![DNA structure, dynamics and recognition 7
Table 1
DNA landmarks
1865 Gregor Mendel publishes his work on plant breeding with the notion of “genes” carrying
transmissible characteristics
1869 “Nuclein” is isolated by Johann Friedrich Miescher in Tübingen in the laboratory of Ernst
Hoppe-Seyler
1892 Meischer writes to his uncle “large biological molecules composed of small repeated
chemical pieces could express a rich language in the same way as the letters of our
alphabet”
1920 Recognition of the chemical difference between DNA and RNA Phoebus Levene proposes
the “tetranucleotide hypothesis”
1938 William Astbury obtains the first diffraction patters of DNA fibres
1944 Oswald Avery (Rockefeller Institute) proves that DNA carries the genetic message by
transforming bacteria
1950 Erwin Chargaff discovers [A]/[G] = [T]/[C]
1953 James Watson and Francis Crick propose the double helix as the structure of DNA based
on the work of Erwin Chargaff, Jerry Donohue, Rosalind Franklin and John Kendrew
1980 Richard Dickerson’s laboratory at UCLA publishes the first crystal structure of a DNA
oligomer
The key to solving the problem came from the observation by Erwin Char-
gaff, that somehow the bases went together in pairs, A with T and G with C.
When the organic chemist Jerry Donahue explained to Jim Watson that most
textbooks of the day were wrong in showing the DNA bases as the so-called enol
tautomers, rather than the keto form (which contains proton accepting carbonyl
groups, rather than proton donating hydroxyl groups), the penny dropped and
Watson was able to plug the base pairs together in the right way and discover that
AT and GC pairs had exactly the same shape.
This implied that they could be build into the centre of a double helix which
could then have a regular structure whatever the sequence of the bases.
This insight became one of the defining moments in 20th century science.
The beauty of the double helix convinced everyone who saw it that it must be
the right answer – not least because it clearly answered the question of how the
genetic message could be copied. Due to base pairing, the two strands of the helix
contained complementary messages: AATCAGTTGA. . . on one strand, lined up
with TTAGTCAACT. . . on the other, separating the two strands and rebuilding
the complementary message led to a new generation with two identical copies
of the original molecule. This mechanism is described in the famous paragraph](https://image.slidesharecdn.com/1020917-250521152704-7102808d/85/Multiple-Aspects-Of-Dna-And-Rna-From-Biophysics-To-Bioinformatics-Chatenay-D-36-320.jpg)
![This ebook is for the use of anyone anywhere in the United States
and most other parts of the world at no cost and with almost no
restrictions whatsoever. You may copy it, give it away or re-use it
under the terms of the Project Gutenberg License included with this
ebook or online at www.gutenberg.org. If you are not located in the
United States, you will have to check the laws of the country where
you are located before using this eBook.
Title: Life of Thomas Paine
Author: Richard Carlile
Release date: July 11, 2012 [eBook #40208]
Most recently updated: October 23, 2024
Language: English
Credits: Produced by David Widger
*** START OF THE PROJECT GUTENBERG EBOOK LIFE OF THOMAS
PAINE ***](https://image.slidesharecdn.com/1020917-250521152704-7102808d/85/Multiple-Aspects-Of-Dna-And-Rna-From-Biophysics-To-Bioinformatics-Chatenay-D-60-320.jpg)
Multiple Aspects Of Dna And Rna From Biophysics To Bioinformatics Chatenay D
- 1. Multiple Aspects Of Dna And Rna From Biophysics To Bioinformatics Chatenay D download https://ebookbell.com/product/multiple-aspects-of-dna-and-rna- from-biophysics-to-bioinformatics-chatenay-d-2041834 Explore and download more ebooks at ebookbell.com
- 2. Here are some recommended products that we believe you will be interested in. You can click the link to download. Various Aspects Of Multiple Zeta Functions In Honor Of Professor Kohji Matsumotos 60th Birthday Hidehiko Mishou Ed https://ebookbell.com/product/various-aspects-of-multiple-zeta- functions-in-honor-of-professor-kohji-matsumotos-60th-birthday- hidehiko-mishou-ed-37143108 Various Aspects Of Multiple Zeta Functions In Honor Of Professor Kohji Matsumotos 60th Birthday Ed Hidehiko Mishou https://ebookbell.com/product/various-aspects-of-multiple-zeta- functions-in-honor-of-professor-kohji-matsumotos-60th-birthday-ed- hidehiko-mishou-37162180 Various Aspects Of Multiple Zeta Functions Aspm84 Ms Japan Mishou H https://ebookbell.com/product/various-aspects-of-multiple-zeta- functions-aspm84-ms-japan-mishou-h-51992448 South Koreas Engagement With Africa A History Of The Relationship In Multiple Aspects 1st Ed 2020 Yongkyu Chang https://ebookbell.com/product/south-koreas-engagement-with-africa-a- history-of-the-relationship-in-multiple-aspects-1st-ed-2020-yongkyu- chang-10806248
- 3. Multipleaspect Analysis Of Semantic Trajectories First International Workshop Master 2019 Held In Conjunction With Ecmlpkdd 2019 Wrzburg Germany September 16 2019 Proceedings Konstantinos Tserpes Chiara Renso Stan Matwin Konstantinos Tserpes https://ebookbell.com/product/multipleaspect-analysis-of-semantic- trajectories-first-international-workshop-master-2019-held-in- conjunction-with-ecmlpkdd-2019-wrzburg-germany- september-16-2019-proceedings-konstantinos-tserpes-chiara-renso-stan- matwin-konstantinos-tserpes-28687232 Multipleaspect Analysis Of Semantic Trajectories Konstantinos Tserpes Chiara Renso Stan Matwin https://ebookbell.com/product/multipleaspect-analysis-of-semantic- trajectories-konstantinos-tserpes-chiara-renso-stan-matwin-59042762 Multipole Theory In Electromagnetism Classical Quantum And Symmetry Aspects With Applications R E Raab https://ebookbell.com/product/multipole-theory-in-electromagnetism- classical-quantum-and-symmetry-aspects-with-applications-r-e- raab-996682 Think Pink Crochet For The Cure Annies Attic Crochet Multiple https://ebookbell.com/product/think-pink-crochet-for-the-cure-annies- attic-crochet-multiple-2202644 Wileyblackwell Companion To Syntax 2nd Multiple https://ebookbell.com/product/wileyblackwell-companion-to-syntax-2nd- multiple-22843928
- 6. Université Joseph Fourier Les Houches Session LXXXII Multiple aspects of DNA and RNA: from Biophysics to Bioinformatics
- 7. Lecturers who contributed to this volume Tom Duke Jacques van Helden Hidde de Jong Jim Kadonaga Alexei Khokhlov Richard Lavery John Marko Alexander Samsonov Maria Samsonova Terence Strick Denis Thieffry Eric Westhof
- 8. ÉCOLE D’ÉTÉ DE PHYSIQUE DES HOUCHES SESSION LXXXII, 2–27 AUGUST 2004 EURO SUMMER SCHOOL NATO ADVANCED STUDY INSTITUTE ÉCOLE THÉMATIQUE DU CNRS MULTIPLE ASPECTS OF DNA AND RNA: FROM BIOPHYSICS TO BIOINFORMATICS Edited by Didier Chatenay, Simona Cocco, Rémi Monasson, Denis Thieffry and Jean Dalibard 2005 Amsterdam – Boston – Heidelberg – London – New York – Oxford Paris – San Diego – San Francisco – Singapore – Sydney – Tokyo
- 9. ELSEVIER B.V. ELSEVIER Inc. ELSEVIER Ltd ELSEVIER Ltd Radarweg 29 525 B Street, Suite 1900 The Boulevard, Langford Lane 84 Theobalds Road P.O. Box 211, 1000 AE San Diego, CA 92101-4495 Kidlington, Oxford OX5 1GB London WC1X 8RR Amsterdam, USA UK UK The Netherlands c 2005 Elsevier B.V. All rights reserved This work is protected under copyright by Elsevier B.V., and the following terms and conditions apply to its use: Photocopying Single photocopies of single chapters may be made for personal use as allowed by national copyright laws. Permis- sion of the Publisher and payment of a fee is required for all other photocopying, including multiple or systematic copying, copying for advertising or promotional purposes, resale, and all forms of document delivery. Special rates are available for educational institutions that wish to make photocopies for non-profit educational classroom use. Permissions may be sought directly from Elsevier’s Rights Department in Oxford, UK: phone (+44) 1865 843830, fax (+44) 1865 853333, e-mail: permissions@elsevier.com. Requests may also be completed on-line via the Elsevier homepage (http://www.elsevier.com/locate/permissions). In the USA, users may clear permissions and make payments through the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA; phone: (+1) (978) 7508400, fax: (+1) (978) 7504744, and in the UK through the Copyright Licensing Agency Rapid Clearance Service (CLARCS), 90 Tottenham Court Road, London W1P 0LP, UK; phone: (+44) 20 7631 5555, fax: (+44) 20 7631 5500. Other countries may have a local reprographic rights agency for payments. Derivative Works Tables of contents may be reproduced for internal circulation, but permission of the Publisher is required for external resale or distribution of such material. Permission of the Publisher is required for all other derivative works, including compilations and translations. Electronic Storage or Usage Permission of the Publisher is required to store or use electronically any material contained in this work, including any chapter or part of a chapter. Except as outlined above, no part of this work may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without prior written permission of the Publisher. Address permissions requests to: Elsevier’s Rights Department, at the fax and e-mail addresses noted above. Notice No responsibility is assumed by the Publisher for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein. Because of rapid advances in the medical sciences, in particular, independent verification of diagnoses and drug dosages should be made. First edition 2005 Library of Congress Cataloging in Publication Data A catalog record is available from the Library of Congress. British Library Cataloguing in Publication Data A catalogue record is available from the British Library. ISBN: 0-444-52081-3 ISSN: 0924-8099 ∞ The paper used in this publication meets the requirements of ANSI/NISO Z39.48-1992 (Permanence of Paper). Printed in The Netherlands.
- 10. ÉCOLE DE PHYSIQUE DES HOUCHES Service inter-universitaire commun à l’Université Joseph Fourier de Grenoble et à l’Institut National Polytechnique de Grenoble Subventionné par le Ministère de l’Éducation Nationale, de l’Enseignement Supérieur et de la Recherche, le Centre National de la Recherche Scientifique, le Commissariat à l’Énergie Atomique Membres du conseil d’administration : Yannick Vallée (président), Paul Jacquet (vice-président), Cécile DeWitt, Thérèse Encrenaz, Bertrand Fourcade, Luc Frappat, Jean-François Joanny, Michèle Leduc, Jean-Yves Marzin, Giorgio Parisi, Eva Pebay-Peyroula, Michel Peyrard, Luc Poggioli, Jean-Paul Poirier, Michel Schlenker, François Weiss, Jean Zinn- Justin Directeur : Jean Dalibard, Laboratoire Kastler Brossel, Paris, France Directeurs scientifiques de la session LXXXII : Didier Chatenay, Strasbourg, France Oleg Krichevsky, Beer-Sheva, Israel Rémi Monasson, Paris, France Simona Cocco, Strasbourg, France Denis Thieffry, Marseille, France
- 11. Previous sessions I 1951 Quantum mechanics. Quantum field theory II 1952 Quantum mechanics. Statistical mechanics. Nuclear physics III 1953 Quantum mechanics. Solid state physics. Statistical mechanics. Elementary particle physics IV 1954 Quantum mechanics. Collision theory. Nucleon–nucleon interaction. Quantum electrodynamics V 1955 Quantum mechanics. Non equilibrium phenomena. Nuclear reactions. Interaction of a nucleus with atomic and molecular fields VI 1956 Quantum perturbation theory. Low temperature physics. Quantum theory of solids. Ferromagnetism VII 1957 Scattering theory. Recent developments in field theory. Nuclear and strong interactions. Experiments in high energy physics VIII 1958 The many body problem IX 1959 The theory of neutral and ionized gases X 1960 Elementary particles and dispersion relations XI 1961 Low temperature physics XII 1962 Geophysics; the earth’s environment XIII 1963 Relativity groups and topology XIV 1964 Quantum optics and electronics XV 1965 High energy physics XVI 1966 High energy astrophysics XVII 1967 Many body physics XVIII 1968 Nuclear physics XIX 1969 Physical problems in biological systems XX 1970 Statistical mechanics and quantum field theory XXI 1971 Particle physics XXII 1972 Plasma physics XXIII 1972 Black holes XXIV 1973 Fluids dynamics XXV 1973 Molecular fluids XXVI 1974 Atomic and molecular physics and the interstellar matter XXVII 1975 Frontiers in laser spectroscopy XXVIII 1975 Methods in field theory XXIX 1976 Weak and electromagnetic interactions at high energy XXX 1977 Nuclear physics with heavy ions and mesons XXXI 1978 Ill condensed matter XXXII 1979 Membranes and intercellular communication XXXIII 1979 Physical cosmology XXXIV 1980 Laser plasma interaction XXXV 1980 Physics of defects XXXVI 1981 Chaotic behaviour of deterministic systems XXXVII 1981 Gauge theories in high energy physics XXXVIII 1982 New trends in atomic physics XXXIX 1982 Recent advances in field theory and statistical mechanics XL 1983 Relativity, groups and topology XLI 1983 Birth and infancy of stars
- 12. XLII 1984 Cellular and molecular aspects of developmental biology XLIII 1984 Critical phenomena, random systems, gauge theories XLIV 1985 Architecture of fundamental interactions at short distances XLV 1985 Signal processing XLVI 1986 Chance and matter XLVII 1986 Astrophysical fluid dynamics XLVIII 1988 Liquids at interfaces XLIX 1988 Fields, strings and critical phenomena L 1988 Oceanographic and geophysical tomography LI 1989 Liquids, freezing and glass transition LII 1989 Chaos and quantum physics LIII 1990 Fundamental systems in quantum optics LIV 1990 Supernovae LV 1991 Particles in the nineties LVI 1991 Strongly interacting fermions and high Tc superconductivity LVII 1992 Gravitation and quantizations LVIII 1992 Progress in picture processing LIX 1993 Computational fluid dynamics LX 1993 Cosmology and large scale structure LXI 1994 Mesoscopic quantum physics LXII 1994 Fluctuating geometries in statistical mechanics and quantum field theory LXIII 1995 Quantum fluctuations LXIV 1995 Quantum symmetries LXV 1996 From cell to brain LXVI 1996 Trends in nuclear physics, 100 years later LXVII 1997 Modeling the Earth’s Climate and its Variability LXVIII 1997 Probing the Standard Model of Particle Interactions LXIX 1998 Topological aspects of low dimensional systems LXX 1998 Infrared space astronomy, today and tomorrow LXXI 1999 The primordial universe LXXII 1999 Coherent atomic matter waves LXXIII 2000 Atomic clusters and nanoparticles LXXIV 2000 New trends in turbulence LXXV 2001 Physics of bio-molecules and cells LXXVI 2001 Unity from duality: Gravity, gauge theory and strings LXXVII 2002 Slow relaxations and nonequilibrium dynamics in condensed matter LXXVIII 2002 Accretion discs, jets and high energy phenomena in astrophysics LXXIX 2003 Quantum Entanglement and Information Processing LXXX 2003 Methods and Models in Neurophysics LXXXI 2004 Nanophysics: Coherence and Transport Publishers: - Session VIII: Dunod, Wiley, Methuen - Sessions IX and X: Herman, Wiley - Session XI: Gordon and Breach, Presses Universitaires - Sessions XII–XXV: Gordon and Breach - Sessions XXVI–LXVIII: North Holland - Session LXIX–LXXVIII: EDP Sciences, Springer - Session LXXIX-LXXXI: Elsevier
