Literature DB >> 15297882

Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.

Luis G Brieba1, Brandt F Eichman, Robert J Kokoska, Sylvie Doublié, Tom A Kunkel, Tom Ellenberger.   

Abstract

Accurate DNA replication involves polymerases with high nucleotide selectivity and proofreading activity. We show here why both fidelity mechanisms fail when normally accurate T7 DNA polymerase bypasses the common oxidative lesion 8-oxo-7, 8-dihydro-2'-deoxyguanosine (8oG). The crystal structure of the polymerase with 8oG templating dC insertion shows that the O8 oxygen is tolerated by strong kinking of the DNA template. A model of a corresponding structure with dATP predicts steric and electrostatic clashes that would reduce but not eliminate insertion of dA. The structure of a postinsertional complex shows 8oG(syn).dA (anti) in a Hoogsteen-like base pair at the 3' terminus, and polymerase interactions with the minor groove surface of the mismatch that mimic those with undamaged, matched base pairs. This explains why translesion synthesis is permitted without proofreading of an 8oG.dA mismatch, thus providing insight into the high mutagenic potential of 8oG.

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Year:  2004        PMID: 15297882      PMCID: PMC516626          DOI: 10.1038/sj.emboj.7600354

Source DB:  PubMed          Journal:  EMBO J        ISSN: 0261-4189            Impact factor:   11.598


  48 in total

Review 1.  DNA polymerases: structural diversity and common mechanisms.

Authors:  T A Steitz
Journal:  J Biol Chem       Date:  1999-06-18       Impact factor: 5.157

Review 2.  An open and closed case for all polymerases.

Authors:  S Doublié; M R Sawaya; T Ellenberger
Journal:  Structure       Date:  1999-02-15       Impact factor: 5.006

3.  XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density.

Authors:  D E McRee
Journal:  J Struct Biol       Date:  1999 Apr-May       Impact factor: 2.867

4.  Rapid automated molecular replacement by evolutionary search.

Authors:  C R Kissinger; D K Gehlhaar; D B Fogel
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-02

5.  Single 8-oxo-guanine and 8-oxo-adenine lesions induce marked changes in the backbone structure of a 25-base DNA strand.

Authors:  D C Malins; N L Polissar; G K Ostrander; M A Vinson
Journal:  Proc Natl Acad Sci U S A       Date:  2000-11-07       Impact factor: 11.205

6.  Structure of the replicating complex of a pol alpha family DNA polymerase.

Authors:  M C Franklin; J Wang; T A Steitz
Journal:  Cell       Date:  2001-06-01       Impact factor: 41.582

7.  Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase eta.

Authors:  L Haracska; S L Yu; R E Johnson; L Prakash; S Prakash
Journal:  Nat Genet       Date:  2000-08       Impact factor: 38.330

8.  Sequence-specific recognition of double helical nucleic acids by proteins.

Authors:  N C Seeman; J M Rosenberg; A Rich
Journal:  Proc Natl Acad Sci U S A       Date:  1976-03       Impact factor: 11.205

Review 9.  Oxyradicals and DNA damage.

Authors:  L J Marnett
Journal:  Carcinogenesis       Date:  2000-03       Impact factor: 4.944

10.  Fidelity of nucleotide insertion at 8-oxo-7,8-dihydroguanine by mammalian DNA polymerase delta. Steady-state and pre-steady-state kinetic analysis.

Authors:  H J Einolf; F P Guengerich
Journal:  J Biol Chem       Date:  2000-11-10       Impact factor: 5.157

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  114 in total

1.  A new proofreading mechanism for lesion bypass by DNA polymerase-λ.

Authors:  Emmanuele Crespan; Giovanni Maga; Ulrich Hübscher
Journal:  EMBO Rep       Date:  2011-12-23       Impact factor: 8.807

2.  Minimalist model for force-dependent DNA replication.

Authors:  Eva X Nong; Stephen J DeVience; Dudley Herschbach
Journal:  Biophys J       Date:  2012-02-21       Impact factor: 4.033

3.  Conformational dynamics of bacteriophage T7 DNA polymerase and its processivity factor, Escherichia coli thioredoxin.

Authors:  Barak Akabayov; Sabine R Akabayov; Seung-Joo Lee; Stanley Tabor; Arkadiusz W Kulczyk; Charles C Richardson
Journal:  Proc Natl Acad Sci U S A       Date:  2010-08-09       Impact factor: 11.205

4.  Synthesis of N2-alkyl-8-oxo-7,8-dihydro-2'-deoxyguanosine derivatives and effects of these modifications on RNA duplex stability.

Authors:  Arunkumar Kannan; Cynthia J Burrows
Journal:  J Org Chem       Date:  2010-12-30       Impact factor: 4.354

5.  Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase η.

Authors:  Timothy D Silverstein; Rinku Jain; Robert E Johnson; Louise Prakash; Satya Prakash; Aneel K Aggarwal
Journal:  Structure       Date:  2010-11-10       Impact factor: 5.006

6.  The use of modified and non-natural nucleotides provide unique insights into pro-mutagenic replication catalyzed by polymerase eta.

Authors:  Jung-Suk Choi; Anvesh Dasari; Peter Hu; Stephen J Benkovic; Anthony J Berdis
Journal:  Nucleic Acids Res       Date:  2015-12-29       Impact factor: 16.971

7.  Error-prone replication bypass of the imidazole ring-opened formamidopyrimidine deoxyguanosine adduct.

Authors:  Yan Sha; Irina G Minko; Chanchal K Malik; Carmelo J Rizzo; R Stephen Lloyd
Journal:  Environ Mol Mutagen       Date:  2017-04-24       Impact factor: 3.216

8.  Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis.

Authors:  Alexandra Vaisman; Hong Ling; Roger Woodgate; Wei Yang
Journal:  EMBO J       Date:  2005-08-18       Impact factor: 11.598

9.  Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation.

Authors:  Benedetta A Sampoli Benítez; Karunesh Arora; Lisa Balistreri; Tamar Schlick
Journal:  J Mol Biol       Date:  2008-10-17       Impact factor: 5.469

10.  Biochemical analysis of active site mutations of human polymerase η.

Authors:  Samuel C Suarez; Renee A Beardslee; Shannon M Toffton; Scott D McCulloch
Journal:  Mutat Res       Date:  2013-03-13       Impact factor: 2.433

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