Removal of Misincorporated Ribonucleotides from Prokaryotic Genomes: An Unexpected Role for Nucleotide Excision Repair

Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection

Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006) · Molecular Systems Biology · doi:10.1038/msb4100050 · Cited by 7,858 · see citing works

Revised methods for the Salmonella mutagenicity test

Maron, D. M., & Ames, B. N. (1983) · Mutation Research/Environmental Mutagenesis and Related Subjects · doi:10.1016/0165-1161(83)90010-9 · Cited by 7,398 · see citing works

Instability and decay of the primary structure of DNA

Lindahl, T. (1993) · Nature · doi:10.1038/362709a0 · Cited by 5,679 · see citing works

MUTANTS OF ESCHERICHIA COLI REQUIRING METHIONINE OR VITAMIN B 12

Davis, B. D., & Mingioli, E. S. (1950) · Journal of Bacteriology · doi:10.1128/jb.60.1.17-28.1950 · Cited by 2,894 · see citing works

A short course in bacterial genetics : a laboratory manual and handbook for Escherichia coli and related bacteria

Miller, J. H. (1992) · Medical Entomology and Zoology · Cited by 2,488 · see citing works

The Y-Family of DNA Polymerases

Ohmori, H., Friedberg, E. C., Fuchs, R. P., Goodman, M. F., Hanaoka, F., Hinkle, D. C., Kunkel, T. A., Lawrence, C. W., Livneh, Z., Nohmi, T., et al. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00278-7 · Cited by 882 · see citing works

Y-family DNA polymerases and their role in tolerance of cellular DNA damage

Sale, J. E., Lehmann, A. R., & Woodgate, R. (2012) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3289 · Cited by 665 · see citing works

Identification of additional genes belonging to the LexA regulon in Escherichia coli

de Henestrosa, A. R. F., Ogi, T., Aoyagi, S., Chafin, D. R., Hayes, J. J., Ohmori, H., & Woodgate, R. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01826.x · Cited by 566 · see citing works

UmuD′ 2 C is an error-prone DNA polymerase, Escherichia coli pol V

Tang, M., Shen, X., Frank, E. G., O’Donnell, M. E., Woodgate, R., & Goodman, M. F. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.16.8919 · Cited by 537 · see citing works

DNA N-glycosidases: properties of uracil-DNA glycosidase from Escherichia coli.

Lindahl, T. L., Ljungquist, S., Siegert, W., Nyberg, B., & Sperens, B. (1977) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)40386-3 · Cited by 522 · see citing works

Enzymatic Removal of Ribonucleotides from DNA Is Essential for Mammalian Genome Integrity and Development

Reijns, M. A. M., Rabe, B., Rigby, R. E., Mill, P., Astell, K. R., Lettice, L. A., Boyle, S., Leitch, A., Keighren, M., Kilanowski, F., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.011 · Cited by 466 · see citing works

A multistep damage recognition mechanism for global genomic nucleotide excision repair

Sugasawa, K., Okamoto, T., Shimizu, Y., Masutani, C., Iwai, S., & Hanaoka, F. (2001) · Genes & Development · doi:10.1101/gad.866301 · Cited by 435 · see citing works

A pSC101-derived plasmid which shows no sequence homology to other commonly used cloning vectors

Churchward, G., Belin, D., & Nagamine, Y. (1984) · Gene · doi:10.1016/0378-1119(84)90207-5 · Cited by 435 · see citing works

Nucleotide excision repair in Escherichia coli

Houten, B. V. (1990) · Microbiological Reviews · doi:10.1128/mr.54.1.18-51.1990 · Cited by 419 · see citing works

Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases

McElhinny, S. A. N., Watts, B. E., Kumar, D., Watt, D. L., Lundström, E.-B., Burgers, P., Johansson, E., Chabes, A., & Kunkel, T. A. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914857107 · Cited by 409 · see citing works

Genome instability due to ribonucleotide incorporation into DNA

McElhinny, S. A. N., Kumar, D., Clark, A. B., Watt, D. L., Watts, B. E., Lundström, E.-B., Johansson, E., Chabes, A., & Kunkel, T. A. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.424 · Cited by 395 · see citing works

Endonuclease IV (nfo) mutant of Escherichia coli

Cunningham, R. P., Saporito-Irwin, S. M., Spitzer, S. G., & Weiss, B. (1986) · Journal of Bacteriology · doi:10.1128/jb.168.3.1120-1127.1986 · Cited by 382 · see citing works

What a difference a decade makes: Insights into translesion DNA synthesis

Yang, W., & Woodgate, R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704219104 · Cited by 377 · see citing works

RecA protein-dependent cleavage of UmuD protein and SOS mutagenesis.

Shinagawa, H., Iwasaki, H., Kato, T., & Nakata, A. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.6.1806 · Cited by 348 · see citing works

Methyl-directed repair of DNA base-pair mismatches in vitro.

