Literature DB >> 19665596

Techniques used to study the DNA polymerase reaction pathway.

Catherine M Joyce1.   

Abstract

A minimal reaction pathway for DNA polymerases was established over 20years ago using chemical-quench methods. Since that time there has been considerable interest in noncovalent steps in the reaction pathway, conformational changes involving the polymerase or its DNA substrate that may play a role in substrate specificity. Fluorescence-based assays have been devised in order to study these conformational transitions and the results obtained have added new detail to the reaction pathway. Copyright (c) 2010 Elsevier B.V. All rights reserved.

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Year:  2009        PMID： 19665596      PMCID： PMC2846202          DOI： 10.1016/j.bbapap.2009.07.021

Source DB:  PubMed          Journal:  Biochim Biophys Acta        ISSN： 0006-3002


  40 in total

1.  Y265H mutator mutant of DNA polymerase beta. Proper teometric alignment is critical for fidelity.

Authors:  A M Shah; S X Li; K S Anderson; J B Sweasy
Journal:  J Biol Chem       Date:  2001-01-11       Impact factor: 5.157

2.  Using 2-aminopurine fluorescence to measure incorporation of incorrect nucleotides by wild type and mutant bacteriophage T4 DNA polymerases.

Authors:  Elizabeth Fidalgo da Silva; Subhrangsu S Mandal; Linda J Reha-Krantz
Journal:  J Biol Chem       Date:  2002-08-19       Impact factor: 5.157

3.  Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.

Authors:  Sean J Johnson; Jeffrey S Taylor; Lorena S Beese
Journal:  Proc Natl Acad Sci U S A       Date:  2003-03-20       Impact factor: 11.205

4.  Global kinetic explorer: a new computer program for dynamic simulation and fitting of kinetic data.

Authors:  Kenneth A Johnson; Zachary B Simpson; Thomas Blom
Journal:  Anal Biochem       Date:  2008-12-25       Impact factor: 3.365

5.  Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM--a flexible, portable system.

Authors:  B A Barshop; R F Wrenn; C Frieden
Journal:  Anal Biochem       Date:  1983-04-01       Impact factor: 3.365

6.  poliota, a remarkably error-prone human DNA polymerase.

Authors:  A Tissier; J P McDonald; E G Frank; R Woodgate
Journal:  Genes Dev       Date:  2000-07-01       Impact factor: 11.361

7.  Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes.

Authors:  J W Arndt; W Gong; X Zhong; A K Showalter; J Liu; C A Dunlap; Z Lin; C Paxson; M D Tsai; M K Chan
Journal:  Biochemistry       Date:  2001-05-08       Impact factor: 3.162

8.  To slip or skip, visualizing frameshift mutation dynamics for error-prone DNA polymerases.

Authors:  Brigette Tippin; Sawami Kobayashi; Jeffrey G Bertram; Myron F Goodman
Journal:  J Biol Chem       Date:  2004-08-31       Impact factor: 5.157

9.  Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase beta.

Authors:  Christopher A Dunlap; Ming-Daw Tsai
Journal:  Biochemistry       Date:  2002-09-17       Impact factor: 3.162

10.  Use of 2-aminopurine fluorescence to examine conformational changes during nucleotide incorporation by DNA polymerase I (Klenow fragment).

Authors:  Vandana Purohit; Nigel D F Grindley; Catherine M Joyce
Journal:  Biochemistry       Date:  2003-09-02       Impact factor: 3.162
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  31 in total

1.  Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.

Authors:  Samra Obeid; Wolfram Welte; Kay Diederichs; Andreas Marx
Journal:  J Biol Chem       Date:  2012-02-07       Impact factor: 5.157

2.  Kinetic analysis of the unique error signature of human DNA polymerase ν.

Authors:  Mercedes E Arana; Olga Potapova; Thomas A Kunkel; Catherine M Joyce
Journal:  Biochemistry       Date:  2011-10-31       Impact factor: 3.162

3.  Divalent Cations Alter the Rate-Limiting Step of PrimPol-Catalyzed DNA Elongation.

Authors:  Wenyan Xu; Wenxin Zhao; Nana Morehouse; Maya O Tree; Linlin Zhao
Journal:  J Mol Biol       Date:  2019-01-08       Impact factor: 5.469

4.  Elucidation of kinetic mechanisms of human translesion DNA polymerase κ using tryptophan mutants.

Authors:  Linlin Zhao; Matthew G Pence; Robert L Eoff; Shuai Yuan; Catinca A Fercu; F Peter Guengerich
Journal:  FEBS J       Date:  2014-08-14       Impact factor: 5.542

5.  Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase ι.

Authors:  Jeong-Yun Choi; Amritaj Patra; Mina Yeom; Young-Sam Lee; Qianqian Zhang; Martin Egli; F Peter Guengerich
Journal:  J Biol Chem       Date:  2016-08-23       Impact factor: 5.157

Review 6.  Chemical and biological consequences of oxidatively damaged guanine in DNA.

Authors:  Sarah Delaney; Daniel A Jarem; Catherine B Volle; Craig J Yennie
Journal:  Free Radic Res       Date:  2012-02-22

Review 7.  Mechanistic cross-talk between DNA/RNA polymerase enzyme kinetics and nucleotide substrate availability in cells: Implications for polymerase inhibitor discovery.

Authors:  Si'Ana A Coggins; Bijan Mahboubi; Raymond F Schinazi; Baek Kim
Journal:  J Biol Chem       Date:  2020-07-31       Impact factor: 5.157

8.  The Closing Mechanism of DNA Polymerase I at Atomic Resolution.

Authors:  Bill R Miller; Lorena S Beese; Carol A Parish; Eugene Y Wu
Journal:  Structure       Date:  2015-07-23       Impact factor: 5.006

9.  Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes.

Authors:  Lucia Greenough; Kelly M Schermerhorn; Laurie Mazzola; Joanna Bybee; Danielle Rivizzigno; Elizabeth Cantin; Barton E Slatko; Andrew F Gardner
Journal:  Nucleic Acids Res       Date:  2015-09-13       Impact factor: 16.971

10.  Induced Fit in the Selection of Correct versus Incorrect Nucleotides by DNA Polymerase β.

Authors:  Beth Moscato; Monalisa Swain; J Patrick Loria
Journal:  Biochemistry       Date:  2015-12-30       Impact factor: 3.162
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