DNA , RNA basic structure and components
- 14. Different topological forms of DNA Genes VI : Figure 5-9
- 15. Negative and positive supercoils • Negative supercoils twist the DNA about its axis in the opposite direction from the clockwise turns of the right-handed (R-H) double helix. – Underwound (favors unwinding of duplex). – Has right-handed supercoil turns. • Positive supercoils twist the DNA in the same direction as the turns of the R-H double helix. – Overwound (helix is wound more tightly). – Has left-handed supercoil turns.
- 16. L= W + T Relationship of writhing number and twist numbers DNA structure: Tertiary Structure: topology of plasmids
- 19. Components of DNA Topology : Twist • Number of times one strand completely wrap around the other strand. • The clockwise turns of R-H double helix generate a positive Twist (T). • The counterclockwise turns of L-H helix (Z form) generate a negative T. • T = Twisting Number B form DNA: + (# bp/10 bp per twist) A form NA: + (# bp/11 bp per twist) Z DNA: - (# bp/12 bp per twist)
- 20. Components of DNA Topology : Writhe • W = Writhing Number • writhe is the number of times the double helix crosses over on itself • Refers to the turning of the axis of the DNA duplex in space • Number of times the duplex DNA crosses over itself Relaxed molecule W=0 Negative supercoils, W is negative Positive supercoils, W is positive
- 21. Relationship between supercoiling and twisting Figure from M. Gellert; Kornberg and Baker
- 22. Two forms of supercoils: a toroidal helix DNA structure: Tertiary Structure: topology of plasmids
- 23. Components of DNA Topology : Linking number • L = Linking Number = total number of times one strand of the double helix (of a closed molecule) encircles (or links) the other. • L = Wr (Writhe)+ Tw(twist)
- 24. L cannot change unless one or both strands are broken and reformed • A change in the linking number, DL, is partitioned between T and W, i.e. • DL=DW+DT • if DL = 0, then DW= -DT
- 25. DNA in most cells is negatively supercoiled • The superhelical density is simply the number of superhelical (S.H.) turns per turn (or twist) of double helix. • Superhelical density = s = W/T = -0.05 for natural bacterial DNA –i.e., in bacterial DNA, there is 1 negative S.H. turn per 200 bp • (calculated from 1 negative S.H. turn per 20 twists = 1 negative S.H. turn per 200 bp)
- 26. Negatively supercoiled DNA favors unwinding • Negative supercoiled DNA has energy stored that favors unwinding, or a transition from B- form to Z DNA. • For s = -0.05, DG=-9 Kcal/mole favoring unwinding Thus negative supercoiling could favor initiation of transcription and initiation of replication.
- 27. Introducing one supercoil into a DNA with 10 duplex turns DNA structure: Tertiary Structure: topology of plasmids
- 29. What can Topoisomerase I do to the DNA? DNA structure: Tertiary Structure: topology of plasmids
- 30. Topoisomerase II (DNA gyrase) DNA structure: Tertiary Structure: topology of plasmids
- 31. DNA structure: Tertiary Structure: topology of plasmids
- 32. Topoisomerase I • Topoisomerases: catalyze a change in the Linking Number of DNA • Topo I = nicking-closing enzyme, can relax positive or negative supercoiled DNA • Makes a transient break in 1 strand • E. coli Topo I specifically relaxes negatively supercoiled DNA. Calf thymus Topo I works on both negatively and positively supercoiled DNA.
- 33. Topoisomerase I: nicking & closing Genes VI : Figure 17-15 One strand passes through a nick in the other strand.
- 34. Topoisomerase II • Topo II = gyrase • Uses the energy of ATP hydrolysis to introduce negative supercoils • Its mechanism of action is to make a transient double strand break, pass a duplex DNA through the break, and then re-seal the break.
- 35. TopoII: double strand break and passage
- 37. RNA vs. DNA: who cares? Base-catalyzed RNA cleavage! -OH Stable backbone Unstable backbone
- 38. RNA transesterification mechanism Base-catalyzed RNA cleavage! transition state + + -OH
- 39. Different bases in RNA and DNA RNA only DNA only DNA and RNA
- 40. RNA chain is made single stranded! Chain is directional. Convention: 5’ 3’. Chemical schematic One-letter code ssDNA can signal DNA damage and promote cell death dsRNA can block protein synthesis and signal viral infections
- 41. Six backbone dihedral angles () per nucleotide in RNA and DNA Is ssDNA floppy or rigid? Is RNA more or less flexible than ssDNA?
- 42. Two orientations of the bases: Anti and syn DNA and RNA Absent from undamaged dsDNA
- 43. -OH, what a difference an O makes! Different functions of DNA and RNA Stores genetic info Stores genetic info ssDNA signals cell death ssRNA OK E.g. mRNA = gene copy dsDNA OK dsRNA (“A” form) signals infe mediates editing, RNA interference, . . . Double helical (B form) Forms complex struct Supercoiled Enzymes (e.g. ribosom Binding sites & scaffo Signals Templates (e.g. telome