Lu, A.-L., Clark, S., & Modrich, P. L. (1983) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.80.15.4639 · Cited by 340 · see citing works

Prokaryotic Nucleotide Excision Repair: The UvrABC System

Truglio, J. J., Croteau, D. L., Van Houten, B., & Kisker, C. (2006) · Chemical Reviews · doi:10.1021/cr040471u · Cited by 340 · see citing works

RNase H2-Initiated Ribonucleotide Excision Repair

Sparks, J. L., Chon, H., Cerritelli, S. M., Kunkel, T. A., Johansson, E., Crouch, R. J., & Burgers, P. M. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.06.035 · Cited by 339 · see citing works

Use of the rpoB gene to determine the specificity of base substitution mutations on the Escherichia coli chromosome.

Garibyan, L., Huang, T. T., Kim, M., Wolff, E., Nguyen, A., Nguyen, T. P. T., Diep, A., Hu, K., Iverson, A., Yang, H., et al. (2003) · DNA Repair · doi:10.1016/s1568-7864(03)00024-7 · Cited by 299 · see citing works

Mutagenic Processing of Ribonucleotides in DNA by Yeast Topoisomerase I

Kim, N., Huang, S.-Y. N., Williams, J. S., Li, Y. C., Clark, A. B., Cho, J.-E., Kunkel, T. A., Pommier, Y., & Jinks-Robertson, S. (2011) · Science · doi:10.1126/science.1205016 · Cited by 291 · see citing works

The overexpression of specialized DNA polymerases in cancer

Albertella, M. R., Lau, A., & O’Connor, M. J. (2005) · DNA repair · doi:10.1016/j.dnarep.2005.01.005 · Cited by 252 · see citing works

Mammalian RNase H2 removes ribonucleotides from DNA to maintain genome integrity

Hiller, B., Achleitner, M., Glage, S., Naumann, R., Behrendt, R., & Roers, A. (2012) · Journal of Experimental Medicine · doi:10.1084/jem.20120876 · Cited by 245 · see citing works

Substrate spectrum of human excinuclease: repair of abasic sites, methylated bases, mismatches, and bulky adducts.

Huang, J. C., Hsu, D. S., Kazantsev, A. G., & Sancar, A. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.25.12213 · Cited by 230 · see citing works

Unlocking the Sugar “Steric Gate” of DNA Polymerases

Brown, J. A., & Suo, Z. (2011) · Biochemistry · doi:10.1021/bi101915z · Cited by 206 · see citing works

Recognition and Repair of Compound DNA Lesions (Base Damage and Mismatch) by Human Mismatch Repair and Excision Repair Systems

Mu, D., Tursun, M., Duckett, D. R., Drummond, J. T., Modrich, P. L., & Sancar, A. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.2.760 · Cited by 197 · see citing works

Excision of misincorporated ribonucleotides in DNA by RNase H (type 2) and FEN-1 in cell-free extracts

Rydberg, B., & Game, J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.262591699 · Cited by 191 · see citing works

Ribonucleotides Are Signals for Mismatch Repair of Leading-Strand Replication Errors

Lujan, S. A., Williams, J. S., Clausen, A. R., Clark, A. B., & Kunkel, T. A. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.03.017 · Cited by 183 · see citing works

RNase H and Postreplication Repair Protect Cells from Ribonucleotides Incorporated in DNA

Lazzaro, F., Novarina, D., Amara, F., Watt, D. L., Stone, J. E., Costanzo, V., Burgers, P., Kunkel, T. A., Plevani, P., & Muzi-Falconi, M. (2012) · Molecular Cell · doi:10.1016/j.molcel.2011.12.019 · Cited by 177 · see citing works

Levels of chromosomally encoded Umu proteins and requirements for in vivo UmuD cleavage

Woodgate, R., & Ennis, D. G. (1991) · Molecular and General Genetics MGG · doi:10.1007/bf00264207 · Cited by 175 · see citing works

Uracil DNA-glycosylase from HeLa cells: general properties, substrate specificity and effect of uracil analogs

Krokan, H. E., & Wittwer, C. U. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.11.2599 · Cited by 175 · see citing works

Okazaki fragment maturation: nucleases take centre stage

Zheng, L., & Shen, B. (2011) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjq048 · Cited by 175 · see citing works

RecA protein of Escherichia coli has a third essential role in SOS mutator activity

Sweasy, J. B., Witkin, E. M., Sinha, N. K., & Roegner-Maniscalco, V. (1990) · Journal of Bacteriology · doi:10.1128/jb.172.6.3030-3036.1990 · Cited by 170 · see citing works

Regulation of SOS mutagenesis by proteolysis.

