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Methods: Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
- Jin Billy Li,
- Yuan Gao,
- John Aach,
- Kun Zhang,
- Gregory V. Kryukov,
- Bin Xie,
- Annika Ahlford,
- Jung-Ki Yoon,
- Abraham M. Rosenbaum,
- Alexander Wait Zaranek,
- Emily LeProust,
- Shamil R. Sunyaev,
- and George M. Church
Genome Res. September 2009 19: 1606-1615; Published in Advance June 12, 2009, doi:10.1101/gr.092213.109
...the polymerase finishes filling the gap, it has to dissociate from the DNA to enable the ligase to close the gap. We used the Stoffel fragment of the AmpliTaq DNA polymerase (Applied Biosystems) that lacks 59!39 exonuclease activity. Fewer circles were formed when 103more or 103 less amount of Stoffel was used...
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LETTER: Microchip Module for Blood Sample Preparation and Nucleic Acid Amplification Reactions
- Po Ki Yuen,
- Larry J. Kricka,
- Paolo Fortina,
- Nicholas J. Panaro,
- Taku Sakazume,
- and Peter Wilding
Genome Res. March 1, 2001 11: 405-412; doi:10.1101/gr.155301
...M MgCl2), 2 μL of dNTPs (10 μM), 1 μL of AmpliTaq Gold DNA polymerase and 83 μL of water. The primer sequence information is as follows: forward primer FACV-3 (5′-TGC CCC ATT ATT TAG CCA GGA G-3′) and reverse primer FACV-5 (5′-ACC CAC AGA AAA TGA TGC CCA G-3′). Finally, the microchip module...
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METHODS: Improved DNA Sequencing Accuracy and Detection of Heterozygous Alleles Using Manganese Citrate and Different Fluorescent Dye Terminators
- Christopher Korch and
- Harry Drabkin
Genome Res. June 1, 1999 9: 588-595; doi:10.1101/gr.9.6.588
...magnesium and the F667Y variant Taq DNA polymerases ( Korch and Drabkin 1999 ). In the present report, we characterize the effects of MnCit addition on all three fluorescent dye-terminator cycle-sequencing procedures from PE/ABI. The uniformity of peak heights is dramatically improved, especially...
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ARTICLES: Detection of p53 gene mutation in cancer tissues by nonradioactive direct sequencing.
- D Bautista,
- P Chaubert,
- J Bertoncini,
- and J Benhattar
Genome Res. October 1994 4: 76-79
.... 1992 . PCR, direct sequencing, and the comparative approach. PCR Methods Applic. 1 : 217 – 221 . 11.. Srivastava, A.K., , Montanaro, V. , Kere. J. Srivastava, A.K., Montanaro, V. and Kere. J. 1992 . Simplified template preparation and improved direct sequencing using Taq polymerase . PCR Methods Applic...
ARTICLE: Sample preparation and PCR amplification from paraffin-embedded tissues.
- C E Greer,
- C M Wheeler,
- and M M Manos
Genome Res. June 1994 3: S113-S122
...for the analysis of point mutations from low-copy number targets. Furthermore, ob- servations made from studying ancient or highly degraded DNA demon- strated that Taq polymerase can " jump" to another template during PCR when the polymerase ncounters trand scission or abasic sites. (26) Such jumping can generate...
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REVIEW: Sequencing of PCR-amplified DNA.
- I S Bevan,
- R Rapley,
- and M R Walker
Genome Res. May 1992 1: 222-228; doi:10.1101/gr.1.4.222
....A., Gelfand, D. and Sninsky. J.J. 1991 . Recent advances in the polymerase chain reaction. Science 252 : 1643 – 1651 . 3. Lee, J.S. 1991 . Alternative dideoxy sequencing of double-stranded DNA by cyclic reactions using Taq polymerase. DNA Cell Biol. 10 : 67 – 73 . 4. Murray, V. 1989 . Improved double...
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METHODS: Determination of Single-Nucleotide Polymorphisms by Real-time Pyrophosphate DNA Sequencing
- Anders Alderborn,
- Anna Kristofferson,
- and Ulf Hammerling
Genome Res. August 1, 2000 10: 1249-1258; doi:10.1101/gr.10.8.1249
...dideoxynucleotides, 10–20 pmoles of primers and Taq polymerase (1.5 units; AmpliTaq Gold, Perkin Elmer). A single fragment type ( ACE , 260 bp) was amplified in a slightly modified reaction (0.875 m m MgCl2, 2.5% v/v of DMSO, and 2.5 units of AmpliTaq Gold). Thermal cycling was performed with an initial denaturation...
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Method: DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
- Anupama Jha,
- Stephanie C. Bohaczuk,
- Yizi Mao,
- Jane Ranchalis,
- Benjamin J. Mallory,
- Alan T. Min,
- Morgan O. Hamm,
- Elliott Swanson,
- Danilo Dubocanin,
- Connor Finkbeiner,
- Tony Li,
- Dale Whittington,
- William Stafford Noble,
- Andrew B. Stergachis,
- and Mitchell R. Vollger
Genome Res. November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
...levels.gDNA methylation with sequence-specific methyltransferasesSamples labeled with the sequence-specific adenine methyltransferases EcoRI (GAATTC; (NEB M0211S), Dam (GATC; NEB M0222S), or TaqI (TCGA; NEB M0219S) were generated as follows: 400 ng of purified gDNA was treated for 1 h with 40 U of Eco...
ARTICLE: Site-directed mutagenesis of herpesvirus glycoprotein phosphorylation sites by recombination polymerase chain reaction.
- Z Yao,
- D H Jones,
- and C Grose
Genome Res. February 1992 1: 205-207; doi:10.1101/gr.1.3.205
...the plasmid template was achieved by adding 1 ng of template DNA, 200 ~M of each dNTP, 25 pmoles of each primer, and 1.25 units of Taq polymerase in a total volume of 50 ~l of Taq polymerase buffer. These samples were overlaid with 50 ~l of mineral oil. Reactants un- derwent 25 cycles of denaturation 1...
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ARTICLE: High-level expression, purification, and enzymatic characterization of full-length Thermus aquaticus DNA polymerase and a truncated form deficient in 5' to 3' exonuclease activity.
- F C Lawyer,
- S Stoffel,
- R K Saiki,
- S Y Chang,
- P A Landre,
- R D Abramson,
- and D H Gelfand
Genome Res. May 1993 2: 275-287; doi:10.1101/gr.2.4.275
...– 400 . 8.. Barnes, W.M. Barnes, W.M. 1992 . The fidelity of Taq polymerase catalyzing PCR is improved by an N-terminal deletion. Gene 112 : 29 – 35 . 9.. Cole, G.E., , McCabe, P.C. , Inlow, D. , Gelfand, D.H. , Ben-Bassat, A. , Innis. M.A. Cole, G.E., McCabe, P.C. Inlow, D. Gelfand, D.H. Ben-Bassat, A...

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