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Sanger sequencing
1. Sanger sequencing
Dr. R. D. Kulkarni, MD
Dept. of Microbiology, SDM College of
Medical Sciences & Hospital, Dharwad -
580009
2. One of the
greatest
women who
ever walked on
earth..!
3.
4.
5. Sanger sequencing
• Frederick Sanger
• British biochemist
• Recipient of the Nobel
Prize TWICE
• 1958 - structure of
proteins, Insulin
• 1980 - determination of
base sequences in
nucleic acids
6. Sanger sequencing
• Sequencing - Method
used to sequence the
stretches of the gens
• Precisely write the
sequence of the
nucleotides as they are
arranged in the stretch
of the DNA
10. dd NTPs
• Specially designed
nucleotides
• Have a hydrogen
atom attached to
the 3' carbon
rather than an OH
group
11. dd NTPs
• They terminate DNA chain elongation as…
– Cannot form a phosphodiester bond with the next
deoxynucleotide
• Each ddNTP has label for different color fluorescence
13. ddNTPs are the terminator molecules…
• dd ATP • dd GTP
• dd CTP • dd TTP
14.
15. • In the actual reaction mixture of dNTPs and ddNTPs
used
• Proportion of the dNTPs and ddNTPs 100 : 1
• Means that 1% of the ddNTPs are fluorescence
labeled terminator molecules
16. Technique
• Gene to be sequenced subjected to standard PCR
• Amplicon will have number of copies of the gene under question
• Now, sequencing PCR is run using this amplicon as template
• To run this reaction we add
– Buffer
– The template i.e. amplicon from the first PCR
– Primer
– BigDye – Polymerase + mixture of ddNTPs and dNTPs
– Double distilled water
• Amplification done
17. • Elongation of strand
• Random addition of dNTPs and ddNTPs
• When ddNTP added strand extension terminates
• Being random - all possible lengths of the DNA
fragments are generated having a terminal
fluorescence labeled ddNTP
• Product of this reaction is subjected to gel
electrophoresis
18. • If ddNTP is added early the fragment will be short
• If ddNTP is added late, fragments will be longer
• Shorter fragments have faster mobility vis-à-vis the bigger
fragments
• Run gel electrophoresis
• Image the gel
• Peaks are generated using software to arrange the
nucleotides based on the fragment length and the
fluorescence labels
• Electropherogram
33. Purification of DNA before sequencing PCR
• DNA amplicon purified before subjecting sequencing PCR
• Purification through Sephadex gel
– Filter plate
– Add Sephadex powder
– Add water to obtain gel
– Centrifuge to remove excess water (2700 rpm x 5 mins)
– Add amplicon to wells
– Centrifuge to collect DNA into catch plate (having cone shaped wells)
– Impurities like ddNTPs, dNTPs, enzymes etc. are caught in Sephadex
– Filtrate is pure DNA - used for sequencing
34. Before fluorescent labels
• Radio labeled ddNTPs were used before the use
of fluorescent ddNTPs
• Reaction was run in quadruplet.
• Each of the four reactions was run with separate
mixtures of dNTPs and ddNTP
– ddGTP / ddCTP / ddATP and ddTTP with dNTPs
• After reaction the electrophoresis was run in four
different lanes and the matching was done using
radiographic reading of the lanes
• Final assembly using algorithms
35. Acinetobacter PCR at SDM
• Genus level
• Scola et al – France
• 100% specificity
• But band at 400 bp rather than at 350 bp as suggested by
Scola
• Discussed with Dr. Scola on Emial – it is highly specific do not
bother about the size of the fragment – but get the amplicon
sequenced
• We got it sequenced
• To our surprise – on sequencing it was 350 bp