Frank, E. G., Ennis, D. G., Gonzalez, M., Levine, A. S., & Woodgate, R. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.19.10291 · Cited by 164 · see citing works

MutS and MutL Activate DNA Helicase II in a Mismatch-dependent Manner

Yamaguchi, M., Dao, V., & Modrich, P. L. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.15.9197 · Cited by 164 · see citing works

Ribonucleotides Misincorporated into DNA Act as Strand-Discrimination Signals in Eukaryotic Mismatch Repair

Ghodgaonkar, M. M., Lazzaro, F., Olivera-Pimentel, M., Borán, M. S., Ćejka, P., Reijns, M. A. M., Jackson, A. P., Plevani, P., Muzi-Falconi, M., & Jiricny, J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.03.019 · Cited by 154 · see citing works

The active form of DNA polymerase V is UmuD′2C–RecA–ATP

Jiang, Q., Karata, K., Woodgate, R., Cox, M. M., & Goodman, M. F. (2009) · Nature · doi:10.1038/nature08178 · Cited by 147 · see citing works

Differential human nucleotide excision repair of paired and mispaired cisplatin-DNA adducts

Moggs, J. G. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.3.480 · Cited by 129 · see citing works

Genetic requirements and mutational specificity of the Escherichia coli SOS mutator activity

Fijałkowska, I. J., Dunn, R. L., & Schaaper, R. M. (1997) · Journal of Bacteriology · doi:10.1128/jb.179.23.7435-7445.1997 · Cited by 116 · see citing works

Altered DNA Polymerase ι Expression in Breast Cancer Cells Leads to a Reduction in DNA Replication Fidelity and a Higher Rate of Mutagenesis

Jin, Y., Chen, Z., Liu, Y., Hickey, R. J., & Malkas, L. H. (2004) · Cancer Research · doi:10.1158/0008-5472.can-04-0603 · Cited by 115 · see citing works

Polymerases Leave Fingerprints: Analysis of the Mutational Spectrum in Escherichia coli rpoB To Assess the Role of Polymerase IV in Spontaneous Mutation

Wolff, E. M., Kim, M., Hu, K., Yang, H., & Miller, J. H. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.9.2900-2905.2004 · Cited by 113 · see citing works

DNA Repair Excision Nuclease Attacks Undamaged DNA

Branum, M. E., Reardon, J. T., & Sancar, A. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m101032200 · Cited by 103 · see citing works

The β-Hairpin Motif of UvrB Is Essential for DNA Binding, Damage Processing, and UvrC-mediated Incisions

Škorvaga, M., Theis, K. W., Mandavilli, B. S., Kisker, C., & Houten, B. V. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m108847200 · Cited by 103 · see citing works

Exonuclease III recognizes urea residues in oxidized DNA.

Kow, Y. W., & Wallace, S. S. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.24.8354 · Cited by 103 · see citing works

Enzymic degradation of uracil-containing DNA. 3. Partial purification and characterization of a uracil DNA N-glycosidase from Bacillus subtilis

Cone, R., Duncan, J., Hamilton, L., & Friedberg, E. C. (1977) · Biochemistry · doi:10.1021/bi00633a024 · Cited by 91 · see citing works

Cho, a second endonuclease involved in Escherichia coli nucleotide excision repair

Moolenaar, G. F., van Rossum-Fikkert, S. E., van Kesteren, M., & Goosen, N. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.032584099 · Cited by 81 · see citing works

Solution Structure of the Dickerson DNA Dodecamer Containing a Single Ribonucleotide

DeRose, E. F., Perera, L., Murray, M. S., Kunkel, T. A., & London, R. E. (2012) · Biochemistry · doi:10.1021/bi201710q · Cited by 65 · see citing works

The C-terminal Zinc Finger of UvrA Does Not Bind DNA Directly but Regulates Damage-specific DNA Binding

Croteau, D. L., DellaVecchia, M. J., Wang, H., Bienstock, R. J., Melton, M. A., & Houten, B. V. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m603093200 · Cited by 51 · see citing works

Mispaired rNMPs in DNA are mutagenic and are targets of mismatch repair and RNases H

Shen, Y., Koh, K. D., Weiss, B., & Storici, F. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2176 · Cited by 50 · see citing works

Repair activity of base and nucleotide excision repair enzymes for guanine lesions induced by nitrosative stress

Nakano, T. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki513 · Cited by 50 · see citing works

In vivo stability of the Umu mutagenesis proteins: a major role for RecA

Frank, E. G., Gonzalez, M., Ennis, D. G., Levine, A. S., & Woodgate, R. (1996) · Journal of Bacteriology · doi:10.1128/jb.178.12.3550-3556.1996 · Cited by 49 · see citing works

DNA polymerase switching: effects on spontaneous mutagenesis inEscherichia coli

Curti, E., McDonald, J. P., Mead, S., & Woodgate, R. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06526.x · Cited by 48 · see citing works

UvrB Domain 4, an Autoinhibitory Gate for Regulation of DNA Binding and ATPase Activity

