Dna sequencing and its types

DNA Sequencing and its
types
A T G C……
Dr. N. Yuvaraj
Assistant Professor
Achariya Arts and Science College
Villianur, Puducherry
yuvaraj.aasc@achariya.org

The process of determining the order of nucleotides adenine (A),
thymine (T), cytosine (C), and guanine (G) along a DNA strand.
We need to know the order of nucleotide bases in a strand of DNA
for sequencing.
All the information required for the growth and development of an
organism is encoded in the DNA of its genome.
So, DNA sequencing is fundamental to genome analysis and
understanding the biological processes in general.

Historical Timeline
1870 – Friedrich Miescher discovers DNA
1940 - Avery: Proposes DNA as ‘Genetic Material’
1953 – Watson & Crick “double helical structure”
1970 - Wu: Sequences λ Cohesive End DNA
1977 – Sanger: Dideoxy Chain Termination
1977 – Gilbert: Chemical Degradation
1986 – Partial Automation
1990 – Cycle Sequencing, Improved Sequencing Enzymes,
Improved fluorescent detection schemes
2002 – NGS: 454 Pyrosequencing

To determine the order of the nucleotide bases adenine, guanine,
cytosine, and thymine in a molecule of DNA two methods
were used
1. Sanger; Chain Termination Sequencing method
2. Maxam and Gilbert; Chemical Sequencing method
These two methods are most popular conventional methods
 Robotics and automated sequencing are based on these
methods

Sanger’s- Chain Termination Sequencing
• It is PCR based method
• A modified DNA replication reaction
• Growing chains are terminated by dideoxynucleotides

The 3′-OH group necessary for formation of the phosphodiester bond is missing in
ddNTPs.

1. Get enough quantity of DNA (Run PCR)
2. Aliqot DNA into four different tubes
3. Prepare PCR reaction mix as below:
• Primer, Taq polymerase, template(ssDNA), dNTPS (All) and
ddNTPs(ddATP, ddGTP,ddCTP & ddTTP respectively)
1. Run PCR
2. Perform Gel Electrophoresis
3. Interpret results
Sanger Sequencing: Process

 A sequencing reaction mix includes labeled primer
and template.
 Dideoxynucleotides are added separately to each of
the four tubes.
Template area to be sequenced
-3′ OH
TCGACGGGC…
5′OP-
Primer
Template

 With addition of enzyme (DNA polymerase), the
primer is extended until a ddNTP is encountered.
 The chain will end with the incorporation of the
ddNTP.
 With the proper dNTP:ddNTP ratio, the chain will
terminate throughout the length of the template.
 All terminated chains will end in the ddNTP added to
that reaction.

The collection of fragments is a sequencing
ladder.
The resulting terminated chains are resolved
by electrophoresis.
Fragments from each of the four tubes are
placed in four separate gel lanes.

Sanger Sequencing: An Example
5’-TACACGATCGA-3’
3’-ATGTGCTAGCT-5’
Denature the sequence
Use only forward primer i.e. use 3’-5’ strand of
DNA

Maxam–Gilbert sequencing method

Maxam–Gilbert sequencing is a method of DNA sequencing
developed by Allan Maxam and Walter Gilbert in 1976–1977.
This method is based on nucleobase-specific partial chemical
modification of DNA and subsequent cleavage of the DNA
backbone at sites adjacent to the modified nucleotides.

Maxam Gilbert Sequencing: Process Summarized
1. Label 5’- end of DNA
2. Aliquot DNA sample in 4 tubes
3. Perform base modification reaction
4. Perform Cleavage reaction
5. Perform Gel Electrophoresis
6. Perform Autoradiography
7. Interpret results

I. Chemical Modification of DNA; radioactive labeling at one 5'
end of the DNA (typically by a kinase reaction using
gamma-32P ATP)
II. Purification of the DNA fragment to be sequenced
III. Chemical treatment generates breaks in DNA
IV. Run on the gel

