In vitro repair enhances amplicon recovery and accuracy from damaged DNA Tom Evans, Ph.D. New...
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Transcript of In vitro repair enhances amplicon recovery and accuracy from damaged DNA Tom Evans, Ph.D. New...
in vitro repair enhances amplicon recovery and accuracy from damaged
DNA
Tom Evans, Ph.D.
New England Biolabs, Inc.
Accessing Genetic Informationpost-mortem
• Variables to Genetic Quality.– Storage state.
• Purified.• in situ.
– Post-mortem interval.– Storage environment.
• Frozen.• Dried.• Ethanol.• Formalin treated.
Accessing Genetic Informationpost-mortem
• Limiting Factor.– DNA extraction efficiency.– PCR/Sequencing inhibitor co-purification.– DNA quality.
Solutions
• Mitochondrial Barcode.– Copy number.
• Minimal Barcode sequence.
• Superior DNA extraction protocols.
• Improve DNA quality.
• More robust analytic techniques/enzymes.
Improve DNA QualityDamages that Inhibit Primer Extension
• Depurination/Depyrimidation.– Most common damage under physiological conditions.
• Oxidative Lesions.– Thymine glycol.– Certain species of oxidized guanine?
• Thymine Dimers.• Nicks.• Double Strand Breaks.• DNA-protein and DNA-DNA cross-links.
DNA DamageMutagenic Lesions
• Deaminated Cytosine.– C to T transition.
• Oxidative Lesions.– 8-oxo-guanine.
• G to T transversion.
Improve DNA QualityGoals
• Full repair in one-pot without sequential enzyme addition, enzyme inactivation, or DNA purification.
• Easy reaction optimization.• Does not hurt the reaction, even if it does not
help.• Full repair.• Not tied to one protocol.
How does it work?Damage Recognition
Endonuclease IV
How does it work?Nick translation
Polymerase (5’-3’ exo+)
How does it work?Nick translation
How does it work?Nick translation
How does it work?Nick translation
How does it work?Nick translation
How does it work?Nick translation
How does it work?Nick translation
How does it work?Nick translation
How does it work?Nick translation
How does it work?Nick translation
How does it work?Polymerase dissociation
How does it work?Nick ligation
Taq DNA ligase
How does it work?Nick ligation
How does it work?Nick ligation
How does it work?Nick ligation
PreCRRepair Spectrum
Repair Spectrum
Abasic sites
Nicks
Gaps
Blocked 3’ Ends
Oxidized Purines
Oxidized Pyrimidines
Thymine Dimers
Deaminated Cytosine
PreCREnzyme Composition
It’s now 7 enzymes.Taq DNA ligase.E. coli endonuclease IV.Bst DNA polymerase I.E. coli Fpg.E. coli Udg.T4 pdg.E. coli endoVIII.
PreCRRepair Spectrum
DOES NOT REPAIR
Double Strand Breaks
DNA-Protein Cross-links
DNA-DNA Cross-links
PreCRUV Damaged DNA
DNA (ng):
3 min UV 4 min UV 5 min UV 10 min UV
5 2.5 1
0.5 5 2.5
1 0.5
5 2.5 1 0.5
5 2.5
1 0.5
5 2.5 1 0.5
5 2.5
1 0.5 5 2.5 1 0.5
5 2.5
1 0.5
PreCR: - + - + - + - +
Oxidized DNA
Clone Amplicon into Expression Plasmid.
Transform intoE. coli.Grow on X-GalPlates.Expose DNA template to light
in the presence of methylene blue.
Use repaired or unrepairedtemplate in PCR.
thermocycler Sequence
PreCROxidatively Damaged DNA
TABLE 1. Base substitution errors after PCR amplification of plasmid DNA (4766 bp amplicon), untreated, treated with methylene blue (MB), and repaired with two different repair mixes at 37oC for 15 min. Substitutionsa Control, no
MB 1)c 25 M MB
4) 50 M MB 2) PreCR-A 25 M MB
5) PreCR-A 50 M MB
3) T21 25 M MB
6) T21 50 M MB
Total bp sequenced
30,128 30,128 N/A 15,064 15,064 15,064 15,064
Per 103 bp 0.03 1.4 N/A 0.13 0.0 0.0 0.0 25 g/µL Methylene Blue 50 g/µL Methylene Blue no repair PreCR-A T21 no repair PreCR-A T21 1) 2) 3) 4) 5) 6)
Oxidatively Damaged DNA Even Worse Damage
PreCR PreCR
0
20
40
60
80
0 20 40 60 80 100 120 140 160
# o
f A
P s
ite
s/1
05 b
p
Citrate Incubation Time (min)
PreCR Activity on AP Sites
pH 5 Incubation Time (min)
PreCR treatment
No treatment
Real World Issues
• Unknown damage.– There are few studies on what is actually wrong with stored
DNA.• Jürgen Zimmermann is characterizing DNA damage in moth
samples, see poster. Poster abstract on page 154.
• Unknown DNA.– Unknown DNA quantities.
• PCR inhibitors.– BSA tube in PreCR Repair Mix helps deal with PCR
inhibitors.
PreCR
• Perception– PreCR allows access (amplification) to
more heavily damaged templates than was possible previously.
Extent of DNA damage
PC
R y
ield maximal
failed0 high
PreCR treateduntreated
Real World Issues
• What is the most common limitation?– DNA extraction.– PCR inhibitors.– DNA Quality.
• Base damage.• Backbone breaks.
Acknowledgements
Barton Slatko Romas Vaisvila Lixin Chen Peter HartlineElizabeth Cantin Katherine MarksDakota Hamill
Mehrdad Hajibabei, University of Guelph.Lee Weigt, NMNH-LAB.Ann Bucklin, University of Connecticut.James Hanken, MCZ, Harvard University.David Blackburn, MCZ, Harvard University.David Schindel, CBOL Executive Secretary.Christoffer Schander, University of Bergen.Jan E. Janecka, Texas A&M University.John V. Planz, UNTHSC.