Wang, H., DellaVecchia, M. J., Škorvaga, M., Croteau, D. L., Erie, D. A., & Houten, B. V. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m601476200 · Cited by 46 · see citing works

Critical amino acids in Escherichia coli UmuC responsible for sugar discrimination and base-substitution fidelity

Vaisman, A., Kuban, W., McDonald, J. P., Karata, K., Yang, W., Goodman, M. F., & Woodgate, R. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks233 · Cited by 43 · see citing works

B-form to A-form conversion by a 3'-terminal ribose: crystal structure of the chimera d(CCACTAGTG)r(G)

Wahl, M. C. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.21.4356 · Cited by 40 · see citing works

Patterns of chromosomal fragmentation due to uracil‐DNA incorporation reveal a novel mechanism of replication‐dependent double‐stranded breaks

Kouzminova, E. A., & Kuzminov, A. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06149.x · Cited by 39 · see citing works

Sequence Context- and Temperature-Dependent Nucleotide Excision Repair of a Benzo[a]pyrene Diol Epoxide-Guanine DNA Adduct Catalyzed by Thermophilic UvrABC Proteins

Ruan, Q., Liu, T., Kolbanovskiy, A., Liu, Y., Ren, J., Škorvaga, M., Zou, Y., Lader, J. M., Malkani, B., Amin, S., et al. (2007) · Biochemistry · doi:10.1021/bi700294k · Cited by 38 · see citing works

Cooperative damage recognition by UvrA and UvrB: Identification of UvrA residues that mediate DNA binding

Croteau, D. L., DellaVecchia, M. J., Perera, L., & Houten, B. V. (2008) · DNA repair · doi:10.1016/j.dnarep.2007.11.013 · Cited by 38 · see citing works

Mechanisms Employed by Escherichia coli to Prevent Ribonucleotide Incorporation into Genomic DNA by Pol V

McDonald, J. P., Vaisman, A., Kuban, W., Goodman, M. F., & Woodgate, R. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1003030 · Cited by 38 · see citing works

Reconstitution of nucleotide excision nuclease with UvrA and UvrB proteins from Escherichia coli and UvrC protein from Bacillus subtilis

Lin, J. J., & Sancar, A. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)45365-8 · Cited by 34 · see citing works

The SOS-dependent upregulation of uvrD is not required for efficient nucleotide excision repair of ultraviolet light induced DNA photoproducts in Escherichia coli

Crowley, D. J., & Hanawalt, P. C. (2001) · Mutation Research/DNA Repair · doi:10.1016/s0921-8777(01)00068-4 · Cited by 29 · see citing works

Enhanced generation of A : T → T : A transversions in a recA730 lexA51(Def) mutant of Escherichia coli

Watanabe‐Akanuma, M., Woodgate, R., & Ohta, T. (1997) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/s0027-5107(96)00189-3 · Cited by 29 · see citing works

Comparative assessment of plasmid and oligonucleotide DNA substrates in measurement of in vitro base excision repair activity

Hou, E. W., Prasad, R., Asagoshi, K., Masaoka, A., & Wilson, S. H. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm639 · Cited by 26 · see citing works

Escherichia coli UmuC active site mutants: Effects on translesion DNA synthesis, mutagenesis and cell survival

Kuban, W., Vaisman, A., McDonald, J. P., Karata, K., Yang, W., Goodman, M. F., & Woodgate, R. (2012) · DNA repair · doi:10.1016/j.dnarep.2012.06.005 · Cited by 25 · see citing works

The post-incision steps of the DNA base excision repair pathway in Escherichia coli: studies with a closed circular DNA substrate containing a single U:G base pair

Sandigursky, M. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.5.1282 · Cited by 17 · see citing works

Efficient processing of TFO-directed psoralen DNA interstrand crosslinks by the UvrABC nuclease

Christensen, L. A., Wang, H., Houten, B. V., & Vásquez, K. M. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn880 · Cited by 16 · see citing works

Uracil-initiated base excision DNA repair synthesis fidelity in human colon adenocarcinoma loVo and Escherichia coli cell extracts

Sanderson, R. J., Bennett, S. E., Sung, J., & Mosbaugh, D. W. (2001) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(01)68098-x · Cited by 9 · see citing works

Reduced sulfhydryls maintain specific incision of BPDE–DNA adducts by recombinant thermoresistant Bacillus caldotenax UvrABC endonuclease

Jiang, G., Škorvaga, M., Houten, B. V., & States, J. C. (2003) · Protein Expression and Purification · doi:10.1016/s1046-5928(03)00137-2 · Cited by 9 · see citing works

Nucleotide excision repair in humans

Spivak, G. (2015) · DNA Repair · doi:10.1016/j.dnarep.2015.09.003 · Cited by 354 · see citing works

Processing ribonucleotides incorporated during eukaryotic DNA replication

Williams, J. S., Lujan, S. A., & Kunkel, T. A. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.37 · Cited by 188 · see citing works