Chemical Modification and Cleavage
Poly nucleotide Kinase radioactive label at one
5' end of the DNA using gamma-32P
5′ G A C G T G C A A C G A A 3′
32P 5′ G A C G T G C A A C G A A 3′

Chemical Modification and Cleavage
Base Modification using Dimethyl sulphate
– Purine
• Adenine
• Guanine
– Only DMS------- G
– DMS+ Formic acid-------G+A
Cleavage of Sugar Phosphate backbone using
Piperidine

Base modification using Hydrazine
– Pyrimidine
• Cytosine
• Thymine
– Hydrazine----- C+T
– Hydrazine + NaCl--------C
Cleavage of Sugar Phosphate backbone using
Piperidine

An Example for
Maxam-Gilbert
Sequencing

The principle behind Next Generation Sequencing (NGS) is
similar to that of Sanger sequencing, which relies on capillary
electrophoresis.
The genomic strand is fragmented, and the bases in each
fragment are identified by emitted signals when the fragments
are ligated against a template strand.
The NGS method uses array-based sequencing which
combines the techniques developed in Sanger sequencing
to process millions of reactions in parallel, resulting in very
high speed and throughput at a reduced cost.

Three general steps in NGS
1. Library preparation: libraries are created using random
fragmentation of DNA, followed by ligation with custom
linkers
2. Amplification: the library is amplified using clonal
amplification methods and PCR
3. Sequencing: DNA is sequenced using one of several
different approaches

LIBRARY PREPARATION
Firstly, DNA is fragmented either enzymatically or by
sonication (excitation using ultrasound) to create smaller
strands.
Adaptors (short, double-stranded pieces of synthetic DNA)
are then ligated to these fragments with the help of DNA
ligase, an enzyme that joins DNA strands.
The adaptors enable the sequence to become bound to a
complementary counterpart.

Adaptors are synthesized so that one end is 'sticky' whilst
the other is 'blunt' (non-cohesive) with the view to joining the
blunt end to the blunt ended DNA.
This could lead to the potential problem of base pairing
between molecules and therefore dimer formation.
To prevent this, the chemical structure of DNA is utilised,
since ligation takes place between the 3′-OH and 5′-P ends.
By removing the phosphate from the sticky end of the
adaptor and therefore creating a 5′-OH end instead, the DNA
ligase is unable to form a bridge between the two termini.

In order for sequencing to be successful, the library fragments
need to be spatially clustered in PCR colonies or ‘colonies' as
they are conventionally known, which consist of many copies of
a particular library fragment.
Since these colonies are attached in a planar fashion, the
features of the array can be manipulated enzymatically in
parallel.
This method of library construction is much faster than the
previous labour intensive procedure of colony picking and E. coli
cloning used to isolate and amplify DNA for Sanger sequencing,
however, this is at the expense of read length of the fragments.

AMPLIFICATION
Library amplification is required so that the received signal
from the sequencer is strong enough to be detected
accurately.
With enzymatic amplification, phenomena such as 'biasing'
and 'duplication' can occur leading to preferential
amplification of certain library fragments.
Instead, there are several types of amplification process
which use PCR to create large numbers of DNA clusters.

Emulsion PCR
Emulsion oil, beads, PCR mix and the library DNA are mixed to
form an emulsion which leads to the formation of micro wells

In order for the sequencing process to be successful, each micro
well should contain one bead with one strand of DNA
(approximately 15% of micro wells are of this composition).
The PCR then denatures the library fragment leading two
separate strands, one of which (the reverse strand) anneals to the
bead.
The annealed DNA is amplified by polymerase starting from the
bead towards the primer site.

The original reverse strand then denatures and is released from
the bead only to re-anneal to the bead to give two separate
strands.
These are both amplified to give two DNA strands attached to the
bead.
The process is then repeated over 30-60 cycles leading to clusters
of DNA.

This technique has been criticized for its time consuming
nature, since it requires many steps (forming and breaking the
emulsion, PCR amplification, enrichment etc) despite its
extensive use in many of the NGS platforms.
It is also relatively inefficient since only around two thirds of
the emulsion micro reactors will actually contain one bead.
Therefore an extra step is required to separate empty
systems leading to more potential inaccuracies.