- 14. Lecturers DUKE Tom, Cavendish Lab., Madingley road, Cambridge CB3 0HE, UK van HELDEN Jacques, Service de Conformation des Macromolécules Biolo- giques et de Bioinformatique, Univ. Libre de Bruxelles, CP 263, Campus Plaine, Boulevard du Triomphe, 1050 Bruxelles, Belgium de JONG Hidde, INRIA Rhône Alpes, 655 avenue de l’Europe, 38330 Montbon- not St Martin, France KADONAGA Jim, Section of Molecular Biology and Center for Molecular Ge- netics, Univ. of California, San Diego, La Jolla, CA 92093-0347 USA KHOKHLOV Alexei, Head of the Chair of Polymer Physics and Crystalophysics, Physics dept., Moscow State Univ., Leninskie Gor, 117234 Moscow, Russia LAVERY Richard, Lab. de Biochimie Théorique, Inst. de Biologie Physico- chimique, 11 rue Pierre et Marie Curie, 75005 Paris, France MARKO John, Dept. Physics, Univ. Illinois, 845 West Taylor Street, Chicago, IL 60607, USA MUKAMEL David, Dept. Physics of Complex Systems, Weizmann Inst., 76100 Rehovot, Israel NOVAK Bela, Group of Computational Molecular Biology, Dept. Agricultural Chemical Technology, Technical Univ., 1521 Budapest, Hungary STRICK Terence, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA SAMSONOVA Maria, Dept. Computational Biology, Center for Advanced Studies, St Petersburg State Polytechnical Univ., 29 Polytechnicheskaya ul., 195251 St Petersburg, Russia TADDEI François, Génétique Moléculaire Évolutive et Médicale, INSERM E9916, Fac. Médecine “Necker – Enfants malades”, Univ. R. Descartes, 156 Rue de Vaugirard, 75730 Paris cedex 15, France WESTHOF Eric, Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Inst. de Biologie Moléculaire et Cellulaire, 15 rue Descartes, 67084 Strasbourg cedex, France ix
- 15. Short lectures and seminar speakers CAVALLI Giacomo, Inst. Génétique Humaine, 141 rue de la Cardonille, 34396 Montpellier, France FERNANDEZ Bastien, CPT/CNRS Luminy Case 907, 13288 Marseille cedex 09, France GAUTHERET Daniel, TAGC INSERM, Luminy case 906, 13288 Marseille cedex 09, France SAMSONOV Alexander, Theoretical Department, The Ioffe Physico-Technical Institute of the Russian Academy of Sciences, St. Petersburg, 194021 Russia Organizers CHATENAY Didier, LPS/ENS, 24 rue Lhomond, 75231 Paris cedex 05, France COCCO Simona, LPS/ENS, 24 rue Lhomond, 75231 Paris cedex 05, France KRICHEVSKY Oleg, Physics dept., Ben Gurion Univ., 84105 Beer Sheva, Israel MONASSON Rémi, LPT/ENS, 24 rue Lhomond, 75231 Paris cedex 05, France THIEFFRY Denis, LGPD/IBDM/CNRS, Campus Luminy, Case 907, 13288 Marseille cedex 9, France DALIBARD Jean, LKB/ENS, 24 rue Lhomond, 75231 Paris cedex 05, France x
- 16. Participants BALDAZZI Valentina, Univ. of Roma “Tor Vergata”, Dept. Physics, via della Ricerca Scientifica1, 00133 Roma, Italy BAULIN Vladimir, LDFC, Univ. Louis Pasteur, 3, rue de l’Université, 67084 Strasbourg cedex, France BOHINC Klemen, Univ. Ljubljana, College for Health Studies, Poljanska 26a, 1000 Ljubljan, Slovenia CANARI Francesco, Univ. Roma “La Sapienza”, Dip. di Chimica, Piazzale A. Moro, box 54-Roma 62, 00185 Roma, Italy CHERTOVICH Alexander, Chair of Physics of Polymers and Crystals, Physics dept., Moscow State Univ., Moscow 119992, Russia CLAUDET Cyril, Lab. Spectrométrie Physique, 140 rue de la Physique, BP 87, 38402 St Martin d’Hères, France CUENDA Sara, Univ. Carlos III de Madrid, Dpto. De Matamaticas, Avda. Uni- versidad, 30, 28911 Madrid, Spain CORA Davide, Univ. Torino, Dept. Theoretical Physics, via Pietro Giuria 1, 10125 Torino, Italy DEREMBLE Cyril, Lab. de Biochimie Théorique, Institut de Biologie Physico- Chimique, 11 rue Pierre et Marie Curie, 75005 Paris, France DONSMARK Jesper, Dept. of Biophysics, Leiden Univ., Niels Bohr weg 2, NL 2333 CA Leiden, The Netherlands DOUARCHE Nicolas, LDFC, 3 rue de l’Université, 67084 Strasbourg, France GABAY Carmit, Ben Gurion Univ., Beer Sheva, 84105, Israel GEURTS Pierre, Univ. Liège, Dept. Electrical and Computer Science, Sart Tilman B28, B-4000 Liège, Belgium GOMEZ ULLATE David, Dip. Matematica, Univ. Bologna, Piazza Porta San Donato, 5, Bologna, 40126, Italy GRIGORYAN Arsen, Dept. Molecular Physics, Yerevan State Univ., Al. Mano- ogian str.1, Yerevan 375025, Armenia HORI Yuko, Dept. Physics, Brandeis Univ., MS 057, P.O. Box 549110, Waltham, MA 02454-9110 USA xi
- 17. IMPARATO Alberto, Dip. di Scienze Fisiche, Univ. di Napoli “Frederico II”, Complesso Universitario di Monte San Angelo, 80126 Napoli, Italy JOLI Flore, Groupe NMR, porte 349, LPBC-CSSB, Univ. Paris 13, 74 rue Mar- cel Cachin, 93017 Bobigny cedex, France JUN Suckjoon, Physics dept., Simon Fraser Univ., Burnaby, B.C V5A 1S6, Canada; FOM Inst. AMOLF, Kruislaan 407, 1098 SJ Amsterdam, The Nether- lands KALOSAKAS George, MPI for Physics of Complex Systems, Nöthnitzer str 38, Dresden 01187, Germany KHIZANISHVILI Ana, E. Andronikashvili Inst. of Physics of Georgia Academy of Sciences, 6 Tamarashvili str, 380077 Tbilisi, Georgia KOSTER Daniel, Kavli Inst. of Nanoscience, Section Molecular Biophysics, Technical Univ. Delft, The Netherlands MANNA Federico, Lab. Physique Mathématique et Théorique, Univ. Montpel- lier II, Sciences et Techniques du Languedoc, Case courrier 70, Place E. Batail- lon, 34095 Montpellier cedex 05, France MARCONE Boris, Dip. Fisica, Univ. degli Studi di Padova, via Marzolo 8, 35131 Padova, Italy MARCONI Daniela, Dept. Physics, Viale Berti Pichat 6/2, Bologna, Italy MARTIGNETTI Loredana, Univ. Di Torino, Dip. Fisica Teorica, VP Giuria, 1, 10125 Torino, Italy MEGRAW Molly, Univ. Pennsylvania, Blockley Hall, Floor 14, 423 Guardian Drive, Philadelphia, PA 19104-6021, USA MESSER Philipp, Inst. Theoretical Physics, Cologne Univ., Zülpicher str. 77, 50937 Köln, Germany MOSCONI Francesco, Univ. Padova, Dept. Physics “G. Galilei”, via F. Marzolo, 8, 35131 Padova, Italy NORMANNO Davide, LENS, European Lab. For Non-Linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy PADINHATEERI Ranjith, Dept. Physics, Indian Inst. of Technology Madras, Chennai 600 036, Tamil Nadu, India PAPAJ Grzegorz, Lab. of Bioinformatics and Protein Engineering, International Inst. of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland xii
- 18. PAPARCONE Raffaella, Dip. Chimica, Univ. “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy REYMOND Nancie, INSA Lyon, Lab. BF 21, Bâtiment Louis Pasteur, 20, av. A. Einstein, 69621 Villeurbanne cedex, France ROSSETTO Vincent, MPI für Physik Komplexer Systeme, Nöthnitzer str 38, 01187 Dresden, Germany ROSVALL Martin, Theoretical Physics, Umea Univ., SE-90187 Umea, Sweden SACHIDANANDAM Ravi, Cold Spring Harbor Lab., 1 Bungtown Road, Free- man Building, Cold Spring Harbor, NY 11724, USA SANKARARAMAN Sumithra, Dept. Physics, Univ. of Illinois, 845 w Taylor street, Chicago, IL 60607, USA SHUSTERMAN Roman, Physics Dept, Ben Gurion Univ., Beer-Sheva, 84105, Israel SKOKO Dunja, Univ. Illinois, 845 W. Tayor str., Physics MC 273, Chicago IL 60607, USA TEIF Vladimir, Inst. Bioorganic Chemistry, Belarus National Academy of Sci- ences, Kuprevich street 5/2, 220141 Minsk, Belarus TKACIK Gasper, 236 Carl Icahn Lab., Princeton Univ., Princeton, NJ 08544, USA TOURLEIGH Yegor, Moscow Lomonosov State Univ., Dept. Biophysics, Lenin- skiye Gory, 1/12, Moscow, 119992, Russia TRUSINA Ala, NORDITA, DK-2100 Copenhagen, Denmark VAFABAKHSH Reza, IASBS, Zanjan, Post box 45195-159, Iran VANDOOLAEGHE Wendy, Polymers and Colloids Group, Cavendish Lab., Univ. Cambridge, Madingley road, Cambridge CB3 0HE, UK WEBER Jérémie, Inst. Curie, Lab. Physico-chimie, 11 Rue Pierre et Marie Curie, 75005 Paris, France WILK Agnieszka, Molecular Biophysics Division, Inst. of Physics, Adam Mick- iewicz Univ., Umultowska 85, 61-614 Poznan, Poland YAN Koon-Kiu, Dept. Physics, Brookhaven National Lab., Upton, NY 11973, USA xiii
- 20. Preface In August 2004, the Ecole de Physique des Houches hosted a Summer School dedicated to biological, physical and computational aspects of nucleic acids. Central to vital processes, these biological molecules have been experimentally studied by molecular biologists for five decades since the discovery of the struc- ture of DNA by J. Watson and F. Crick in 1953. Recent progresses, such as the development of DNA arrays, manipulations at the single molecule level, the availability of huge genomic databases, have foster the need for theoretical mod- eling. In particular, a global understanding of the structure and function of DNA and RNA require the concerted development and application of proper experi- mental and theoretical approaches, involving methods and tools from different disciplines, including physics. The aim of this Summer School was precisely to provide a comprehensive overview of these issues at the interface between physics, biology and information science. The Summer School encompassed three main sections: 1) Biochemistry and Biology of DNA/RNA; 2) Biophysics: from Experiments to modeling and theory; 3) Bioinformatics. The present book follows the same organization, and is mainly intended to ad- vanced graduate students or young researchers willing to acquire a broad inter- disciplinary understanding of the multiple aspects of DNA and RNA. The first section comprises an introduction to biochemistry and biology of nucleic acids. The structure and function of DNA are reviewed in R. Lavery’s chapter. The next contribution, by V. Fritsch and E. Westhof, concentrates on the folding properties of RNA molecules. The cellular processes involving these molecules are reviewed by J. Kadonaga, with special emphasis on the regulation of tran- scription of DNA. These chapters do not require any preliminary knowledge in the field, except that of elementary biology and chemistry. The second section covers the biophysics of DNA and RNA, starting with ba- sics in polymer physics with the contribution by R. Khokhlov. Advances in the understanding of electrophoresis, a technique of crucial importance in everyday molecular biology, are then exposed in T. Duke’s contribution. Finally a large xv
- 21. space is devoted to the presentation of recent experimental and theoretical pro- gresses in the field of single molecule studies. T. Strick’s contribution presents a detailed description of the various micro-manipulation techniques, and reviews recent experiments on the interactions between DNA and proteins (helicases, topoisomerases, etc.). The theoretical modeling of single molecules is presented by J. Marko, with a special attention paid to the elastic and topological properties of DNA. The third section presents provides an overview of the main computational ap- proaches to integrate, analyze and simulate molecular and genetic networks. First J. van Helden introduces a series of statistical and computational methods al- lowing the identification of short nucleic fragments putatively involved in the regulation of gene expression from sets of promoter sequences controlling co- expressed genes. Next the chapter by Samsonova et al. connects the issue of transcriptional regulation with that of the control of cell differentiation and pat- tern formation during embryonic development. This contribution ties the issues of data integration, image processing and dynamical modeling, focusing on a simple model organism (the fly). Finally, H. de Jong and D. Thieffry review a series of mathematical approaches to model the dynamical behaviour of complex genetic regulatory networks. This contribution includes brief descriptions and references to successful applications of these approaches, including the work of B. Novak, one of the teachers of the school, on the dynamical modeling of cell cycle in different model organisms, from yeast to mammals. To complete the different chapters of this volume, the material corresponding to additional seminars and lectures, as well as to the public lecture in Les Houches by D. Chatenay can be download from the Summer School web page, at the url: http://w3houches.ujf-grenoble.fr/sessions_ete/ete-82/session-82.html The organization of the summer school and the publication of this volume could not be achieved without the invaluable contributions of the speakers and authors, all deserving warm thanks. We also express our gratitude to I. Lelièvre and B. Rousset for their diligent help in the organization of the School. Furthermore, we gratefully acknowledge the generous financial support from the CNRS, the NATO, and the European Union. Finally, we thank the attendees for the friendly and warm atmosphere that they were able to create during this 82th Session of the Les Houches Summer School. D. Chatenay, S. Cocco, R. Monasson, D. Thieffry and J. Dalibard xvi
- 22. CONTENTS Lecturers ix Short lectures and seminar speakers x Organizers x Participants xi Preface xv Course 1. DNA structure, dynamics and recognition, by Richard Lavery 1 1. Introduction to the DNA double helix 5 2. Biophysical studies of DNA – structure and stability 16 3. DNA dynamics 21 4. Deformations of the double helix 25 5. DNA recognition 33 Course 2. Introduction to non-Watson–Crick base pairs and RNA folding, by V. Fritsch and E. Westhof 41 1. Definitions 45 2. The annotation of non-Watson–Crick base pairs and of RNA motifs 52 3. RNA–RNA recognition motifs 56 4. Roles of RNA motifs in RNA-protein recognition 61 5. Conclusions 69 References 69 xvii
- 23. Contents Course 3. Regulation of transcription by RNA polymerase II, by James T. Kadonaga 73 1. Introduction 77 2. DNA regulatory elements 79 3. Basal/general transcription factors 81 4. Sequence-specific DNA-binding factors 83 5. Chromatin and transcription 85 6. Conclusions and speculations 87 References 89 Course 4. Basic concepts of statistical physics of polymers, by A.R. Khokhlov and E.Yu. Kramarenko 91 1. Introduction to polymer physics 95 1.1. Fundamentals of physical viewpoint in polymer science 95 1.2. Flexibility of a polymer chain. Flexibility mechanisms 96 1.2.1. Rotational-isomeric flexibility mechanism 96 1.2.2. Persistent flexibility mechanism 98 1.2.3. Freely-jointed flexibility mechanism 98 1.3. Types of polymer molecules 98 1.4. Physical states of polymer materials 100 1.5. Polymer solutions 101 2. Single ideal polymer chain 102 2.1. Definition of ideal polymer chain 102 2.2. Size of ideal freely-jointed chain. Entangled coil 102 2.3. Size of ideal chain with fixed valency angle 104 2.4. Kuhn segment length of a polymer chain 105 2.5. Persistent length of a polymer chain 106 2.6. Stiff and flexible chains 107 2.7. Gaussian distribution for the end-to-end vector for ideal chain 108 3. High elasticity of polymer networks 109 3.1. The property of high elasticity 109 3.2. Elasticity of a single ideal chain 111 3.3. Elasticity of a polymer network (rubber) 113 4. Viscoelasticity of entangled polymer fluids 116 4.1. Main properties of entangled polymer fluids 116 4.2. Viscosity of fluids 117 4.3. The property of viscoelasticity 118 4.4. Theory of reptations 119 xviii