Ribonucleotides in DNA: Origins, repair and consequences

Williams, J. S., & Kunkel, T. A. (2014) · DNA repair · doi:10.1016/j.dnarep.2014.03.029 · Cited by 170 · see citing works

Bacterial DNA excision repair pathways

Wozniak, K. J., & Simmons, L. A. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00694-0 · Cited by 110 · see citing works

Sources of spontaneous mutagenesis in bacteria

Schroeder, J. W., Yeesin, P., Simmons, L. A., & Wang, J. D. (2017) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2017.1394262 · Cited by 101 · see citing works

An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis

Million‐Weaver, S., Samadpour, A. N., Moreno-Habel, D. A., Nugent, P., Brittnacher, M., Weiss, E. J., Hayden, H. S., Miller, S. I., Liachko, I., & Merrikh, H. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1416651112 · Cited by 82 · see citing works

How the misincorporation of ribonucleotides into genomic DNA can be both harmful and helpful to cells

Potenski, C. J., & Klein, H. L. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku773 · Cited by 79 · see citing works

Unveiling the non-repair face of the Base Excision Repair pathway in RNA processing: A missing link between DNA repair and gene expression?

Antoniali, G., Malfatti, M. C., & Tell, G. (2017) · DNA repair · doi:10.1016/j.dnarep.2017.06.008 · Cited by 65 · see citing works

Guardians of the mycobacterial genome: A review on DNA repair systems in Mycobacterium tuberculosis

Singh, A. (2017) · Microbiology · doi:10.1099/mic.0.000578 · Cited by 63 · see citing works

Topoisomerase I Alone Is Sufficient to Produce Short DNA Deletions and Can Also Reverse Nicks at Ribonucleotide Sites

Huang, S.-Y. N., Ghosh, S., & Pommier, Y. G. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.653345 · Cited by 62 · see citing works

Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2

Malfatti, M. C., Balachander, S., Antoniali, G., Koh, K. D., Saint-Pierre, C., Gasparutto, D., Chon, H., Crouch, R. J., Storici, F., & Tell, G. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx723 · Cited by 59 · see citing works

Genome-wide mapping of embedded ribonucleotides and other noncanonical nucleotides using emRiboSeq and EndoSeq

Ding, J., Taylor, M. S., Jackson, A. P., & Reijns, M. A. M. (2015) · Nature Protocols · doi:10.1038/nprot.2015.099 · Cited by 47 · see citing works

Ribonuclease H2 in health and disease

Reijns, M. A. M., & Jackson, A. P. (2014) · Biochemical Society Transactions · doi:10.1042/bst20140079 · Cited by 45 · see citing works

Investigating the mechanisms of ribonucleotide excision repair in Escherichia coli

Vaisman, A., McDonald, J. P., Noll, S., Huston, D., Loeb, G., Goodman, M. F., & Woodgate, R. (2014) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2014.01.005 · Cited by 43 · see citing works

RNase HII Saves rnhA Mutant Escherichia coli from R-Loop-Associated Chromosomal Fragmentation

Kouzminova, E. A., Kadyrov, F. F., & Kuzminov, A. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.08.004 · Cited by 40 · see citing works

Ribonucleotide discrimination by translesion synthesis DNA polymerases

Vaisman, A., & Woodgate, R. (2018) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2018.1483889 · Cited by 38 · see citing works

Mutagenic cost of ribonucleotides in bacterial DNA

Schroeder, J. W., Randall, J. R., Hirst, W. G., O’Donnell, M. E., & Simmons, L. A. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1710995114 · Cited by 37 · see citing works

Mycobacterium smegmatis DinB2 misincorporates deoxyribonucleotides and ribonucleotides during templated synthesis and lesion bypass

Ordonez, H., & Shuman, S. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1027 · Cited by 37 · see citing works

Current perspectives on mechanisms of ribonucleotide incorporation and processing in mammalian DNA

Sassa, A., Yasui, M., & Honma, M. (2019) · Genes and Environment · doi:10.1186/s41021-019-0118-7 · Cited by 34 · see citing works

RADAR-seq: A RAre DAmage and Repair sequencing method for detecting DNA damage on a genome-wide scale

Zatopek, K. M., Potapov, V., Maduzia, L. L., Alpaslan, E., Chen, L., Evans, T. C., Ong, J. L., Ettwiller, L. M., & Gardner, A. F. (2019) · DNA Repair · doi:10.1016/j.dnarep.2019.06.007 · Cited by 31 · see citing works

Ribonucleotides in bacterial DNA

Schroeder, J. W., Randall, J. R., Matthews, L. A., & Simmons, L. A. (2014) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2014.981647 · Cited by 29 · see citing works

Ribonucleotide incorporation into DNA during DNA replication and its consequences