Bridge PCR
The surface of the flow cell is densely coated with primers
that are complementary to the primers attached to the DNA
library fragments.
The DNA is then attached to the surface of the cell at
random where it is exposed to reagents for polymerase based
extension.
On addition of nucleotides and enzymes, the free ends of
the single strands of DNA attach themselves to the surface of
the cell via complementary primers, creating bridged
structures.

Enzymes then interact with the bridges to make them
double stranded, so that when the denaturation occurs, two
single stranded DNA fragments are attached to the surface
in close proximity.
Repetition of this process leads to clonal clusters of
localized identical strands.
In order to optimize cluster density, concentrations of
reagents must be monitored very closely to avoid
overcrowding.

SEQUENCING
Several competing methods of Next Generation Sequencing
have been developed by different companies.
1. 454 Pyrosequencing
2. Ion torrent semiconductor sequencing
3. Sequencing by ligation (SOLiD)
4. Reversible terminator sequencing (Illumina)
 3′-O-blocked reversible terminators
3′-unblocked reversible terminators

1. 454 Pyrosequencing
Pyrosequencing is based on the 'sequencing by synthesis'
principle, where a complementary strand is synthesized in
the presence of polymerase enzyme.
In contrast to using dideoxynucleotides to terminate chain
amplification (as in Sanger sequencing), pyrosequencing
instead detects the release of pyrophosphate when
nucleotides are added to the DNA chain.

It initially uses the emulsion PCR technique to construct the
colonies required for sequencing and removes the
complementary strand.
Next, a ssDNA sequencing primer hybridizes to the end of
the strand (primer-binding region), then the four different
dNTPs are then sequentially made to flow in and out of the
wells over the colonies.
When the correct dNTP is enzymatically incorporated into
the strand, it causes release of pyrophosphate

In the presence of ATP sulfurylase and adenosine, the
pyrophosphate is converted into ATP.
This ATP molecule is used for luciferase-catalysed conversion
of luciferin to oxyluciferin, which produces light that can be
detected with a camera.
The relative intensity of light is proportional to the amount of
base added (i.e. a peak of twice the intensity indicates two
identical bases have been added in succession).

Pyrosequencing, developed by 454 Life Sciences, was one of
the early successes of Next-generation sequencing; indeed,
454 Life Sciences produced the first commercially available
Next-generation sequencer.
However, the method was eclipsed by other technologies
and, in 2013, new owners Roche announced the closure of
454 Life Sciences and the discontinuation of the 454
pyrosequencing platform.

2. Ion torrent semiconductor sequencing
Ion torrent sequencing uses a "sequencing by synthesis"
approach, in which a new DNA strand, complementary to
the target strand, is synthesized one base at a time.
A semiconductor chip detects the hydrogen ions produced
during DNA polymerization

Following colony formation using emulsion PCR, the DNA
library fragment is flooded sequentially with each nucleoside
triphosphate (dNTP), as in pyrosequencing.
The dNTP is then incorporated into the new strand if
complementary to the nucleotide on the target strand.
Each time a nucleotide is successfully added, a hydrogen ion
is released, and it detected by the sequencer's pH sensor.
As in the pyrosequencing method, if more than one of the
same nucleotide is added, the change in pH/signal intensity is
correspondingly larger.

Ion torrent sequencing is the first commercial technique not to use
fluorescence and camera scanning.
It is therefore faster and cheaper than many of the other methods.
Unfortunately, it can be difficult to enumerate the number of
identical bases added consecutively.
For example, it may be difficult to differentiate the pH change for a
homo repeat of length 9 to one of length 10, making it difficult to
decode repetitive sequences.