- 24. Contents 4.5. The method of gel-electrophoresis in application to DNA molecules 122 4.6. Gel permeation chromatography 124 References 125 Course 5. The physics of DNA electrophoresis, by T.A.J. Duke 127 1. Importance of DNA sorting in biology and how physics can help 131 2. Physical description of DNA 133 3. Electrophoretic force 134 4. DNA sequencing: gel electrophoresis of single-stranded DNA 135 4.1. Reptative dynamics 136 4.2. Biased reptation 137 4.3. Repton model 140 4.4. Strategies for DNA sequencing 141 5. Gel electrophoresis of long double-stranded DNA molecules 142 5.1. Complex dynamics in constant fields 142 5.2. Pulsed-field gel electrophoresis: separation of restriction fragments 144 5.3. Difficulty of separating very large molecules 147 6. Obstacle courses on microchips 148 6.1. Collision of a DNA molecule with an obstacle 149 6.2. Efficient pulsed-field fractionation in silicon arrays 150 6.3. Continuous separation in asymmetric pulsed fields 152 6.4. Asymmetric sieves for sorting DNA 154 6.5. Rapid continuous separation in a divided laminar flow 156 7. Summary 158 References 158 Course 6. Single-molecule studies of DNA mechanics and DNA/protein interactions, by T.R. Strick 161 1. Introduction 165 2. The interest of physicists for DNA 166 2.1. Ease of handling 166 2.2. DNA as a model polymer 167 2.3. Introduction to single-molecule DNA manipulation techniques 168 2.3.1. Strategies and forces involved 168 2.3.2. Measurement techniques 170 3. Force measurements 172 3.1. Measuring forces with Brownian motion 172 3.2. Advantages and disadvantages of the manipulation techniques 174 xix
- 25. Contents 4. Mechanical properties and behavior of DNA 175 4.1. Tertiary structures in DNA 175 4.2. Topological formalism 176 4.3. DNA supercoiling in vivo 177 4.3.1. DNA unwinding and helix destabilisation 177 4.3.2. DNA topoisomerases 177 4.3.3. Supercoiling and transcription 178 4.4. DNA elasticity in the absence of torsion (σ = 0) 178 4.4.1. Results 179 4.4.2. Theoretical models 180 4.5. Mechanical properties of supercoiled DNA 180 4.5.1. Results 181 4.5.2. Interpretation 181 4.5.3. The buckling instability in DNA 183 4.6. Stretching single-strand DNA 184 4.7. Conclusions on the mechanical properties of nucleic acids 185 5. RNA polymerases 186 5.1. An introduction to transcription 186 5.2. Historical overview: transcription elongation, or RNA polymerase as a linear motor 188 5.3. RNA polymerase as a torquing device: the case of transcription initiation 189 6. DNA topoisomerases 193 6.1. Type I and Type II topoisomerases 193 6.2. Eukaryotic topoisomerase II 195 6.2.1. Enzymatic cycle 195 6.3. Prokaryotic topoisomerase IV 196 6.4. Experimental results: D. melanogaster topoisomerase II 196 6.4.1. Calibrating the experiment 196 6.4.2. Crossover clamping in the absence of ATP 197 6.4.3. Low ATP concentrations: detecting a single enzymatic cycle 198 6.4.4. High ATP concentration 199 6.4.5. Determining Vsat, the saturated reaction velocity 200 6.4.6. Effect of the stretching force 201 6.4.7. Relaxation of negatively supercoiled DNA 202 6.4.8. Topo II only removes crossovers in DNA 202 6.5. A comparison with E. coli topo IV 203 6.5.1. Experiments on braided DNA molecules 204 6.6. Conclusions on type II topoisomerases 204 7. Conclusions and future prospects 205 References 205 xx
- 26. Contents Course 7. Introduction to single-DNA micromechanics, by John F. Marko 211 1. Introduction 215 2. The double helix is a semiflexible polymer 217 2.1. Structure 217 2.2. DNA bending 219 2.2.1. Discrete-segment model of a semiflexible polymer 219 2.2.2. Bending elasticity and the persistence length 221 2.2.3. End-to-end distance 222 2.2.4. DNA loop bending energies 223 2.2.5. Site-juxtaposition probabilities 224 2.2.6. Permanent sequence-driven bends 225 2.3. Stretching out the double helix 225 2.3.1. Small forces ( kBT /A = 0.08 pN) 227 2.3.2. Larger forces ( kBT /A = 0.08 pN) 227 2.3.3. Free energy of the semiflexible polymer 229 2.3.4. Really large forces ( 10 pN) 230 3. Strand separation 231 3.1. Free-energy models of strand separation 232 3.1.1. Sequence-dependent models 233 3.1.2. Free energy of internal ‘bubbles’ 234 3.1.3. Small internal bubbles may facilitate sharp bending 235 3.2. Stretching single-stranded nucleic acids 236 3.3. Unzipping the double helix 238 3.3.1. Effect of torque on dsDNA end 240 3.3.2. Fixed extension versus fixed force for unzipping 241 4. DNA topology 242 4.1. DNA supercoiling 242 4.1.1. Twist rigidity of the double helix 242 4.1.2. Writhing of the double helix 243 4.1.3. Simple model of plectonemic supercoiling 244 4.2. Twisted DNA under tension 248 4.3. Forces and torques can drive large structural reorganizations of the double helix 250 4.4. DNA knotting 251 4.4.1. Cells contain active machinery for removal of knots and other entanglements of DNA 252 4.4.2. Knotting a molecule is surprisingly unlikely 252 4.4.3. Condensation-resolution mechanism for disentangling long molecules 253 xxi
- 27. Contents 5. DNA-protein interactions 254 5.1. How do sequence-specific DNA-binding proteins find their targets? 255 5.1.1. Three-dimensional diffusion to the target 255 5.1.2. Nonspecific interactions can accelerate targeting 256 5.2. Single-molecule study of DNA-binding proteins 257 5.2.1. DNA-looping protein: equilibrium ‘length-loss’ model 257 5.2.2. Loop formation kinetics 258 5.2.3. DNA-bending proteins 259 5.2.4. Analytical calculation for compaction by DNA-bending proteins 262 5.2.5. Effects of twisting of DNA by proteins 264 5.2.6. Surprising results of experiments 265 6. Conclusion 266 References 268 Course 8. The analysis of regulatory sequences, by J. van Helden 271 1. Forewords 275 1.1. Scope of the course 275 1.2. Web site and practical sessions 275 2. Transcriptional regulation 275 2.1. The non-coding genome 275 2.2. Transcriptional regulation 276 3. Representations of regulatory elements 279 3.1. String-based representations 279 3.2. Matrix-based representation 280 4. Pattern discovery 283 4.1. Introduction 283 4.2. Study cases 283 5. String-based pattern discovery 284 5.1. Analysis of word occurrences 284 5.2. Analysis of dyad occurrences (spaced pairs of words) 291 5.3. Strengths and weaknesses of word- and dyad-based pattern discovery 293 6. String-based pattern matching 294 7. Matrix-based pattern discovery 296 7.1. Consensus: a greedy approach 297 7.2. Gibbs sampling 297 7.3. Strengths and weaknesses of matrix-based pattern discovery 299 xxii
- 28. Contents 8. Concluding remarks 301 9. Practical sessions 302 10. Appendices 302 10.1. IUPAC ambiguous nucleotide code 302 Course 9. A survey of gene circuit approach applied to modelling of segment determination in fruit fly, by M.G. Samsonova, A.M. Samsonov, V.V. Gursky and C.E. Vanario-Alonso 305 1. Preamble 309 2. Introduction 309 3. The biology of segment determination 310 4. Method description 311 4.1. The gene circuit modelling framework 311 4.2. Quantitative expression data 313 4.3. Optimization by Parallel Lam Simulated Annealing (PLSA) and Optimal Steepest Descent Algorithm (OSDA) 314 4.4. Selection of gene circuits 314 4.5. Software and bioinformatics 315 5. Analysis of regulatory mechanisms controlling segment determination 315 5.1. Regulatory interactions in gap gene system 315 5.2. Stripe forming architecture of the gap gene system 318 6. Pattern formation and nuclear divisions are uncoupled in Drosophila segmentation 318 7. Conclusions 320 References 321 Course 10. Modeling, analysis, and simulation of genetic regulatory networks: from differential equations to logical models, by Hidde de Jong and Denis Thieffry 325 1. Introduction 329 2. Ordinary differential equations 331 2.1. Models and analysis 331 2.2. Analysis of regulatory networks involved in cell-cycle control, cir- cadian rhythms, and development 334 xxiii
- 29. Contents 3. Piecewise-linear differential equations 335 3.1. Models and analysis 335 3.2. Simulation of the initiation of sporulation in Bacillus subtilis 339 4. Logical models 343 4.1. Models and analysis 343 4.2. Modeling of the lysis-lysogeny decision during the infection of Escherichia coli by bacteriophage lambda 345 4.3. Extensions of logical modeling 349 5. Conclusions 350 References 351 xxiv
- 30. Course 1 DNA STRUCTURE, DYNAMICS AND RECOGNITION Richard Lavery Laboratoire de Biochimie Théorique, CNRS UPR 9080 Institut de Biologie Physico-Chimique 13 rue Pierre et Marie Curie, Paris 75005, France D. Chatenay, S. Cocco, R. Monasson, D. Thieffry and J. Dalibard, eds. Les Houches, Session LXXXII, 2004 Multiple aspects of DNA and RNA: from Biophysics to Bioinformatics c 2005 Elsevier B.V. All rights reserved 1
- 32. Contents 1. Introduction to the DNA double helix 5 2. Biophysical studies of DNA – structure and stability 16 3. DNA dynamics 21 4. Deformations of the double helix 25 5. DNA recognition 33 3
- 33. This page intentionally left blank
- 34. 1. Introduction to the DNA double helix We live in the age of genomes and the DNA double helix which carries the ge- netic code has become a universally recognized icon. Today, the genomes of several hundred organisms have already been sequenced. Their size in base pairs (bp), the fundamental building block of the genetic code, is very variable, only 600,000 bp for mycoplasma genitalium, but roughly 3,300,000,000 bp for the hu- man genome. The scale of these numbers means that “Mb”, or mega-base pairs, has become the most common unit. Since the distance between two successive base pairs within DNA is roughly 0.34 nm (or 3.4 Å, where an Å is 10−10 m), the human genome is roughly 1 m long. Despite this length, the whole genome is packed into the nucleus of every one of our cells, a structure having a diameter on the order of 1 µm. DNA has a persistence length of roughly 500 Å (150 bp), which means that 1m of isolated DNA would form a random coil with a diameter of roughly 200 µm. This implies that something else must contribute to packing DNA into our cells, and this, as we will see later, is one of the roles of a wide va- riety of proteins which interact with the double helix (the protein-DNA complex found in the nucleus is termed chromatin). Despite the very real complexity of cellular functioning, the sequencing of entire genomes means that it is becoming feasible, at least for the simplest organ- isms, to build lists of all the proteins encoded in the DNA message, to understand how the production of these proteins is controlled (initially through the subtle in- terplay of the proteins, known as transcription factors, controlling DNA→RNA transcription) and how these proteins interact with one another or act upon other molecules present within the cell, leading to energy storage, molecular synthesis, and so on. A number of projects are now targeting the construction of “min- imal organisms” either in the laboratory (http://www.biomedcentral.com/news/ 20021122/05/) or within the computer (http://www.e-cell.org/). These efforts, which would have been impossible without genome sequencing, should bring us to a much deeper understanding of the true nature of life – a striking contrast to the definition I learnt in school, which was an acronym based simply on the observable characteristics of living organisms: “MERRING” (movement, excre- tion, reproduction, respiration, irritability, nutrition and growth). Let’s start the story of the DNA double helix by looking briefly at the his- tory of its discovery. Although the Austrian monk, Gregor Mendel’s work turned 5
- 35. 6 R. Lavery out to be the true foundation of genetics, it was Freidrich Meischer who actu- ally first isolated the carrier of the genetic message, DNA. He termed the mole- cule, or rather the molecular complex (somewhat degraded chromatin), he iso- lated “nuclein”. Meischer, who had some difficulty publishing his work despite the fact that his boss Ernst Hoppe-Seyler was the founder of the first journal of biochemistry, showed great insight in imagining that a biological polymer (or biopolymer) might carry a message, coded in the linear organization of its monomeric building blocks. Nevertheless, it would take almost 60 years un- til this role was demonstrated for DNA. Part of the delay was due to the great organic chemist Phoebus Levene, did much of the pioneering work necessary to identify the molecular components of DNA (deoxyribonucleic acid) and how they were distinguished from RNA (ribonucleic acid). Unfortunately, he con- cluded that the four bases which occur along the DNA polymer, adenine (A), cytosine (C), guanine (G) and thymine (T) were probably organized in a tedious regular repeat: ACGTACGT. . . . This so-called tetranucleotide hypothesis im- plied that DNA could not be an information carrier, and led to proteins, which were known to have irregular sequences formed from 20 different amino acids, appearing to be much more attractive candidates as information storage mole- cules. With DNA research now seen as a side-track, it took many years before the pioneering work of Oswald Avery (ironically working at the Rockefeller In- stitute where Levine had formulated his tetranucleotide hypothesis) showed that injections of DNA led to genetic transformations in bacteria and put DNA back in the limelight. Converting the chemical structure of DNA into a molecular conformation turned out to be a difficult task. A key step involved obtaining X-ray diffrac- tion patterns for fibres, which could be easily pulled by inserting a glass rod into a solution of DNA. The earliest diffraction patters were obtained by William Ast- bury, but this work was perfected by Rosalind Franklin, working alongside John Kendrew in University College, London. While Rosalind Franklin attempted to solve the structure of DNA by laborious crystallographic techniques, Francis Crick and James Watson in Cambridge set about model building, using data from Francis Crick’s earlier work on the theory of diffraction, which enabled them to identify the signature of a helical structure within the DNA fibre patterns. The first model of Watson and Crick was a disaster which meant that they had to continue their work in secret in order to avoid the wrath of William Bragg, the director of the Cavendish laboratory. They were not alone in making early mis- takes, since Linus Pauling, one of the greatest structural chemists, also published a model of DNA (a triple helix with the bases on the outside) which was clearly incorrect. His mistake was to assume that the phosphate groups of DNA would be neutral and could hydrogen bond together. In fact, the phosphates are ionised in aqueous solution and therefore repel one another.