Zhou, Z.-X., Williams, J. S., Lujan, S. A., & Kunkel, T. A. (2021) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2020.1869175 · Cited by 30 · see citing works

RNase HIII Is Important for Okazaki Fragment Processing in Bacillus subtilis

Randall, J. R., Nye, T. M., Wozniak, K. J., & Simmons, L. A. (2019) · Journal of Bacteriology · doi:10.1128/jb.00686-18 · Cited by 27 · see citing works

Redundancy in ribonucleotide excision repair: Competition, compensation, and cooperation

Vaisman, A., & Woodgate, R. (2015) · DNA repair · doi:10.1016/j.dnarep.2015.02.008 · Cited by 29 · see citing works

Substrate Specificity for Bacterial RNases HII and HIII Is Influenced by Metal Availability

Randall, J. R., Hirst, W. G., & Simmons, L. A. (2017) · Journal of Bacteriology · doi:10.1128/jb.00401-17 · Cited by 25 · see citing works

New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps

Malfatti, M. C., Antoniali, G., Codrich, M., Burra, S., Mangiapane, G., Dalla, E., & Tell, G. (2019) · Mutagenesis · doi:10.1093/mutage/gez051 · Cited by 26 · see citing works

Unlocking the steric gate of DNA polymerase η leads to increased genomic instability in Saccharomyces cerevisiae

Donigan, K. A., Cerritelli, S. M., McDonald, J. P., Vaisman, A., Crouch, R. J., & Woodgate, R. (2015) · DNA repair · doi:10.1016/j.dnarep.2015.07.002 · Cited by 27 · see citing works

Ultraviolet-induced RNA:DNA hybrids interfere with chromosomal DNA synthesis

Kouzminova, E. A., & Kuzminov, A. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab147 · Cited by 24 · see citing works

RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome wide

Schroeder, J. W., Hurto, R. L., Randall, J. R., Wozniak, K. J., Timko, T. A., Nye, T. M., Wang, J. D., Freddolino, P. L., & Simmons, L. A. (2023) · Science Advances · doi:10.1126/sciadv.adi5945 · Cited by 21 · see citing works

Investigation of bacterial nucleotide excision repair using single-molecule techniques

Houten, B. V., & Kad, N. M. (2014) · DNA repair · doi:10.1016/j.dnarep.2013.10.012 · Cited by 22 · see citing works

Ribonucleotides as nucleotide excision repair substrates

Cai, Y., Geacintov, N. E., & Broyde, S. B. (2013) · DNA repair · doi:10.1016/j.dnarep.2013.10.010 · Cited by 22 · see citing works

Impact of Ribonucleotide Backbone on Translesion Synthesis and Repair of 7,8-Dihydro-8-oxoguanine

Sassa, A., Çağlayan, M., Rodriguez, Y., Beard, W. A., Wilson, S. H., Nohmi, T., Honma, M., & Yasui, M. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.738732 · Cited by 21 · see citing works

DNA polymerase η contributes to genome-wide lagging strand synthesis

Kreisel, K., Engqvist, M. K. M., Kalm, J., Thompson, L. J., Boström, M., Navarrete, C., McDonald, J. P., Larsson, E., Woodgate, R., & Clausen, A. R. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1291 · Cited by 20 · see citing works

RNA polymerase drives ribonucleotide excision DNA repair in E. coli

Hao, Z., Gowder, M., Proshkin, S., Bharati, B. K., Epshtein, V., Svetlov, V., Shamovsky, I., & Nudler, E. (2023) · Cell · doi:10.1016/j.cell.2023.04.029 · Cited by 19 · see citing works

Differential Activities of DNA Polymerases in Processing Ribonucleotides during DNA Synthesis in Archaea

Lemor, M., Kong, Z., Henry, E., Brizard, R., Laurent, S., Bossé, A., & Henneke, G. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.10.004 · Cited by 18 · see citing works

In vitro reconstitution of an efficient nucleotide excision repair system using mesophilic enzymes from Deinococcus radiodurans

Seck, A., Bonis, S. D., Saint‐Pierre, C., Gasparutto, D., Ravanat, J., & Timmins, J. (2022) · Communications Biology · doi:10.1038/s42003-022-03064-x · Cited by 18 · see citing works

Analysis of Ribonucleotide Removal from DNA by Human Nucleotide Excision Repair

Lindsey‐Boltz, L. A., Kemp, M. G., Hu, J., & Sancar, A. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.695254 · Cited by 17 · see citing works

A DinB Ortholog Enables Mycobacterial Growth under dTTP-Limiting Conditions Induced by the Expression of a Mycobacteriophage-Derived Ribonucleotide Reductase Gene

Ghosh, S., Samaddar, S., Kirtania, P., & GUPTA, S. K. (2015) · Journal of Bacteriology · doi:10.1128/jb.00669-15 · Cited by 17 · see citing works