3. Sequencing by ligation (SOLiD)
SOLiD is an enzymatic method of sequencing that uses DNA ligase,
an enzyme used widely in biotechnology for its ability to ligate
double-stranded DNA strands .
Emulsion PCR is used to immobilize/amplify a ssDNA primer-
binding region (known as an adapter) which has been conjugated to
the target sequence (i.e. the sequence that is to be sequenced) on a
bead.
These beads are then deposited onto a glass surface − a high
density of beads can be achieved which in turn, increases the
throughput of the technique.

Once bead deposition has occurred, a primer of length N is
hybridized to the adapter, then the beads are exposed to a
library of 8-mer probes which have different fluorescent dye
at the 5' end and a hydroxyl group at the 3' end.
Bases 1 and 2 are complementary to the nucleotides to be
sequenced whilst bases 3-5 are degenerate and bases 6-8 are
inosine bases.
Only a complementary probe will hybridize to the target
sequence, adjacent to the primer.

DNA ligase is then uses to join the 8-mer probe to the
primer.
A phosphorothioate linkage between bases 5 and 6 allows
the fluorescent dye to be cleaved from the fragment using
silver ions.
This cleavage allows fluorescence to be measured (four
different fluorescent dyes are used, all of which have different
emission spectra) and also generates a 5’-phosphate group
which can undergo further ligation.

Once the first round of sequencing is completed, the extension
product is melted off and then a second round of sequencing is
performed with a primer of length N−1.
Many rounds of sequencing using shorter primers each time (i.e.
N−2, N−3 etc) and measuring the fluorescence ensures that the
target is sequenced.

Due to the two-base sequencing method (since each base is
effectively sequenced twice), the SOLiD technique is highly
accurate (at 99.999% with a sixth primer, it is the most accurate of
the second generation platforms) and also inexpensive.
It can complete a single run in 7 days and in that time can
produce 30 Gb of data.
Unfortunately, its main disadvantage is that read lengths are
short, making it unsuitable for many applications.

4. Reversible terminator sequencing (Illumina)
Reversible terminator sequencing differs from the traditional
Sanger method in that, instead of terminating the primer
extension irreversibly using dideoxynucleotide, modified
nucleotides are used in reversible termination.
Whilst many other techniques use emulsion PCR to amplify
the DNA library fragments, reversible termination uses bridge
PCR, improving the efficiency of this stage of the process.

a. 3′-O-blocked reversible terminators
The mechanism uses a sequencing by synthesis approach,
elongating the primer in a stepwise manner.
Firstly, the sequencing primers and templates are fixed to
a solid support.
The support is exposed to each of the four DNA bases,
which have a different fluorophore attached (to the
nitrogenous base) in addition to a 3’-O-azidomethyl group

Only the correct base anneals to the target and is subsequently
ligated to the primer.
The solid support is then imaged and nucleotides that have not
been incorporated are washed away and the fluorescent branch is
cleaved using TCEP (tris(2-carboxyethyl)phosphine).
TCEP also removes the 3’-O-azidomethyl group, regenerating 3’-
OH, and the cycle can be repeated.

b. 3′-unblocked reversible terminators
The reversible termination group of 3′-unblocked reversible
terminators is linked to both the base and the fluorescence
group, which now acts as part of the termination group as well
as a reporter.
This method differs from the 3′-O-blocked reversible
terminators method in three ways: firstly, the 3’-position is not
blocked (i.e. the base has free 3’-OH); the fluorophore is the
same for all four bases; and each modified base is flowed in
sequentially rather than at the same time.

The main disadvantage of these techniques lies with their
poor read length, which can be caused by one of two
phenomena.
In order to prevent incorporation of two nucleotides in a
single step, a block is put in place, however in the event of no
block addition due to a poor synthesis, strands can become out
of phase creating noise which limits read length.
Noise can also be created if the fluorophore is unsuccessfully
attached or removed.

These problems are prevalent in other sequencing methods
and are the main limiting factors to read length.
This technique was pioneered by Illumina, with their HiSeq
and MiSeq platforms.
HiSeq is the cheapest of the second generation sequencers
with a cost of $0.02 per million bases.
It also has a high data output of 600 Gb per run which takes
around 8 days to complete.

Dna sequencing and its types

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