Literature DB >> 22147421

Liquid chromatography-mass spectrometry analysis of DNA polymerase reaction products.

Goutam Chowdhury1, F Peter Guengerich.   

Abstract

This unit describes experimental and analytical procedures for characterizing the efficiency and fidelity of translesion DNA synthesis across various DNA damages by DNA polymerases in vitro. This procedure utilizes primer extension assays followed by LC-MS and LC-MS/MS analysis of the extension products. Detailed explanations for the analysis of the LC-MS/MS data for deciphering the nucleotide sequences of the DNA fragments are also presented. This approach provides a significant improvement over conventional methods, as it allows detection of misincorporation, as well as frameshift products.
© 2011 by John Wiley & Sons, Inc.

Entities:  

Mesh：

Substances：

Year:  2011        PMID： 22147421      PMCID： PMC3678528          DOI： 10.1002/0471142700.nc0716s47

Source DB:  PubMed          Journal:  Curr Protoc Nucleic Acid Chem        ISSN： 1934-9270


  9 in total

1.  DNA adduct bypass polymerization by Sulfolobus solfataricus DNA polymerase Dpo4: analysis and crystal structures of multiple base pair substitution and frameshift products with the adduct 1,N2-ethenoguanine.

Authors:  Hong Zang; Angela K Goodenough; Jeong-Yun Choi; Adriana Irimia; Lioudmila V Loukachevitch; Ivan D Kozekov; Karen C Angel; Carmelo J Rizzo; Martin Egli; F Peter Guengerich
Journal:  J Biol Chem       Date:  2005-06-17       Impact factor: 5.157

2.  Direct detection and mapping of sites of base modification in DNA fragments by tandem mass spectrometry.

Authors:  Goutam Chowdhury; F Peter Guengerich
Journal:  Angew Chem Int Ed Engl       Date:  2008       Impact factor: 15.336

Review 3.  Interactions of carcinogen-bound DNA with individual DNA polymerases.

Authors:  F Peter Guengerich
Journal:  Chem Rev       Date:  2006-02       Impact factor: 60.622

4.  Purification of oligonucleotides using denaturing polyacrylamide gel electrophoresis.

Authors:  A Ellington; J D Pollard
Journal:  Curr Protoc Mol Biol       Date:  2001-05

5.  Tandem mass spectrometry-based detection of c4'-oxidized abasic sites at specific positions in DNA fragments.

Authors:  Goutam Chowdhury; F Peter Guengerich
Journal:  Chem Res Toxicol       Date:  2009-07       Impact factor: 3.739

6.  DNA polymerase insertion fidelity. Gel assay for site-specific kinetics.

Authors:  M S Boosalis; J Petruska; M F Goodman
Journal:  J Biol Chem       Date:  1987-10-25       Impact factor: 5.157

7.  Translesion synthesis across O6-alkylguanine DNA adducts by recombinant human DNA polymerases.

Authors:  Jeong-Yun Choi; Goutam Chowdhury; Hong Zang; Karen C Angel; Choua C Vu; Lisa A Peterson; F Peter Guengerich
Journal:  J Biol Chem       Date:  2006-10-18       Impact factor: 5.157

8.  Interpretation of oligonucleotide mass spectra for determination of sequence using electrospray ionization and tandem mass spectrometry.

Authors:  J Ni; C Pomerantz; J Rozenski; Y Zhang; J A McCloskey
Journal:  Anal Chem       Date:  1996-07-01       Impact factor: 6.986

9.  Replication past the N5-methyl-formamidopyrimidine lesion of deoxyguanosine by DNA polymerases and an improved procedure for sequence analysis of in vitro bypass products by mass spectrometry.

Authors:  Plamen P Christov; Karen C Angel; F Peter Guengerich; Carmelo J Rizzo
Journal:  Chem Res Toxicol       Date:  2009-06       Impact factor: 3.739
  9 in total
  15 in total

1.  Replication of the 2,6-diamino-4-hydroxy-N(5)-(methyl)-formamidopyrimidine (MeFapy-dGuo) adduct by eukaryotic DNA polymerases.

Authors:  Plamen P Christov; Kinrin Yamanaka; Jeong-Yun Choi; Kei-ichi Takata; Richard D Wood; F Peter Guengerich; R Stephen Lloyd; Carmelo J Rizzo
Journal:  Chem Res Toxicol       Date:  2012-07-06       Impact factor: 3.739

2.  Quantitative measurement of transcriptional inhibition and mutagenesis induced by site-specifically incorporated DNA lesions in vitro and in vivo.

Authors:  Changjun You; Yinsheng Wang
Journal:  Nat Protoc       Date:  2015-08-20       Impact factor: 13.491

3.  Backbone Flexibility Influences Nucleotide Incorporation by Human Translesion DNA Polymerase η opposite Intrastrand Cross-Linked DNA.

Authors:  Derek K O'Flaherty; F Peter Guengerich; Martin Egli; Christopher J Wilds
Journal:  Biochemistry       Date:  2015-12-16       Impact factor: 3.162

4.  Mutagenic Bypass of an Oxidized Abasic Lesion-Induced DNA Interstrand Cross-Link Analogue by Human Translesion Synthesis DNA Polymerases.

Authors:  Wenyan Xu; Adam Ouellette; Souradyuti Ghosh; Tylor C O'Neill; Marc M Greenberg; Linlin Zhao
Journal:  Biochemistry       Date:  2015-12-14       Impact factor: 3.162

5.  O6-2'-Deoxyguanosine-butylene-O6-2'-deoxyguanosine DNA Interstrand Cross-Links Are Replication-Blocking and Mutagenic DNA Lesions.

Authors:  Wenyan Xu; Daniel Kool; Derek K O'Flaherty; Ashley M Keating; Lauralicia Sacre; Martin Egli; Anne Noronha; Christopher J Wilds; Linlin Zhao
Journal:  Chem Res Toxicol       Date:  2016-11-04       Impact factor: 3.739

Review 6.  Steady-state kinetic analysis of DNA polymerase single-nucleotide incorporation products.

Authors:  Derek K O'Flaherty; F Peter Guengerich
Journal:  Curr Protoc Nucleic Acid Chem       Date:  2014-12-12

7.  Mechanisms of Insertion of dCTP and dTTP Opposite the DNA Lesion O6-Methyl-2'-deoxyguanosine by Human DNA Polymerase η.

Authors:  Amitraj Patra; Qianqian Zhang; F Peter Guengerich; Martin Egli
Journal:  J Biol Chem       Date:  2016-09-30       Impact factor: 5.157

8.  Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1,N6-Ethenodeoxyadenosine by Human Translesion DNA Polymerase η.

Authors:  Amritraj Patra; Yan Su; Qianqian Zhang; Kevin M Johnson; F Peter Guengerich; Martin Egli
Journal:  J Biol Chem       Date:  2016-05-16       Impact factor: 5.157

9.  Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase κ.

Authors:  Oliver P Yockey; Vikash Jha; Pratibha P Ghodke; Tianzuo Xu; Wenyan Xu; Hong Ling; P I Pradeepkumar; Linlin Zhao
Journal:  Chem Res Toxicol       Date:  2017-10-23       Impact factor: 3.739

10.  Impact of 1,N 6-ethenoadenosine, a damaged ribonucleotide in DNA, on translesion synthesis and repair.

Authors:  Pratibha P Ghodke; F Peter Guengerich
Journal:  J Biol Chem       Date:  2020-03-25       Impact factor: 5.157
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.