UvrC Coordinates an O 2 -Sensitive [4Fe4S] Cofactor

Silva, R. M. B., Grodick, M. A., & Barton, J. K. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.0c01671 · Cited by 16 · see citing works

Ribonucleotides and Transcription-Associated Mutagenesis in Yeast

Cho, J.-E., & Jinks-Robertson, S. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.08.005 · Cited by 14 · see citing works

Bacillus subtilis PcrA Helicase Removes Trafficking Barriers

Álamo, M. M., Carrasco, B., Torres, R., & Alonso, J. C. (2021) · Cells · doi:10.3390/cells10040935 · Cited by 14 · see citing works

Processing of a single ribonucleotide embedded into DNA by human nucleotide excision repair and DNA polymerase η

Sassa, A., Tada, H., Takeishi, A., Kaho, H., Suzuki, M., Tsuda, M., Sasanuma, H., Takeda, S., Sugasawa, K., Yasui, M., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-50421-8 · Cited by 12 · see citing works

The Deletion of rnhB in Mycobacterium smegmatis Does Not Affect the Level of RNase HII Substrates or Influence Genome Stability

Minias, A. E., Brzostek, A. M., Minias, P., & Dziadek, J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0115521 · Cited by 11 · see citing works

The Impact of RNA-DNA Hybrids on Genome Integrity in Bacteria

McLean, E. K., Nye, T. M., Lowder, F. C., & Simmons, L. A. (2022) · Annual Review of Microbiology · doi:10.1146/annurev-micro-102521-014450 · Cited by 11 · see citing works

AUF1 Recognizes 8-Oxo-Guanosine Embedded in DNA and Stimulates APE1 Endoribonuclease Activity

Malfatti, M. C., Codrich, M., Dalla, E., DˈAmbrosio, C., Storici, F., Scaloni, A., & Tell, G. (2023) · Antioxidants and Redox Signaling · doi:10.1089/ars.2022.0105 · Cited by 9 · see citing works

Escherichia coli DNA replication: the old model organism still holds many surprises

Łazowski, K., Woodgate, R., & Fijałkowska, I. J. (2024) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuae018 · Cited by 10 · see citing works

Role of RNase H enzymes in maintaining genome stability in Escherichia coli expressing a steric-gate mutant of pol VICE391

Walsh, E. M., Henrikus, S. S., Vaisman, A., Makiela‐Dzbenska, K., Armstrong, T. J., Łazowski, K., McDonald, J. P., Goodman, M. F., van Oijen, A. M., Jonczyk, P., et al. (2019) · DNA repair · doi:10.1016/j.dnarep.2019.102685 · Cited by 10 · see citing works

The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response

Erill, I., Campoy, S., Kılıç, S., & Barbé, J. (2016) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2016.00033 · Cited by 10 · see citing works

Novel Escherichia coli active site dnaE alleles with altered base and sugar selectivity

Vaisman, A., Łazowski, K., Reijns, M. A. M., Walsh, E. M., McDonald, J. P., Moreno, K. C., Quiros, D. R., Schmidt, M., Kranz, H. D., Yang, W., et al. (2021) · Molecular Microbiology · doi:10.1111/mmi.14779 · Cited by 8 · see citing works

Antisense inhibition of the Escherichia coli NrdAB aerobic ribonucleotide reductase is bactericidal due to induction of DNA strand breaks

Campion, C., Charbon, G., Thomsen, T. T., Nielsen, P. E., & Løbner‐Olesen, A. (2021) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkab305 · Cited by 7 · see citing works

How RNA impacts DNA repair

Tsao, N., Ashour, M. E., & Mosammaparast, N. (2023) · DNA repair · doi:10.1016/j.dnarep.2023.103564 · Cited by 7 · see citing works

Ligase A and RNase HI Participate in Completing Replication on the Chromosome in Escherichia coli

Wendel, B. M., Hernandez, A. J., Courcelle, C. T., & Courcelle, J. (2021) · DNA · doi:10.3390/dna1010003 · Cited by 6 · see citing works

Strand specificity of ribonucleotide excision repair inEscherichia coli

Łazowski, K., Faraz, M., Vaisman, A., Ashton, N. W., Jonczyk, P., Fijałkowska, I. J., Clausen, A. R., Woodgate, R., & Makiela‐Dzbenska, K. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad038 · Cited by 6 · see citing works

NER enzymes maintain genome integrity and suppress homologous recombination in the absence of exogenously induced DNA damage in Pseudomonas putida

Sidorenko, J., Ukkivi, K., & Kivisaar, M. (2014) · DNA repair · doi:10.1016/j.dnarep.2014.11.001 · Cited by 6 · see citing works

Nucleotide Excision Repair Pathway in Mycobacteria

Thakur, M., & Muniyappa, K. (2019) · Springer eBooks · doi:10.1007/978-981-32-9413-4_16 · Cited by 6 · see citing works