- 36. DNA structure, dynamics and recognition 7 Table 1 DNA landmarks 1865 Gregor Mendel publishes his work on plant breeding with the notion of “genes” carrying transmissible characteristics 1869 “Nuclein” is isolated by Johann Friedrich Miescher in Tübingen in the laboratory of Ernst Hoppe-Seyler 1892 Meischer writes to his uncle “large biological molecules composed of small repeated chemical pieces could express a rich language in the same way as the letters of our alphabet” 1920 Recognition of the chemical difference between DNA and RNA Phoebus Levene proposes the “tetranucleotide hypothesis” 1938 William Astbury obtains the first diffraction patters of DNA fibres 1944 Oswald Avery (Rockefeller Institute) proves that DNA carries the genetic message by transforming bacteria 1950 Erwin Chargaff discovers [A]/[G] = [T]/[C] 1953 James Watson and Francis Crick propose the double helix as the structure of DNA based on the work of Erwin Chargaff, Jerry Donohue, Rosalind Franklin and John Kendrew 1980 Richard Dickerson’s laboratory at UCLA publishes the first crystal structure of a DNA oligomer The key to solving the problem came from the observation by Erwin Char- gaff, that somehow the bases went together in pairs, A with T and G with C. When the organic chemist Jerry Donahue explained to Jim Watson that most textbooks of the day were wrong in showing the DNA bases as the so-called enol tautomers, rather than the keto form (which contains proton accepting carbonyl groups, rather than proton donating hydroxyl groups), the penny dropped and Watson was able to plug the base pairs together in the right way and discover that AT and GC pairs had exactly the same shape. This implied that they could be build into the centre of a double helix which could then have a regular structure whatever the sequence of the bases. This insight became one of the defining moments in 20th century science. The beauty of the double helix convinced everyone who saw it that it must be the right answer – not least because it clearly answered the question of how the genetic message could be copied. Due to base pairing, the two strands of the helix contained complementary messages: AATCAGTTGA. . . on one strand, lined up with TTAGTCAACT. . . on the other, separating the two strands and rebuilding the complementary message led to a new generation with two identical copies of the original molecule. This mechanism is described in the famous paragraph
- 37. 8 R. Lavery Fig. 1. Base pairs. of Watson and Crick’s 1953 paper in Nature beginning “It has not escaped our notice . . .”. Despite the success of the double helix, it should be remarked there is actually not much information in a fibre diffraction pattern. The model of Watson and Crick was therefore very much a model. One problem it appeared to present was related to replicating the genetic message. In order to copy the strands of the double helix it is necessary to separate them. This is not trivial since the double helical structure implies that the two strands are interwound and cross over one another roughly every 10 base pairs. Separating the stands therefore requires un- winding them and not just pulling them apart. Given the duplication time seen in bacteria, simple calculations suggested that unwinding speeds would be so high that the corresponding centrifugal forces would lead to breaking chemical bonds. This independently led groups in New Zealand and in India to propose a so-called side-by-side model, where crossovers were avoided by making a dou- ble helix composed of alternate left- and right-handed segments. This model, which solved the centrifugal force problem, fitted the fibre diffraction data and was also compatible with early electron micrographs. The final solution came from Richard Dickerson’s first single crystal structure of a DNA fragment (with the sequence CGCGAATTCGCG). It provided the first high-resolution view of DNA and it confirmed all the aspects of Watson and Crick’s model. However, it also showed that a specific base sequence could locally deform the double helix. This slightly mars its beauty, but, as we shall see later, is an important factor in recognizing specific target sites within genomic DNA. In order to understand DNA structure in more detail, we should now step back to its building blocks. Figure 2 shows the chemical constitution of DNA. The bases which we have already seen are divided in two families: adenine and
- 38. DNA structure, dynamics and recognition 9 Fig. 2. DNA backbone. guanine belong to the purine family (abbreviated as Pur or R) and have two con- jugated rings; cytosine and thymine, which only have single rings, belong to the pyrimidine family (abbreviated as Pyr or Y). If, like a mathematician friend of mine, you can’t remember which is which, just imagine yourself cleaning a DNA model with a “Rag” (puRine = Adenine and Guanine). The bases are linked to a 5-membered sugar ring through the so-called glycosidic bond. This bond links the N9 atom of purine bases or the N1 atom of pyrimidine bases to the C1 atom of the sugar. The sugar is called a deoxyribose. Together the sugar and the base constitute a nucleoside. (Before you get bored with chemical jargon, remember that when a base becomes a nucleoside it changes its name: adenosine, cytidine, guanidine and thymidine.) When we add a phosphate group (via a “phospho- diester bond”) to the sugar ring a nucleoside becomes a nucleotide. Nucleotides can be linked together to form a polymer chain, since each sugar has two possible phosphate binding sites, the C3 atom and the C5 atom. Note that this implies that a polynucleotide chain has a direction. Conventionally, chains are written in
- 39. 10 R. Lavery the 5-3 direction, which can be identified by drawing a vector from the C5 atom to the C3 atom of any sugar moiety within the chain. (This direction is down- wards in figure 2.) This conventional directionality also applies to sequences and thus CGCGAATTCGAG implies 5-CGCGAATTCGCG-3. When two polynu- cleotide chains are put together to form a double helix, the complementarity al- ready discussed for the base sequences also extends to the chain directions: one chain goes up and the other goes down, making DNA an antiparallel double he- lix. Therefore each end of the double helix is composed of a 5 and a 3 strand terminus. Before continuing our visit of DNA, it is worth remarking that the chemical differences between DNA and RNA are limited to the addition of a hydroxyl group at the C2 atom of the sugar ring (turning a deoxyribose into a ribose) and the removal of a methyl group at the C5 atom of thymine (making it into another pyrimidine, named uracil). Although the chemical differences between DNA and RNA do not seem to be very important, the structural and biological differences are significant, as you will learn from other courses in this series. Looking at figure 1, we see that the glycosidic bonds which link the bases to the backbone sugar groups (symbolized by the solid black circles) both lie on the same side of the base pairs. This means that the sugar-phosphate backbones are closer together on this side and that, when the two strands of DNA are wound up into a double helix, this side will form a narrower groove than the opposing side. The narrow groove is conventionally termed the minor groove and the opposing groove is known as the major groove. These differences are quite important when we think about other molecules, and notably proteins, binding to the double helix, since there is more space to reach in and contact the bases on the major groove side. The difference between the grooves becomes clear in the view of the conventional B form of DNA shown in Fig. 3. The minor groove can be seen in the centre of this figure. (In passing, the A and B notations for DNA date from the fibre diffraction studies of Rosalind Franklin. A transition from the “A” to the “B” form was seen as the relative humidity of the fibres increased.) B-DNA has a diameter of roughly 20 Å. The base pairs are perpendicular to the helical axis and separated by roughly 3.4 Å. There is a twist of roughly 34◦ between successive base pairs, implying that there are roughly 10.5 bp per full turn of the helix. Note that B-DNA is a right-handed double helix and, as already mentioned, the strands run in opposite directions. To orient yourself, it is useful to remember that, if we look into the minor groove of B-DNA, the 5-3 direction of the strand on the left will point upwards, while that of the strand on the right will point downwards. If we look into the major groove, these directions will be reversed. If we study the DNA backbones in more detail, we will see that there are six single bond rotations for each nucleotide along the sugar-phosphate pathway.
- 40. DNA structure, dynamics and recognition 11 Fig. 3. B-DNA. Table 2 Backbone dihedral angles α : O3 – P – O5 – C5 g− β : P – O5 – C5 – C4 t γ : O5 – C5 – C4 – C3 g+ δ : C5 – C4 – C3 – O3 g+ ε : C4 – C3 – O3 – P t ζ : C3 – O3 – P – O5 g− χ : O4 – C1 – N1 – C2 g− (Pyr) O4 – C1 – N9 – C4 g− (Pur) These dihedrals are denoted by the Greek letters α through ζ. A further single bond, the glycosidic bond χ, positions the base with respect to the sugar ring. Seven single bonds per nucleotide means that a single DNA chain is potentially very flexible and indeed studies of single chains show a persistence length equiv- alent to a single nucleotide unit. Much of this flexibility is lost in forming the double helix because of the pairing and stacking interactions involving the bases, but DNA still retains considerable conformational freedom, allowing for tran- sitions between distinct conformational states (termed allomorphs) and also for considerable thermal fluctuation. Table 2 gives the definitions of the backbone dihedrals and shows there most common conformations in B-DNA. (The nota-
- 41. 12 R. Lavery tions g−, t and g+, where g stands for gauche and t for trans, refer to dihedral angles corresponding to staggered conformations around 60◦, 180◦ and −60◦ re- spectively.) We must also discuss briefly the sugar rings themselves. The optimal va- lence angles of these 5-membered rings lead them to be most stable in non-planar “puckered” conformations. With respect to the mean plane formed by the ring atoms, these conformations have either two adjacent atoms out of plane, one on each side of the mean plane, or one atom out of-plane, leading to a so-called “en- velope” conformation. There are a total of 10 major pucker states. These puckers are named after the atom which is most displaced from the ring plane and are termed “endo” if this atom lies on the same side as the C5 exocyclic atom (or the nucleic acid base) and “exo” if the lie on the opposite side. Given the chemi- cal environment of the sugar rings within DNA, two puckers turn out to be most stable. C2-endo is preferred in B-DNA, while C3-endo is preferred in A-DNA. (Shakespeare’s famous “2B or not 2B” is a good way to remember which pucker goes with which form.) In publications concerning DNA structure, you will also see that sugar pucker described in terms of phase and amplitude. The variables come from the so-called pseudorotational representation of ring pucker, which treats the ring deformation as a sort of standing wave. The phase angle then characterizes the atom most displaced from the mean plane and the amplitude characterizes the extent of its displacement. The phase angles corresponding to the C3-endo and C2-endo forms are around 20◦ and 160◦ respectively. If you imagine these angles plotted on a 360◦ compass, you will understand why C3- endo is sometimes referred to as a “north” pucker, while C2-endo is “ “south” pucker. The last thing its worth knowing about sugars is that the lowest energy route from south to north puckers goes though east direction, which corresponds to a O4-endo pucker. This is due to steric hindrance which occurs between the C5 atom and the base bound to C1 if you try and push the O4 atom below the mean plane (corresponding, as I’m sure you have already worked out, to an O4-exo pucker). I have already remarked that DNA can exist in more than one allomorphic form. Although the B form is the most common, transitions to other forms can take place as the result of physico-chemical changes (notably, differences in the solvent/salt environment) or as the result of physical constraints such as super- coiling and transitions are also be influenced by the base sequence. The A form of DNA, which was identified early on as occurring at low humidity, can be in- duced by changing to a water/alcohol mixture and is also favoured by high GC content. A-DNA is distinguished by a larger diameter than B-DNA (by roughly 4 Å), and a smaller rise (2.56 Å). The base pairs are also inclined with respect to the helical axis and, whereas in B-DNA the helical axis passes roughly through the centre of the base pairs, in A-DNA the base pairs are shifted almost 5 Å to-
- 42. DNA structure, dynamics and recognition 13 Fig. 4. A-, B- and Z-DNA structures. wards the minor groove side. This means, as you can see on, the left of figure 4, that the minor groove becomes wide and shallow and the major groove is now deep and narrow. Despite these differences, the groove names derived from B- DNA (and based on the location of the glycosidic bonds) are maintained for the A form. In response to the change in position of the base pairs, there are also changes in the conformations of the backbones, the most important of which is a change in the sugar puckers from C2-endo to C3-endo. Note that A-DNA is still a right-handed, antiparallel helix. The B to A transition can occur rapidly and in a cooperative manner since it only requires minor conformational rearrangements. Local transitions to the A form of DNA probably occur within the cell and can certainly be induced by binding specific proteins. Another important allomorphic form which you should know about is called Z-DNA. This form was originally detected by changes in the circular dichroism spectra for poly(dCG) sequences in high ionic concentrations. Z-DNA, shown on the right of figure 4, is notable in being a left-handed helix. It is less well known that, compared to B-DNA, the base pairs in Z-DNA have been turned through 180◦ around their long axis. The difficulty of carrying out such a rotation for a set of stacked base pairs explains why the transition from B to Z is much slower than from B to A, and that this transition generally starts at one point and works
- 43. 14 R. Lavery it way along the double helix, base pair by base pair. One other unusual feature of Z-DNA is the relative position of the base and the sugar. When the base pair is turned over, the rotation for purine nucleotides occurs at the glycosidic bond, leading the base to be positioned over the sugar ring. This rotation is chemically termed an anti to syn transition. If we were to try the same rotation with a pyrimidine base, we would find that we generate steric hindrance between the base and the sugar. As a result, when Z-DNA is formed, the rotation at pyrimidines involves not only the base, but also the sugar ring. This coupled rotation leads to the characteristic zigzag conformation of the backbone which gave Z-DNA its name. Z-DNA is favoured by GC alternating base sequences (or, more weakly, by alternating purine-pyrimidine sequences) and can be induced at usual ionic strengths by applying negative supercoils to DNA. Whether Z-DNA exists in biological systems is unproved (although antibodies binding Z-DNA have been isolated), but its ability to relax negative supercoiling is certainly an attractive property. Before ending this introduction, it is important to note that the DNA can adopt a much wider variety of structures than the limited forms of the double helix dis- cussed above. Firstly, as shown in figure 5, there are other ways to put bases together than the conventional “Watson–Crick” pairs. These alternate forms open the way for building more complex structures with three or even four DNA strands. Both of the latter possibilities, known respectively as triplex and quadru- plex DNA, have biological and biotechnological interest. DNA triplexes occur naturally with the cell. They are also an attractive route towards artificial tran- scription control, since binding an appropriate single polynucleotide to a DNA duplex can inhibit transcription. This technique is known as the anti-gene strat- egy. The related technique of targeting a polynucleotide against a single stranded RNA to form a duplex is known as the anti-sense strategy. Since exogenous single strands are rapidly degraded within the cell, and also because the forma- tion of duplex or triplex structures corresponds to a thermodynamic equilibrium, chemists have gone to considerable lengths to create modified nucleotides that will survive longer and bind better. If you are interested in this area, look up the work of Peter Nielsen on PNA (peptide nucleic acid) where the sugar-phosphate backbone has been replaced with modified peptide linkages, without damaging the possibility of base pairing with conventional polynucleotides. A final structure which should be mentioned is the so-called Holliday junction (figure 6) which can be formed as a response to negative superhelical stress at inverted sequence repeats. Stress leads to local unpairing and the extrusion of two single strands which can then reform base pairs leading to a four helix junction. Although these junctions are conventionally drawn as square planar structures, they can fold up into a more compact tetrahedral form in the presence of Mg2+ ions.
