Literature DB >> 25916710

Measuring ribonucleotide incorporation into DNA in vitro and in vivo.

Anders R Clausen1, Jessica S Williams, Thomas A Kunkel.   

Abstract

Ribonucleotides are incorporated into genomes by DNA polymerases, they can be removed, and if not removed, they can have deleterious and beneficial consequences. Here, we describe an assay to quantify stable ribonucleotide incorporation by DNA polymerases in vitro, and an assay to probe for ribonucleotides in each of the two DNA strands of the yeast nuclear genome.

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Year:  2015        PMID： 25916710      PMCID： PMC5321556          DOI： 10.1007/978-1-4939-2596-4_9

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  11 in total

1.  Proofreading of ribonucleotides inserted into DNA by yeast DNA polymerase ɛ.

Authors:  Jessica S Williams; Anders R Clausen; Stephanie A Nick McElhinny; Brian E Watts; Erik Johansson; Thomas A Kunkel
Journal:  DNA Repair (Amst)       Date:  2012-06-08

2.  Structure of Saccharomyces cerevisiae DNA polymerase epsilon by cryo-electron microscopy.

Authors:  Francisco J Asturias; Iris K Cheung; Nasim Sabouri; Olga Chilkova; Daniel Wepplo; Erik Johansson
Journal:  Nat Struct Mol Biol       Date:  2005-12-20       Impact factor: 15.369

Review 3.  Unlocking the sugar "steric gate" of DNA polymerases.

Authors:  Jessica A Brown; Zucai Suo
Journal:  Biochemistry       Date:  2011-01-26       Impact factor: 3.162

4.  Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases.

Authors:  Stephanie A Nick McElhinny; Brian E Watts; Dinesh Kumar; Danielle L Watt; Else-Britt Lundström; Peter M J Burgers; Erik Johansson; Andrei Chabes; Thomas A Kunkel
Journal:  Proc Natl Acad Sci U S A       Date:  2010-03-01       Impact factor: 11.205

5.  Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase δ.

Authors:  Anders R Clausen; Sufang Zhang; Peter M Burgers; Marietta Y Lee; Thomas A Kunkel
Journal:  DNA Repair (Amst)       Date:  2012-12-12

6.  Topoisomerase 1-mediated removal of ribonucleotides from nascent leading-strand DNA.

Authors:  Jessica S Williams; Dana J Smith; Lisette Marjavaara; Scott A Lujan; Andrei Chabes; Thomas A Kunkel
Journal:  Mol Cell       Date:  2013-01-31       Impact factor: 17.970

7.  Ribonucleotides are signals for mismatch repair of leading-strand replication errors.

Authors:  Scott A Lujan; Jessica S Williams; Anders R Clausen; Alan B Clark; Thomas A Kunkel
Journal:  Mol Cell       Date:  2013-04-18       Impact factor: 17.970

8.  Genome instability due to ribonucleotide incorporation into DNA.

Authors:  Stephanie A Nick McElhinny; Dinesh Kumar; Alan B Clark; Danielle L Watt; Brian E Watts; Else-Britt Lundström; Erik Johansson; Andrei Chabes; Thomas A Kunkel
Journal:  Nat Chem Biol       Date:  2010-08-22       Impact factor: 15.040

9.  The major roles of DNA polymerases epsilon and delta at the eukaryotic replication fork are evolutionarily conserved.

Authors:  Izumi Miyabe; Thomas A Kunkel; Antony M Carr
Journal:  PLoS Genet       Date:  2011-12-01       Impact factor: 5.917

10.  Mismatch repair balances leading and lagging strand DNA replication fidelity.

Authors:  Scott A Lujan; Jessica S Williams; Zachary F Pursell; Amy A Abdulovic-Cui; Alan B Clark; Stephanie A Nick McElhinny; Thomas A Kunkel
Journal:  PLoS Genet       Date:  2012-10-11       Impact factor: 5.917
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  6 in total

1.  Facile preparation of model DNA interstrand cross-link repair intermediates using ribonucleotide-containing DNA.

Authors:  Jin Tang; Feng Tang; Linlin Zhao
Journal:  DNA Repair (Amst)       Date:  2022-01-31

2.  A role for Rad5 in ribonucleoside monophosphate (rNMP) tolerance.

Authors:  Menattallah Elserafy; Iman El-Shiekh; Dalia Fleifel; Reham Atteya; Abdelrahman AlOkda; Mohamed M Abdrabbou; Mostafa Nasr; Sherif F El-Khamisy
Journal:  Life Sci Alliance       Date:  2021-08-18

3.  High density of unrepaired genomic ribonucleotides leads to Topoisomerase 1-mediated severe growth defects in absence of ribonucleotide reductase.

Authors:  Susana M Cerritelli; Jaime Iranzo; Sushma Sharma; Andrei Chabes; Robert J Crouch; David Tollervey; Aziz El Hage
Journal:  Nucleic Acids Res       Date:  2020-05-07       Impact factor: 16.971

4.  Incision of damaged DNA in the presence of an impaired Smc5/6 complex imperils genome stability.

Authors:  Jie Peng; Wenyi Feng
Journal:  Nucleic Acids Res       Date:  2016-08-17       Impact factor: 16.971

5.  Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA.

Authors:  Anna-Karin Berglund; Clara Navarrete; Martin K M Engqvist; Emily Hoberg; Zsolt Szilagyi; Robert W Taylor; Claes M Gustafsson; Maria Falkenberg; Anders R Clausen
Journal:  PLoS Genet       Date:  2017-02-16       Impact factor: 5.917

6.  Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae.

Authors:  Éva Hegedüs; Endre Kókai; Péter Nánási; László Imre; László Halász; Rozenn Jossé; Zsuzsa Antunovics; Martin R Webb; Aziz El Hage; Yves Pommier; Lóránt Székvölgyi; Viktor Dombrádi; Gábor Szabó
Journal:  Nucleic Acids Res       Date:  2018-11-16       Impact factor: 16.971
  6 in total

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