Processing of matched and mismatched rNMPs in DNA by archaeal ribonucleotide excision repair

Reveil, M., Chapel, L., Vourc’h, B., Bossé, A., Vialle, L., Brizard, R., Moalic, Y., Jebbar, M., & Henneke, G. (2023) · iScience · doi:10.1016/j.isci.2023.108479 · Cited by 5 · see citing works

Ribonucleotide Misincorporation and Reverse Transcriptase Activities of Plasmodium falciparum Apicoplast DNA Polymerase

Nieto, N. S., Parrott, E. E., & Nelson, S. W. (2022) · Biochemistry · doi:10.1021/acs.biochem.2c00450 · Cited by 3 · see citing works

Model DNA for investigation of mechanism of nucleotide excision repair

Evdokimov, A. N., Lavrik, O. I., & Petruseva, I. O. (2014) · Biopolymers and Cell · doi:10.7124/bc.000893 · Cited by 3 · see citing works

<scp> <i>Bacillus subtilis</i> RNase HII </scp> Is Inefficient at Processing Guanosine Monophosphate and Damaged Ribonucleotides

Cresti, J. R., & Simmons, L. A. (2026) · Molecular Microbiology · doi:10.1111/mmi.70047 · Cited by 2 · see citing works

Genome-wide ribonucleotide detection in <i>Archaea</i>

Moalic, Y., Reveil, M., Kundnani, D. L., Balachander, S., Yang, T., Gombolay, A., Ranjbarian, F., Brizard, R., Durand, P., Myllykallio, H., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1231 · Cited by 2 · see citing works

DNA repair gene ERCC1 polymorphisms and glioma susceptibility among Chinese population: a meta-analysis.

Jiang, C., Shen, F., Du, J.-M., Wang, X., Su, J., Liu, Z., & Huang, X. (2015) · PubMed Central · Cited by 2 · see citing works

High Flexibility of RNaseH2 Catalytic Activity with Respect to Non-Canonical DNA Structures

Dede, M., Napolitano, S., Melati, A., Pirota, V., Maga, G., & Crespan, E. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22105201 · Cited by 2 · see citing works

DNA polymerase I: structure, activity, and function in bacterial DNA replication and repair

Lowder, F. C., & Simmons, L. A. (2026) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2026.2682122 · Cited by 1 · see citing works

Ribonucleotide errors, RNase HII, and ribonucleotide excision repair

Cresti, J. R., & Simmons, L. A. (2026) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2026.2704628

SURVEY AND SUMMARY How the misincorporation of ribonucleotides into genomic DNA can be both harmful and helpful to cells

Potenski, C. J., & Klein, H. L. (2014)

Obecność rybonukleotydów w DNA ma antagonistyczne znaczenie dla utrzymania stabilności genetycznej organizmów

Łazowski, K., & Makiela‐Dzbenska, K. (2019) · Postępy Biochemii · doi:10.18388/pb.2019_247

Genome instability in bacteria and archaea: Strategies for maintaining genome stability

Golubov, A. (2021) · Elsevier eBooks · doi:10.1016/b978-0-323-85679-9.00004-0

Quantitation, base identity and distribution of stably incorporated ribonucleotides in nuclear and mitochondrial DNA from murine tissuesPreprint

Kreisel, K., Kalm, J., Bandaru, S., Ala, C., Akyürek, L. M., & Clausen, A. R. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.20.485043

Influence de la variation de la concentration intracellulaire des désoxyribonucléotides et rubbonucléotides sur la stabilité génomique chez Pyrococcus abyssi

Lemor, M. (2017) · doi:10.70675/c008e746z3c84z45e6zb8f1z9f96609cbe22

Investigating the mechanisms of ribonucleotide excision repair in Escherichia coli

Vaisman, A., McDonald, J. P., Noll, S., Huston, D., Loeb, G., Goodman, M. F., & Woodgate, R. (2014) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2014.01.005 · Cited by 43 · see citing works

Mechanisms Employed by Escherichia coli to Prevent Ribonucleotide Incorporation into Genomic DNA by Pol V

McDonald, J. P., Vaisman, A., Kuban, W., Goodman, M. F., & Woodgate, R. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1003030 · Cited by 38 · see citing works

Ribonucleotides as nucleotide excision repair substrates

Cai, Y., Geacintov, N. E., & Broyde, S. B. (2013) · DNA repair · doi:10.1016/j.dnarep.2013.10.010 · Cited by 22 · see citing works

Ribonucleotide errors, RNase HII, and ribonucleotide excision repair

Cresti, J. R., & Simmons, L. A. (2026) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2026.2704628

Redundancy in ribonucleotide excision repair: Competition, compensation, and cooperation

Vaisman, A., & Woodgate, R. (2015) · DNA repair · doi:10.1016/j.dnarep.2015.02.008 · Cited by 29 · see citing works