- 44. DNA structure, dynamics and recognition 15 Fig. 5. Types of base pairing.
- 45. 16 R. Lavery Fig. 6. Schematic Holliday junction. 2. Biophysical studies of DNA – structure and stability Probably the most important technique for studying DNA has already been dis- cussed in the preceding section, namely X-ray diffraction. While the X-ray diffraction of DNA fibres only gave partial structural information, the advent of solid phase synthesis techniques made it possible to routinely prepare suf- ficient quantities of pure DNA oligomers (typically 10 or 12 base pairs long) to grow single crystals and obtain high-resolution data. (It is now possible to buy long oligomers with defined sequences. Automated synthesis has progressed to the point where Craig Venter’s company is considering synthesizing the en- tire genome of a “minimal” organism containing several hundred thousand base pairs.) Crystallisation remains an art dependent on finding exactly the right solvent, salt and temperature conditions. Robots have however made these searches less tedious and intense synchrotron radiation has allowed results to be obtained from smaller and smaller crystals. The quality of X-ray structures is defined by two factors: the resolution, which is dependent on the diffraction behaviour of the crystal and the R-factor which tests the quality of the calculated structure by comparing its predicted diffraction pattern with that observed experimentally. Good results correspond to a resolution of at least 2.5 Å and an R-factor below 0.25. The very best crystals diffract to roughly 1 Å and yield electron density maps that enable individual atoms, including hydrogens, to be distinguished. Although X-ray diffraction is undoubtedly the best technique available for determining the fine structure of DNA, the very process of forming crystals does run the risk of deforming the oligomers. Such deformations can notably affect helix bending and these problems have hindered the use of crystallography as
- 46. DNA structure, dynamics and recognition 17 a means for understanding sequence-induced structural changes in the double helix. The crystalline environment can also favour allomorphic transitions for some sequences (notably B→A) and other changes are also found more locally in the sugar-phosphate backbone conformations. Thus it is not clear that the crystalline conformation of an oligomer will necessarily reflect its conformation in solution, although a good match is found in many cases. NMR spectroscopy (which studies atomic spin inversions) offers the possibil- ity of studying DNA structure in solution and thus of avoiding crystal packing effects, however it does not provide the same quantity of information as X-ray diffraction. The two principal families of NMR experiments are termed COSY (COrrelation SpectroscopY) and NOESY (Nuclear Overhauser Effect Spectros- copY). COSY experiments give access to dihedral angles, while NOESY ex- periments provide through-space interatomic distances. (It remains difficult to directly exploit chemical shift data, although progress is being made in the quan- tum chemical calculations necessary to understand how local electronic struc- ture influences the shielding of individual atomic spin centres.) Both COSY and NOESY methods require an initial analysis step where individual spectral peaks are assigned to specific chemical groups within specific nucleotides – using a stepwise procedure exploiting the chemical connectivity of the oligomer. Be- cause peaks often overlap it is generally necessary to use pulse sequences which enable the spectra to be spread out over 2 or sometimes 3 dimensions. Since most NMR experiments study the spin inversions of hydrogen atoms, only a sub- set of the dihedral angles in the DNA backbone are accessible. Likewise, the distance dependence of NOESY coupling limits the detection of atomic interac- tions to distances below roughly 5 Å. This information is insufficient to obtain a 3D structure and means that model building, constrained to fit the available experimental data, is an indispensable part of NMR studies. In contrast to X-ray diffraction, it is not possible to define a single resolution for NMR structures. Since a variety of models generally fit the spectral data (re- flecting, in large part, the thermal motions of the oligomers in solution), NMR results are generally presented as an ensemble of 10 or 20 related conforma- tions. While local elements of these structures (glycosidic angles, sugar puckers, base hydrogen bonding, . . .) are generally well defined, more subtle, long-range characteristics, such as axis bending, are more difficult to get at because they are sensitive to even small imprecisions in the data. A new NMR technique, termed RDC (residual dipolar coupling), offers a way of accessing longer inter- atomic distances and should result in considerable improvements for DNA. To date, only a few RDC studies have been carried out and it is too early to judge the quantitative improvement they represent. As a result of both X-ray diffraction and NMR spectroscopy, a large num- ber of DNA oligomer structures are now available in the PDB (Protein Data
- 47. 18 R. Lavery Base, http://www.rcsb.org/pdb/) and NDB databases (Nucleic acid Data Base, http://ndbserver.rutgers.edu/). These databases are now grouped together under the RCSB (Research Collaboratory for Structural Bioinformatics) run by Helen Berman’s group at Rutgers University. They also contain many DNA-ligand and DNA-protein complexes. Both databases provide tools for rapidly locating and for analyzing chosen structures and they represent a very valuable, and freely available, research resource. Given the difficulties associated with both X-ray diffraction and NMR spec- troscopy, lower resolution techniques can still play a significant role in DNA biophysical studies of DNA. Amongst these are UV (Ultra-Violet) and IR (Infra- Red) spectroscopy. UV radiation is sufficiently energetic to induce electronic transitions. Large molecules such as DNA do not give well-defined UV spectra, but rather large bands which are sensitive to changes in molecular disorder. This makes UV spectroscopy a useful tool for studying DNA melting, since the ab- sorbance curve versus temperature (generally measured at a wavelength around 260 nm) gives access to Tm, the temperature at which 50% of the sampled has denatured from a double helix to disordered single strands. UV experiments on DNA fragments of known sequences show that higher GC content leads to a higher Tm. If you refer back to figure 1, you can see that this can be explained by the fact that GC base pairs are bound together by three hydrogen bonds, while AT pairs only have two. We will return to a more detailed discussion of double helix stability shortly. A second use of UV radiation involves fluorescent resonance energy transfer (or FRET) between a fluorophore and a quencher group. An appropriate choice of these two groups enables short-range resonant interactions to inhibit the UV fluorescence of the fluorophore. If the two groups become spatially separated, this fluorescence is re-established. Attaching the two groups to appropriate posi- tions in a DNA molecule enables FRET to be used as a powerful molecular ruler for distances up to the order of 10 Å. Less energetic IR radiation is sensitive to bond vibrations and IR spectroscopy of DNA can therefore be used to define certain overall structural characteristics such as the dominant anti-syn state of the glycosidic bonds or the percentages of various sugar ring puckers. Raman FTIR (Fourier Transform Infra-Red spec- troscopy) is the most common type of IR experiment since it avoids interference from water vibrations. Another useful tool for studying DNA is CD (Circular dichroism). This type of spectroscopy measures how a molecule selectively absorbs left- or right- handed circularly polarised light. It is sensitive to molecular chirality and, in the case of DNA, was notably used to predict that the Z form was a left-handed double helix. It can provide data on the orientation of the base pairs with respect to the helical axis, but quantitative interpretation of the data is not easy since it
- 48. DNA structure, dynamics and recognition 19 Table 3 Energetics of DNA Stabilising factors: Base pairing (electrostatics/LJ) Base stacking (hydrophobic) Ion binding (electrostatics) Solvation entropy Destabilising factors: Phosphate repulsion (electrostatics) Solvation enthalpy (electrostatics/LJ) DNA strand entropy is still difficult to calculate the theoretical CD spectra corresponding to a given molecular conformation. I should lastly mention the technique of neutron scattering (in either the elastic or inelastic regimes), which is gives access to information on dynamic fluctua- tions occurring in the picosecond to nanosecond timescale. This is a particularly interesting range for modellers since it corresponds to the timescale covered by molecular dynamics simulations. However, this technique has not been widely used for studying DNA. It should be remarked that one of its drawbacks is that it requires large quantities of the sample molecule. I would now like to turn to a more general discussion of the stability of the DNA double helix. Many factors contribute to the equilibrium between the single and double stranded forms of DNA as shown in table 3. Amongst the stabilizing factors, most people immediately think of base pair hydrogen bonding. However, it should be remembered that in aqueous solution the bases are already interact- ing with water molecules before they come together to form base pairs. This balance means that a single base pair hydrogen bond contributes only roughly 1 kcal.mol−1 to stabilizing the double helix, compared to roughly 5 kcal.mol−1 if its formation enthalpy is measured in vacuum. (Note, in passing, that hydrogen bond stability results mainly from dipolar electrostatic interactions, but it also has a roughly 30% dispersion component, treated by the Lennard-Jones term in force fields.) In fact, the double helix is more significantly stabilized by base stacking than by base pairing. This can be deduced from the fact that free bases in water stack on top of one another rather than forming hydrogen bonded pairs. Stacking en- ables the bases to remove the hydrophobic π-clouds of their conjugated rings from solution, without hindering access to the hydrophilic groups (involved in hydrogen bonding) around their peripheries. It should also be noted that stack- ing acts not only “vertically” between the successive bases in each strand of the double helix, but also “diagonally” between the neighbouring bases in opposing strands. This means that the total stacking between two successive base pairs
- 49. 20 R. Lavery is composed of four contributions, two vertical and two diagonal. Depending on the nature of the base pairs and the overall conformation of the double helix, the diagonal contributions can actually dominate the total stacking interaction. The next stabilizing factor is ion binding. Counter-ions are indispensable for overcoming the electrostatic repulsion between the anionic phosphates which are regularly spaced along each of the backbones of DNA. Their importance can be judged from the fact that the DNA double helix is not stable in pure water. Al- though water has a high dielectric constant (≈80), this alone is not enough to overcome the phosphate-phosphate repulsion. The importance of electrostatics for DNA is also illustrated by the fact that its stability is enormously increased when one of its strands is replaced by the neutral “peptide nucleic acid” syn- thesized by Peter Nielsen (which was already mentioned earlier). The resulting hybrid is stable for hours in boiling water, in striking contrast to normal DNA. The last stabilizing factor to be considered is solvent entropy. This results from the fact that bringing together two single strands requires desolvation of their interacting faces. This releases a large number of previously bound water mole- cules into solution, with a consequent gain in entropy. Desolvation however also has a negative side, since removing the water molecules causes an enthalpy loss, a significantly destabilizing factor. A further disadvantage of forming a double helix is that loss of flexibility in the single strands (remember that the persistence length of DNA changes from roughly 4 Å to 500 Å upon forming a double helix) which represents an entropy penalty. Each of the terms we have discussed can amount to hundreds of kcal.mol−1 for even a short DNA oligomer. It is a subtle balance between these large con- tributions which leads finally to a stable helix. A good way to get a feeling for the balances involved is provided by a thermodynamic study carried out in Ken Breslauer’s group (see figure 7). The results of this study, which concern a 13 bp fragment of DNA with the sequence CGCATGAGTACGC, enable us to break down the helix-coil transition into two steps, the passage from a double-stranded helix (ds) into two helical single strands (s1 and s2) and then the passage of each of these strands to a disordered coil. The numbers given in figure 7 show that the double helix is stabilized by 20 kcal.mol−1, but that this number actually hides opposing enthalpy and entropy changes which are roughly five times larger. If we now look at the single strands, their helical forms (h) are still stabilized en- thalpically with respect to random coils (r) by roughly 30 kcal.mol−1 (almost exclusively due to base stacking). This term is however almost exactly compen- sated by the entropic loss associated with helical ordering. As a result, single strand ordering is easily disrupted by thermal agitation at room temperature. Even for double helices, the overall balance of the enthalpic and entropic terms we have just discussed means that DNA (like most biological complexes) is only moderately stable at room temperature. This is an advantage in most cases, mak-
- 50. DNA structure, dynamics and recognition 21 Fig. 7. Double helix to coil transitions (values in kcal.mol−1). ing it easy to locally separate the two strands of a double helix in order to translate or replicate the genetic message. This ease can be increased further by negatively supercoiling, a strategy used by most living organisms. However, this moderate stability can become a liability when things get hot. This explains the fact that thermophiles need to keep their DNA positively supercoiled to avoid it unravel- ling. 3. DNA dynamics Although experimental studies provide overall information on DNA dynamics (for example, through the atomic fluctuations probed by crystallographic B-fac- tors), molecular simulations provide the only fully detailed information on dy- namics and, in particular, offer the only hope at present of obtaining a compre- hensive view of base sequence effects on dynamics. I would therefore like to spend a little time describing how simulations are carried out and what data they have provided so far. The starting point for such simulations is an energy functional (or force field) which gives the conformational energy of a molecule as a function of the rela- tive positions of its constituent atoms. Such force fields are empirical, although their terms are based on the various physical interactions which play a role in de- termining molecular structure. Their terms can be divided into those describing
- 51. 22 R. Lavery Fig. 8. Force field terms. the interactions of chemically bonded atoms and those dealing with longer-range (termed, non-bonded) interactions. Typical functional forms are shown in fig- ure 8. In the first group we find bond length, valence angle and dihedral terms which depend respectively on the relative positions of two, three or four linearly bonded atoms. The first two of these terms are generally quadratic functions, while the third is based on a cosine function. Each must be parameterized to re- produce the appropriate experimental (or quantum chemically calculated) value of the bond length, valence angle or dihedral (or set of symmetrically equiva- lent dihedrals) and be associated with an appropriate force constant determining the flexibility of the corresponding value. Such parameters need to be obtained for each chemically distinct class of bonds, valence angles or dihedrals, classes which are in turn determined by the “classes” of atom which compose them. Non-bonded interactions are generally limited to a Coulomb term describing the electrostatic interactions between fractional charges on each of the atoms and a Lennard-Jones term describing short-range interatomic repulsion and disper- sion interactions. The fractional atomic charges within a molecule are gener- ally determined by a fitting procedure aimed at reproducing the quantum chem- ically calculated electrostatic potential surrounding the molecule. (In the case of macromolecules, this procedure is actually applied to overlapping molecular fragments.) Lennard-Jones terms, including short range repulsion and dispersion, are obtained for interactions between all necessary atomic “classes”, generally by fitting to data from the crystalline phases of small organic molecules. The reason for using the term atomic “classes” is that, given the empirical nature of force fields, it is not enough to have one set of parameters for a given atom type. It is necessary, for example, to distinguish aromatic and aliphatic carbon atoms, and amine and imine nitrogens, etc. Modern force fields typically contain around 50 atomic classes. For more details see the book by Leach cited at the end of this chapter.
- 52. DNA structure, dynamics and recognition 23 Fig. 9. MD protocol. Carrying out a molecular dynamics simulation involves integrating Newton’s equation of motion in time, using an appropriate force field to obtain the energy of the system and the forces acting on each atom. The integration has to be made in finite steps which must be smaller than the faster fluctuations occurring in the system. Since the vibrations of chemical bonds involving hydrogen have a char- acteristic time of a few femtoseconds (fs), the dynamics time step is generally set to 1-2 fs. Since DNA, like other biomacromolecules, is only stable in salty water, simulations must take into account a layer of water molecules contain- ing counterions surrounding the solute molecule. This greatly increases the size of the system to be treated. As an example, a 15 base pair DNA double helix (containing roughly 1000 atoms) requires a solvent shell of roughly 5000 water molecules. The simulated system is contained within a box, which is typically a rectangular prism or a truncated octahedron. Artefacts linked to edge-effects are avoided by symmetrically reproducing the box in all directions. These so-called “periodic boundary conditions” mean that a solvent molecule or ion leaving the simulation box on one side will simultaneously re-enter the box on the opposite side. Having set up the initial conformation of the system, and generally carried out energy minimization to ensure that there are no close atomic contacts, the sys- tem can be gently heated (by increasing the atomic velocities) until the desired simulation temperature is reached (figure 9). The so-called production phase of the simulation can then be carried out in various thermodynamic ensembles,
- 53. 24 R. Lavery Fig. 10. MD time series. the most common being the isothermal-isobaric ensemble (NPT), where both the temperature and the pressure of the simulated system are controlled by respec- tively modulating the atomic velocities and the size of the simulation cell. Given the computational cost of molecular dynamic simulations for macromolecular systems, production runs are typically limited to a few tens of nanoseconds. What do we get out of such simulations? Firstly, it is possible to analyze in detail the way a DNA fragment fluctuates at room temperature. This can be done by making a movie of the simulation, superposing snapshots drawn from the simulation or studying time series of the backbone or helical parameters describ- ing the fragment (figure 10 shows examples for sugar puckering and fluctuations in groove width). The results show that DNA undergoes dramatic fluctuations which considerably exceed those deduced by looking at an ensemble of DNA crystal structures. These fluctuations apply to both local backbone parameters (such as sugar puckers, phosphodiester dihedrals) and to helical parameters (such as rise and twist). They also show how base sequence can influence the structure and dynamics of the double helix and they have notably helped to understand how some sequences can induce bending of the helical axis (see below). By changing the solvent conditions it has also been possible to study spontaneous
- 54. DNA structure, dynamics and recognition 25 transitions between the A and B forms of DNA and it is also possible to study slower processes, such as base pair opening, by using constraints which force the simulation to sample what would otherwise be extremely rare events. I will return to this later. An international group of laboratories (ABC, the Ascona B-DNA Consortium) has recently been formed to carry out enough DNA simulations to be able to get a comprehensive view of sequence effects. The initial stage of this project involved 15 ns simulations on a group of 39 oligomers. Each oligomer contained a tetranucleotide repeating sequence and these sequences were chosen so that the whole dataset would provide information on the 136 unique tetranucleotide sequences which can be formed from AT, TA, CG and GC base pairs. The project is far from finished, but the initial results have already led to some surprises, notably that the phosphodiester backbones can adopt finite set of conformational substates and that the barriers separating some of these substates are high enough to hinder proper sampling within a multi-nanosecond timescale. It has also been shown that ion distributions around DNA converge very slowly and that different monovalent ions have different influences on both backbone transitions and on the overall structure of DNA fragments. 4. Deformations of the double helix Before discussing the major deformations that DNA undergoes, it is worth saying a few words about how to analyze its deformed conformations. Since DNA is a double helix it is useful to speak in terms of helical parameters. The names and geometrical sense of the various helical parameters is shown in figure 11. Fig. 11. Helical parameters.
- 55. Other documents randomly have different content
- 59. The Project Gutenberg eBook of Life of Thomas Paine
- 60. This ebook is for the use of anyone anywhere in the United States and most other parts of the world at no cost and with almost no restrictions whatsoever. You may copy it, give it away or re-use it under the terms of the Project Gutenberg License included with this ebook or online at www.gutenberg.org. If you are not located in the United States, you will have to check the laws of the country where you are located before using this eBook. Title: Life of Thomas Paine Author: Richard Carlile Release date: July 11, 2012 [eBook #40208] Most recently updated: October 23, 2024 Language: English Credits: Produced by David Widger *** START OF THE PROJECT GUTENBERG EBOOK LIFE OF THOMAS PAINE ***
- 61. LIFE OF THOMAS PAINE WRITTEN PURPOSELY TO BIND WITH HIS WRITINGS
- 62. By Richard Carlile SECOND EDITION. 1821. LIFE OF THOMAS PAINE The present Memoir is not written as a thing altogether necessary, or what was much wanted, but because it is usual and fitting in all collections of the writings of the same Author to accompany them with a brief account of his life; so that the reader might at the same time be furnished with a key to the Author's mind, principles, and works, as the best general preface. On such an occasion it does not become the Compiler to seek after the adulation of friends, or the slander of enemies; it is equally unnecessary to please or perplex the reader with either; for when an author has passed the bar of nature, it behoves us not to listen to any tales about what he was, or what he did, but to form our judgments of the utility or non-utility
- 63. of his life, by the writings he has left behind him. Our business is with the spirit or immortal part of the man. If his writings be calculated to render him immortal, we have nothing to do with the body that is earthly and corruptible, and which passes away into the common mass of regenerating matter. Whilst the man is living, we are justified in prying into his actions to see whether his example corresponds with his precept, but when dead, his writings must stand or fall by the test of reason and its influence on public opinion. The excess of admiration and vituperation has gone forth against the name and memory of the Author of Rights of Man, and Age of Reason, but it shall be the endeavour of the present Compiler to steer clear of both, and to draw from the reader an acknowledgement that here the Life and Character of Paine is fairly stated, and that here the enquirer after truth may find that which he most desires—an unvarnished statement. Thomas Paine was born at Thetford, in the county of Norfolk, in England, on the 29th of January, 1737. He received such education as the town could afford him, until he was thirteen years of age, when his father, who was a staymaker, took him upon the shop- board. Before his twentieth year, he set out for London to work as a journeyman, and from London to the coast of Kent. Here he became inflamed with the desire of a trip to sea, and he accordingly served in two privateers, but was prevailed upon by the affectionate remonstrances of his father, who had been bred a Quaker, to relinquish the sea-faring life. He then set up as a master stay maker at Sandwich, in the county of Kent, when he was about twenty-three years of age. It appears that he had a thorough distaste for this trade, and having married the daughter of an exciseman, he soon began to turn his attention to that office. Having qualified himself he soon got appointed, but from some unknown cause his commission scarcely exceeded a year. He then filled the office of an usher at two different schools in the suburbs of London, and by his assiduous application to study, and by his regular attendance at certain astronomical and mathematical lectures in London, he became a proficient in those sciences, and from this moment his mind, which
- 64. was correct and sound, began to expand, and here that lustre began to sparkle, which subsequently burst into a blaze, and gave light both to America and Europe. He again obtained an appointment in the Excise, and was stationed at Lewes, in Sussex, and in this town the first known production of his pen was printed and published. He had displayed considerable ability in two or three poetical compositions, and his fame beginning to spread in this neighbourhood, he was selected by the whole body of excisemen to draw up a case in support of a petition they were about to present to Parliament for an increase of salary. This task he performed in a most able and satisfactory manner, and although this incident drew forth his first essay at prose composition, it would have done honour to the first literary character in the country; and it did not fail to obtain for Mr. Paine universal approbation. The Case of the Officers of Excise is so temperately stated, the propriety of increasing their salaries, which were then but small, urged with such powerful reasons and striking convictions, that although we might abhor such an inquisitorial system of excise as has long disgraced this country, we cannot fail to admire the arguments and abilities of Mr. Paine, who was then an exciseman, in an endeavour to increase their salaries. He was evidently the child of nature from the beginning, and the success of his writings was mainly attributable to his never losing sight of this infallible guide. In his recommendation to Government to increase the salaries of excisemen, he argues from natural feelings, and shews the absolute necessity of placing a man beyond the reach of want, if honesty be expected in a place of trust, and that the strongest inducement to honesty is to raise the spirit of a man, by enabling and encouraging him to make a respectable appearance. This Case of the Officers of Excise procured Mr. Paine an introduction to Oliver Goldsmith, with whom he continued on terms of intimacy during his stay in England. His English poetical productions consisted of The Death of Wolfe, a song; and the humourous narrative, about The Three Justices and Farmer Short's Dog. At least, these two pieces are all that we now have in print. I
- 65. have concisely stated Mr. Paine's advance to manhood and fame considering the act but infantile in being elaborate upon the infancy and youth of a public character who displays nothing extraordinary until he reaches manhood. My object here is not to make a volume, but to compress all that is desirable to be known of the Author, in as small a compass as possible. Mr. Paine was twice married, but obtained no children: his first wife he enjoyed but a short time, and his second he never enjoyed at all, as they never cohabited, and before Mr. Paine left England they separated by mutual consent, and by articles of agreement. Mr. Paine often said, that he found sufficient cause for this curious incident, but he never divulged the particulars to any person, and, when pressed to the point, he would say that it was nobody's business but his own. In the autumn of 1774, being then out of the Excise, he was introduced to the celebrated Dr. Franklin, then on an embassy to England respecting the dispute with the Colonies, and the Doctor was so much pleased with Mr. Paine, that he pointed his attention to America as the best mart for his talents and principles, and gave him letters of recommendation to several friends. Mr. Paine took his voyage immediately, and reached Philadelphia just before Christmas. In January he had become acquainted with a Mr. Aitkin, a bookseller, who it appears started a magazine for the purpose of availing himself of Mr. Paine's talents. It was called the Pennsylvania Magazine, and, from our Author's abilities, soon obtained a currency that exceeded any other work of the kind in America. Many of Mr. Paine's productions in the papers and magazines of America have never reached this country so as to be republished, but such as we have are extremely beautiful, and compel us to admit, that his literary productions are as admirable for style, as his political and theological are for principle. From his connection with the leading characters at Philadelphia, Mr. Paine immediately took a part in the politics of the Colonies, and being a staunch friend to the general freedom and happiness of the human race, he was the first to advise the Americans to assert their independence. This he did in his famous pamphlet, intitled Common
- 66. Sense, which for its consequences and rapid effect was the most important production that ever issued from the press. This pamphlet appeared at the commencement of the year 1776, and it electrified the minds of the oppressed Americans. They had not ventured to harbour the idea of independence, and they dreaded war so much as to be anxious for reconciliation with Britain. One incident which gave a stimulus to the pamphlet Common Sense was, that it happened to appear on the very day that the King of England's speech reached the United States, in which the Americans were denounced as rebels and traitors, and in which speech it was asserted to be the right of the Legislature of England to bind the Colonies in all cases whatsoever! Such menace and assertion as this could not fail to kindle the ire of the Americans, and Common Sense came forward to touch their feelings with the spirit of independence in the very nick of time. On the 4th of July, in the same year, the independence of the United States was declared, and Paine had then become so much an object of esteem, that he joined the army, and was with it a considerable time. He was the common favourite of all the officers, and every other liberal-minded man, that advocated the independence of his country, and preferred liberty to slavery. It does not appear that Paine held any rank in the army, but merely assisted with his advice and presence as a private individual. Whilst with the army, he began, in December of the same year, to publish his papers intitled The Crisis. These came out as small pamphlets and appeared in the newspapers, they were written occasionally, as circumstances required. The chief object of these seems to have been to encourage the Americans, to stimulate them to exertion in support and defence of their independence, and to rouse their spirits after any little disaster or defeat. Those papers, which also bore the signature of Common Sense, were continued every three or four months until the struggle was over. In the year 1777, Mr. Paine was called away from the army by an unexpected appointment to fill the office of Secretary to the Committee for Foreign Affairs. In this office, as all foreign
- 67. correspondence passed through his hands, he obtained an insight into the mode of transacting business in the different Courts of Europe, and imbibed much important information. He did not continue in it above two years, and the circumstance of his resignation seems to have been much to his honour as an honest man. It was in consequence of some peculation discovered to have been committed by one Silas Deane who had been a commissioner from the United States to some part of Europe. The discovery was made by Mr. Paine, and he immediately published it in the papers, which gave offence to certain members of the Congress, and in consequence of some threat of Silas Deane, the Congress shewed a disposition to censure Mr. Paine without giving him a hearing, who immediately protested against such a proceeding, and resigned his situation. However, he carried no pique with him into his retirement, but was as ardent as ever in the cause of independence and a total separation from Britain. He published several plans for an equal system of taxation to enable the Congress to recruit the finances and to reinforce the army, and in the most clear and pointed manner, held out to the inhabitants of the United States, the important advantages they would gain by a cheerful contribution towards the exigencies of the times, and at once to make themselves sufficiently formidable, not only to cope with, but to defeat the enemy. He reasoned with them on the impossibility of any army that Britain could send against them, being sufficient to conquer the Continent of America. He again and again explained to them that nothing but fortitude and exertion was necessary on their part to annihilate in one campaign the forces of Britain, and put a stop to the war. It is evident, and admitted on all sides, that these writings of Mr. Paine became the main spring of action in procuring independence to the United States. Notwithstanding the little disagreement he had with the Congress, it was ready at the close of the war to acknowledge his services by a grant of three thousand dollars, and he also obtained from the State of New York, the confiscated estate of some slavish lory and royalist, situate at New Rochelle. This estate contained three hundred acres
- 68. of highly, cultivated land, and a large and substantial stone built house. The State of Pennsylvania, in which he first published Common Sense and The Crisis, presented him with £500 sterling; and the State of Virginia had come to an agreement for a liberal grant, but in consequence of Mr. Paine's interference and resistance to some claim of territory made by that State, in his pamphlet, intitled Public Good, he lost this grant by a majority of one vote. This pamphlet is worthy of reading, but for this single circumstance, and nothing can more strongly argue the genuine patriotism and real disinterestedness of the man, than his opposing the claims of this State at a moment when it was about to make him a more liberal grant than any other State had done. It was in the year 1779, that Mr. Paine resigned his office as Secretary to the Committee for Foreign Affairs, and in the year 1781, he was, in conjunction with a Colonel Laurens, dispatched to France to try to obtain a loan from that government. They succeeded in their object, and returned to America with two millions and a half of livres in silver, and stores to the united value of sixteen millions of livres. This circumstance gave such vigour to the cause of the Americans, that they shortly afterwards brought the Marquis Cornwallis to a capitulation. Six millions of livres were a present from France, and ten millions were borrowed from Holland on the security of France. In this trip to France, Mr. Paine not only accomplished the object of his embassy, but he also made a full discovery of the traitorous conduct of Silas Deane, and, on his return fully justified himself before his fellow citizens, in the steps he had taken in that affair, whilst Deane was obliged to shelter himself in England from the punishment due to his crimes. In a number of the Crisis, Mr. Paine says, it was the cause of independence to the United States, that made him an author; by this it has been argued, that he could not have written The Case of the Officers of Excise before going to America, but this I consider to be easy of explanation. As the latter pamphlet was published by the subscriptions of the officers of excise, and as it was a mere statement of their case, drawn up at their request and suggestion,
- 69. Mr. Paine might hardly consider himself, intitled to the name of author for such a production which had but a momentary and partial object. He might have considered himself as the mere amanueusis of the body of excisemen, and, to have done nothing more than state their complaint and sentiments. It does not appear that the pamphlet was printed for sale, or that the writer ever had, or thought to have, any emolument from it. It must have been in this light that Mr. Paine declined the character of an Author on the account of that pamphlet, for no man need be ashamed to father it either for principle or style. In the same manner might be considered his song On the Death of General Wolfe, his Reflections on the Death of Lord Clive, and several other essays and articles that appeared in the Pennsylvania Magazine, and the different newspapers of America, all of which had obtained celebrity as something superior to the general rank of literature that had appeared in the Colonies, and yet even on this ground he also relinquished the title of an author. To be sure, a man who writes a letter to his relatives or friends is an author, but Mr. Paine thought the word of more import, and did not call himself an author until he saw the benefits he had conferred on his fellow-citizens and mankind at large, by his well-timed Common Sense and Crisis. During the struggle for independence, the Abbe Raynal, a French author, had written and published what he called a History of the Revolution, or Reflections on that History, in which he had made some erroneous statements, probably guided by the errors, wilful or accidental, in the European newspapers. Mr. Paine answered the Abbe in a letter, and pointed out all his misstatements, with a hope of correcting the future historian. This letter is remarkably well written, and abounds with brilliant ideas and natural embellishments. Ovid's classical and highly admired picture of Envy, can scarcely vie with the picture our Author has drawn of Prejudice in this letter. It will be sure to arrest the reader's attention, therefore I will not mar it by an extract. Mr. Paine never deviated from the path of nature, and he was unquestionably as bright an ornament as ever our
- 70. Common Parent held up to mankind. He studied Nature in preference to books, and thought and compared as well as read. The hopes of the British Government having been baffled in the expected reduction of the Colonies, and being compelled to acknowledge their independence, Mr. Paine had now leisure to turn to his mechanical and philosophical studies. He was admitted a member of the American Philosophical Society, and appointed Master of Arts, by the University of Philadelphia, and we find nothing from his pen in the shape of a pamphlet until the year 1786, He then published his Dissertations on Governments, the Affairs of the Bank, and Paper Money. The object of this pamphlet was to expose the injustice and ingratitude of the Congress in withdrawing the charter of incorporation from the American Bank, and to show, that it would rather injure than benefit the community. The origin of this Bank having been solely for the carrying on of the war with vigour, and to furnish the army with necessary supplies, at a time when the want of food and clothing threatened a mutiny, Mr. Paine condemned the attempt to suppress it as an act of ingratitude. At a moment when the United States were overwhelmed with a general gloom by repeated losses and disasters, and by want of vigour to oppose the enemy, Mr. Paine proposed a voluntary contribution to recruit the army, and sent his proposal, and five hundred dollars as a commencement, to his friend Mr. M'Clenaghan. The proposal was instantly embraced, and such was the spirit by which it was followed, that the Congress established the leading subscribers into a Bank Company, and gave them a charter. This incident might be said to have saved America for that time, and as Mr. Paine has fairly shown that the Bank was highly advantageous to the interest of the United States at the time of its suppression, and that the act proceeded from party spleen, we cannot fail to applaud the spirit of this pamphlet, although it was an attack on the conduct of the Congress. It forms another proof that our Author never suffered his duty and principle to be biassed by his interest. In the year 1787, Mr. Paine returned to Europe, and first proceeded to Paris, where he obtained considerable applause for the
- 71. construction of a model of an iron bridge which he presented to the Academy of Sciences. The iron bridge is now becoming general in almost all new erections, and will doubtless, in a few years, supersede the more tedious and expensive method of building bridges with stone. How few are those who walk across the bridge of Vauxhall and call to mind that Thomas Paine was the first to suggest and recommend the use of the iron bridge: he says, that he borrowed the idea of this kind of bridge from seeing a certain species of spider spin its web*! In the mechanical arts Mr. Paine took great delight, and made considerable progress. In this, as in his political and theological pursuits, to ameliorate the condition, and to add to the comforts, of his fellow men, was his first object and final aim. * The famous iron bridge of one arch at Sunderland was the first result of this discovery, although another gentleman claimed the invention and took credit for it with impunity, in consequence of the general prejudice against the name and writings of Mr. Paine. It is a sufficient attestation of this fact, to say, that the Sunderland bridge was cast at the foundery of Mr. Walker, at Rotheram, in 'Yorkshire, where Mr. Paine had made his first experiment on an extensive scale. From Paris Mr. Paine returned to England after an absence of thirteen years, in which time he had lost his father, and found his mother in distress. He hastened to Thetford to relieve her, and settled a small weekly sum upon her to make her comfortable. He spent a few weeks in his native town, and wrote the pamphlet, intitled Prospects on the Rubicon, c. at this time, which appears to have been done as much for amusement and pastime as any thing else, as it has no peculiar object, like most of his other writings, and the want of that object is visible throughout the work. It is more of a general subject than Paine was in the habit of indulging in, and its publication in England produced but little attraction. France, at this moment, had scarcely begun to indicate her determination to reform her government. England was engaged in the affairs of the Stadt-holder of Holland; and there seemed a confusion among the principal governments of
- 72. Europe, but no disposition for war. Mr. Paine having become intimate with Mr. Walker, a large iron- founder of Rotheram, in Yorkshire, retired thither for the purpose of trying the experiment of his bridge. The particulars of this experiment, with an explanation of its success, the reader will find fully developed in his letter to Sir George Staunton. This letter was sent to the Society of Arts in the Adelphi, and was about to be printed in their transactions, but the appearance of the First Part of Rights of Man, put a stop to its publication in that shape, and afforded us a lesson that bigotry and prejudice form a woeful bar to science and improvement. For the expence of this bridge Mr. Paine had drawn considerable sums from a Mr. Whiteside, an American merchant, on the security of his American property, but this Mr. Whiteside becoming a bankrupt, Mr. Paine was suddenly arrested by his assignees, but soon liberated by two other American merchants becoming his bail, until he could make arrangements for the necessary remittances from America. During the American war, Mr. Paine had felt a strong; desire to come privately into England, and publish a pamphlet on the real state of the war, and display to the people of England the atrocities of that cause they were so blinded to support. He had an impression that this step would have more effect to stop the bloody career of the English Government, than all he could write in America, and transmit to the English newspapers. It was with difficulty that his friends got him to abandon this idea, and after he had succeeded in obtaining the loan from the French Government, he proposed to Colonel Laurens to return alone, and let him go to England for this purpose. The Colonel, however, positively refused to return without him, and in this purpose he was overcome by the force of friendship. Still the same idea lingered in his bosom after the Americans had won their independence. Mr. Paine loved his country and countrymen, and was anxious to assist them in reforming their Government. The attack which Mr. Burke made upon the French Revolution soon gave him an opportunity of doing this, and the
- 73. production of Rights of Man will ever rank Mr. Paine among the first and best of writers on political economy. The friend and companion of Washington and Franklin could not fail to obtain an introduction to the leading political characters in England, such as Burke, Horne Tooke, and the most celebrated persons of that day. Burke had been the opponent of the English Government during the American war, and was admired as the advocate of constitutional freedom. Pitt, the most insidious and most destructive man that ever swayed the affairs of England, saw the necessity of tampering with Burke, and found him venal. It was agreed between them that Burke should receive a pension in a fictitious name, but outwardly continue his former character, the better to learn the dispositions of the leaders in the opposition, as to the principles they might imbibe from the American revolution, and the approaching revolution in France. This was the master-piece of Pitt's policy, he bought up all the talent that was opposed to his measures, but instead of requiring a direct support, he made such persons continue as spies on their former associates, and thus was not only informed of all that was passing, but, by his agents, was enabled to stifle every measure that was calculated to affect him, by interposing the advice of his bribed opponents and pseudo-patriots. It was thus Mr. Paine was drawn into the company of Burke, and even a correspondence with him on the affairs of France; and it was not until Pitt saw the necessity of availing himself of the avowed apostacy of Burke, and of getting him to make a violent attack upon the French revolution, that Mr. Paine discovered his mistake in the man. It is beyond question that Burke's attack on the French Revolution had a most powerful effect in this country, and kindled a hatred without shewing a cause for it, but still, as honest principle will always outlive treachery, it drew forth from Mr. Paine his Rights of Man which will stand as a lesson to all people in all future generations whose government might require reformation. Vice can triumph but for a moment, whilst the triumph of virtue is perpetual.
- 74. The laws of England have been a great bar to the propagation of sound principles and useful lessons on Government, for whatever might have been the disposition and abilities of authors, they have been compelled to limit that disposition and those abilities to the disposition and abilities of the publisher. Thus it has been difficult for a bold and honest man to find a bold and honest publisher; even in the present day it continues to be the same, and the only effectual way of going to work is, for every author to turn printer and publisher as well. Without this measure every good work has to be mangled according to the humour of the publisher employed. It was thus Mr. Paine found great difficulty in procuring a publisher even for his First Part of Rights of Man. It was thus the great and good Major Cartwright found it necessary during the Suspension of the Habeas Corpus to take a shop and sell his own pamphlets. I do not mean to say that there is a fault in publishers, the fault lays elsewhere, for it is well known that as soon as a man finds himself within the walls of a gaol for any patriotic act, those outside trouble themselves but little about him. It is the want of a due encouragement which the nation should bestow on all useful and persecuted publishers. I may be told that this last observation has a selfish appearance, but let the general statement be first contradicted, then I will plead guilty to selfish views. Mr. Paine would not allow any man to make any the least alteration or even correction in his writings. He carried this disposition so far as to refuse a friend to correct an avowed grammatical error. He would say that he only wished to be known as what he really was, without being decked with the plumes of another. I admire and follow this part of his principles, as well as most of his others, and I hold the act to be furtive and criminal, where one man prunes, mangles, and alters the writings of another. It is a vicious forgery, and merits punishment. If a man durst not publish the whole of the writings of another, he had far better leave them altogether, until another more bold and honest shall be found to undertake the task. Every curtailment must tend to misrepresent; and whatever may be the motive, the act is dishonest.
- 75. Mr. Paine had been particularly intimate with Burke, and I have seen an original letter of Burke to a friend, wherein he expressed the high gratification and pleasure he felt at having dined at the Duke of Portland's with Thomas Paine the great political writer of the United States, and the author of Common Sense. Whether the English ministers had formed any idea or desire to corrupt Paine by inviting him to their tables, it is difficult to say, but not improbable; one thing is certain, that, if ever they had formed the wish, they were foiled in their design, for the price of £1000, which Chapman, the printer of the Second Part of Rights of Man, offered Mr. Paine for his copyright, is a proof that he was incorruptible on this score. Mr. Paine was evidently much pleased with his intimacy with Burke, for it appears he took considerable pains to furnish him with all the correspondence possible on the affairs of France, little thinking that he was cherishing a viper, and a man that would hand those documents over to the minister; but such was the case, until Mr. Burke was compelled to display his apostacy in the House of Commons, and to bid his former associates beware of him. Mr. Paine promised the friends of the French Revolution, that he would answer Burke's pamphlet, as soon as he saw it; and it would be difficult to say, whether Burke's Reflections on the French Revolution, or Paine's Rights of Man, had the more extensive circulation. One thing we know, Burke's book is buried with him, whilst Rights of Man, stitl blazes and obtains an extensive circulation yearly, since it has been republished. Its principles will be co-existent with the human race, and the more they are known the more will they be admired. Nature assisted by Reason form their base: the only stable foundation on which the welfare of mankind can be erected. I have circulated near 5000 copies since November, 1817. The publication of Rights of Man, formed as great an era in the politics of England, as Common Sense had done in America: the difference is only this, the latter had an opportunity of being acted upon instantly, whilst the former has had to encounter corruption and persecution; but that it will finally form the base of the English
- 76. Government, I have neither fear or doubt. Its principles are so self- evident, that they flash conviction on the most unwilling mind that gives the work a calm perusal. The First Part of Rights of Man passed unnoticed, as to prosecution, neither did Burke venture a reply. The proper principles of Government, where the welfare of the community is the object of that Government, as the case should always be, are so correctly and forcibly laid down in Rights of Man, that the book will stand, as long as the English language is spoken, as a monument of political wisdom and integrity. It should be observed, that Mr. Paine never sought profit from his writings, and when he found that Rights of Man had obtained a peculiar attraction he gave up the copyright to whomsoever would print it, although he had had so high a price offered for it. He would always say that they were works of principle, written solely to ameliorate the condition of mankind, and as soon as published they were common property to any one that thought proper to circulate them. I do not concur in the propriety of Mr. Paine's conduct on this occasion, because, as he was the Author, he might as well have put the Author's profit into his pocket, as to let the bookseller pocket the profit of both. His pamphlets were never sold the cheaper for his neglecting to take his profit as an Author; but, it is now evident that Mr. Paine, by neglecting that affluence which he might have honestly and honourably possessed, deprived himself in the last dozen years of his life of the power of doing much good. It is not to be denied that property is the stamina of action and influence, and is looked up to by the mass of mankind in preference to principle in poverty. But there comes another danger and objection, that is, that the holders of much property are but seldom found to trouble themselves about principle. Their principle seldom goes a step beyond profession. But where principle and property unite, the individual becomes a host. The First Part of Rights of Man, has not that methodical arrangement which is to be found in the Second Part, but an apology arises for it, Mr. Paine had to tread the wilderness of rhapsodies, that Burke had prepared for him. The part is, however, interspersed
- 77. with such delightful ornaments, and such immutable principles, that the path does not become tedious. Perhaps no other volume whatever has so well defined the causes of the French Revolution, and the advantages that would have arisen from it had France been free from the corrupting influence of foreign powers. But I must recollect that my business here is to sketch the Life of Mr. Paine, I wish to avoid any thing in the shape of quotation from his writings, as I am of opinion, that the reader will glean their beauties from the proper source with more satisfaction; and no Life of Paine that can be compiled will ever express half so much of the man, as his own writings, as a whole, speak for themselves, and almost seem to say the hand that made us is divine. After some difficulty a publisher was found for Rights of Man in Mr. Jordan, late of 166, Fleet Street The First Part appeared on the 13th of March, 1791, and the Second Part on the 16th of February in the following year. The Government was paralyzed at the rapid sale of the First Part, and the appearance of the Second. The attempt to purchase having failed, the agents of the Government next set to work to ridicule it, and to call it a contemptible work. Whig and Tory members in both Houses of Parliament affected to sneer at it, and to laud our glorious constitution as a something impregnable to the assaults of such a book. However, Whig and Tory members had just began to be known, and their affected contempt of Rights of Man, served but as advertisements, and greatly accelerated its sale. In the month of May, 1792, the King issued his proclamation, and the King's Devil his ex officio information, on the very same day, against Rights of Man. This in some measure impeded its sale, or occasioned it to be sold in a private manner; through which means it is impossible to give effectual circulation to any publication. One part of the community is afraid to sell and another afraid to purchase under such conditions. It is not too much to say, that if Rights of Man had obtained two or three years free circulation in England and Scotland, it would have produced a similar effect to what Common Sense did in the United States of America. The French Revolution had set the people of England and Scotland to think, and Rights of
- 78. Man was just the book to furnish materials for thinking. About this time he also wrote his Letter to the Addressers, and several letters to the Chairmen of different County Meetings, at which those addresses were voted. Mr. Paine had resolved to defend the publication of Rights of Man in person, but in the month of September, a deputation from the inhabitants of Calais waited upon him to say, that they had elected him their deputy to the National Convention of France. This was an affair of more importance than supporting Rights of Man, before a political judge and a packed jury, and, accordingly, Mr. Paine set off for France with the deputation, but not without being exposed to much insult at Dover; where the Government spies had apprised the Custom House Officers of his arrival, and some of those spies were present to overhaul all his papers. It was said, that Mr. Paine had scarcely embarked twenty minutes before a warrant came to Dover, from the Home Department to arrest him. Be this as it may, Mr. Paine had more important scenes allotted to him. On reaching the opposite Shore the name of Paine was no sooner announced than the beach was crowded;-all the soldiers on duty Were drawn up; the officer of the guard embraced him on landing, and presented him with the national cockade, which a handsome young woman, who was standing by, begged the honour of fixing in his hat, and returned it to him, expressing a hope that he would continue his exertions in the behalf of Liberty, France, and the Rights of Man. A salute was then fired from the battery; to announce the arrival of their new representative. This ceremony being over, he walked to Deisseiu's, in the Rue de l'Egalite (formerly Rue de Roi), the men, women, and children crowding around him, and calling out Vive Thomas Paine! He was then conducted to the Town Hall, and there presented to the Municipality, who with the greatest affection embraced their representative. The Mayor addressed him in a short speech, which was interpreted to him by his friend and conductor, M. Audibert, to which Mr. Paine laying his hand on his heart, replied, that his life should be devoted to their service.
- 79. At the inn, he was waited upon by the different persons in authority, and by the President of the Constitutional Society, who desired he would attend their meeting of that night: he cheerfully complied with the request, and the whole town would have been there, had there been room: the hall of the 'Minimes' was so crowded that it was with the greatest difficulty they made way for Mr. Paine to the side of the President. Over the chair he sat in, was placed the bust of Mirabeau, and the colours of France, England, and America united. A speaker acquainted him from the tribune with his election, amidst the plaudits of the people. For some minutes after this ceremony, nothing was heard but Vive la Nation! Vive Thomas Paine in voices male and Female. On the following day, an extra meeting was appointed to be held in the church in honour of their new Deputy to the Convention, the Minimes being found quite suffocating from the vast concourse of people which had assembled on the previous occasion. A play was performed at the theatre on the evening after his arrival, and a box was specifically reserved for the author of 'Rights of Man,' the object of the English Proclamation. Mr. Paine was likewise elected as deputy for Abbeville, Beauvais, and Versailles, as well as for the department of Calais, but the latter having been the first in their choice, he preferred being their representative. On reaching Paris, Mr. Paine addressed a letter to the English Attorney General, apprizing him of the circumstances of his departure from England, and hinting to him, that any further prosecution of Rights of Man, would form a proof that the Author was not altogether the object, but the book, and the people of England who should approve its sentiments. A hint was also thrown out that the events of France ought to form a lesson to the English Government, on its attempt to arrest the progress of correct principles and wholesome truths. This letter was in some measure due to the Attorney General, as Mr. Paine had written to him in England on the commencement of the prosecution assuring him, that he should defend the work in person. Notwithstanding the
- 80. departure of Mr. Paine, as a member of the French National Convention, the information against Rights of Man was laid before a jury, on the 2d of December in the same year, and the Government, and its agents, were obliged to content themselves with outlawing Mr. Paine, and punishing him, in effigy, throughout the country! Many a faggot have I gathered in my youth to burn old Tom Paine! In the West of England, his name became quite a substitute for that of Guy Faux. Prejudice, so aptly termed by Mr. Paine, the spider of the mind, was never before carried to such a height against any other individual; and what will future ages think of the corrupt influence of the English Government at the close of the eighteenth century, when it could excite the rancour of a majority of the nation against such a man as Thomas Paine! We now find Mr. Paine engaged in new and still more important scenes. His first effort as a member of the National Convention, was to lay the basis of a self-renovating constitution, and to repair the defects of that which had been previously adopted: but a circumstance very soon occurred, which baffled all his good intentions, and brought him to a narrow escape from the guillotine. It was his humane and strenuous opposition to the putting Louis the XVIth to death. The famous or infamous manifesto issued by the Duke of Brunswick, in July 1792, had roused such a. spirit of hatred towards the Royal Family of France, and all other Royal Families, that nothing short of their utter destruction could appease the majority of the French nation. Mr. Paine willingly voted for the trial of Louis as a necessary exposure of Court intrigue and corruption; but when he found a disposition to destroy him at once, in preference to banishment, he exposed the safety of his own person in his endeavour to save the life of Louis. Mr. Paine was perfectly a humane man, he deprecated the punishment of death on any occasion whatever. His object was to destroy the monarchy, but not the man who had filled the office of monarch. The following anecdote is another unparalleled instance of humanity, and the moral precept of returning good for evil. Mr. Paine happened to be dining one day with about twenty friends at a Coffee
- 81. House in the Palais Egalité, now the Palais Royal, when unfortunately for the harmony of the company, a Captain in the English service contrived to introduce himself as one of the party. The military gentleman was a strenuous supporter of what is called in England, the constitution in church and state, and a decided enemy of the French Revolution. After the cloth was drawn, the conversation chiefly turned on the state of affairs in England, and the means which had been adopted by the government to check the increase of political knowledge. Mr. Paine delivered his opinions very freely, and much to the satisfaction of every one present, with the exception of Captain Grimstone, who returned his arguments by calling him a traitor to his country, with a variety of terms equally opprobrious. Mr. Paine treated his abuse with much good humour, which rendered the Captain so furious, that he walked up to the part of the room where Mr. Paine was sitting, and struck him a violent blow, which nearly knocked him off his seat. The cowardice of this behaviour from a stout young man towards a person of Mr. Paine's age (he being then upwards of sixty) is not the least disgraceful part of the transaction. There was, however, no time for reflections of this sort; an alarm was instantly given, that the Captain had struck a Citizen Deputy of the Convention, which was considered an insult to the nation at large; the offender was hurried into custody, and it was with the greatest difficulty that Mr. Paine prevented him from being executed on the spot. It ought to be observed, that an act of the Convention had awarded the punishment of death to any one who should be convicted of striking a deputy; Mr. Paine was therefore placed in a very unpleasant situation. He immediately applied to Barrere, at that time president of the Committee of Public Safety, for a passport for his imprudent adversary, who after much hesitation complied with his request. It likewise occasioned Mr. Paine considerable personal inconvenience to procure his liberation; but even this was not sufficient; the Captain was without friends, and pennyless, and Mr. Paine generously supplied him with money to defray his travelling expences.
- 82. Louis fell under the guillotine, and Mr. Paine's deprecation of that act brought down upon him the hatred of the whole Robespierrean party. The reign of terror now commenced in France; every public man who breathed a sigh for Louis was denounced a traitor to the nation, and as such was put to death. Every man who complained of the despotism and violence of the party in power, was hurried to a prison, or before the Revolutionary Tribunal and to immediate execution. Mr. Paine, although a Member of the Convention, was first excluded on the ground of being a foreigner, and then thrown into prison because he had been born in England! His place of confinement was the Luxembourg; the time, about eleven months, during which he was seized with a most violent fever, that rendered him insensible to all that was passing, and to which circumstance he attributes his escape from the guillotine. About this period Mr. Paine wrote his first and second part of Age of Reason. The first part was written before he went to the Luxembourg, as in his passage thither he deposited the manuscript with Joel Barlow. The second part he wrote during his confinement, and at a moment when he could not calculate on the preservation of his life for twenty-four hours: a circumstance which forms the best proof of his sincerity, and his conviction of the fallacy and imposture of all established religions: Throughout this work he has also trod the path of nature, and has laid down some of the best arguments to shew the existence of an Omnipotent Being, that ever were penned. Those who are in the habit of running down every thing that does not tally with their antiquated opinions, or the prejudices in which they have been educated, have decried Mr. Paine as an Atheist! Of all the men who ever wrote, Mr. Paine was the most remote from Atheism, and has advanced stronger arguments against the belief of no God, than any who have gone before him, or have lived since. If there be any chance of the failure of Mr. Paine's theological writings as a standard work, it will be on the ground of their being more superstitious than otherwise. However, their beauties, I doubt not, will at all times be a sufficient apology for a few trifling defects. Mr. Paine has been taxed with inconsistency in
- 83. Welcome to our website – the perfect destination for book lovers and knowledge seekers. We believe that every book holds a new world, offering opportunities for learning, discovery, and personal growth. That’s why we are dedicated to bringing you a diverse collection of books, ranging from classic literature and specialized publications to self-development guides and children's books. More than just a book-buying platform, we strive to be a bridge connecting you with timeless cultural and intellectual values. With an elegant, user-friendly interface and a smart search system, you can quickly find the books that best suit your interests. Additionally, our special promotions and home delivery services help you save time and fully enjoy the joy of reading. Join us on a journey of knowledge exploration, passion nurturing, and personal growth every day! ebookbell.com