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Article ; Online: Efficient replication of human nuclear DNA.

Kunkel, Thomas A

2022 Volume 32, Issue 9, Page(s) 797–798

MeSH term(s)	Cell Nucleus ; DNA ; DNA Replication ; Humans ; Virus Replication
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2022-07-20
Publishing country	England
Document type	Journal Article
ZDB-ID	1319303-x
ISSN	1748-7838 ; 1001-0602
ISSN (online)	1748-7838
ISSN	1001-0602
DOI	10.1038/s41422-022-00690-2
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Zs.A 5283: Show issues

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Article ; Online: Ribonucleotide Incorporation by Eukaryotic B-Family Replicases and Its Implications for Genome Stability.

Williams, Jessica S / Kunkel, Thomas A

Annual review of biochemistry

2022 Volume 91, Page(s) 133–155

Abstract: Our current view of how DNA-based genomes are efficiently and accurately replicated continues to evolve as new details emerge on the presence of ribonucleotides in DNA. Ribonucleotides are incorporated during eukaryotic DNA replication at rates that make ...

Abstract	Our current view of how DNA-based genomes are efficiently and accurately replicated continues to evolve as new details emerge on the presence of ribonucleotides in DNA. Ribonucleotides are incorporated during eukaryotic DNA replication at rates that make them the most common noncanonical nucleotide placed into the nuclear genome, they are efficiently repaired, and their removal impacts genome integrity. This review focuses on three aspects of this subject: the incorporation of ribonucleotides into the eukaryotic nuclear genome during replication by B-family DNA replicases, how these ribonucleotides are removed, and the consequences of their presence or removal for genome stability and disease.
MeSH term(s)	DNA/genetics ; DNA/metabolism ; DNA Repair ; DNA Replication ; Eukaryota/genetics ; Eukaryota/metabolism ; Genomic Instability ; Nucleotidyltransferases/genetics ; Ribonucleotides/genetics ; Ribonucleotides/metabolism
Chemical Substances	Ribonucleotides ; DNA (9007-49-2) ; Nucleotidyltransferases (EC 2.7.7.-)
Language	English
Publishing date	2022-03-14
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Intramural
ZDB-ID	207924-0
ISSN	1545-4509 ; 0066-4154
ISSN (online)	1545-4509
ISSN	0066-4154
DOI	10.1146/annurev-biochem-032620-110354
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Article ; Online: Extrinsic proofreading.

Zhou, Zhi-Xiong / Kunkel, Thomas A

DNA repair

2022 Volume 117, Page(s) 103369

Abstract: The high fidelity of replication of the nuclear DNA genome in eukaryotes involves three processes. Correct rather than incorrect dNTPs are almost always incorporated by the three major replicases, DNA polymerases α, δ and ε. When an incorrect base is ... ...

Abstract	The high fidelity of replication of the nuclear DNA genome in eukaryotes involves three processes. Correct rather than incorrect dNTPs are almost always incorporated by the three major replicases, DNA polymerases α, δ and ε. When an incorrect base is occasionally inserted, the latter Pols δ and ε also have a 3 ´ to 5 ´ exonuclease activity that can remove the mismatch to allow correct DNA synthesis to proceed. Lastly, rare mismatches that escape proofreading activity and are present in newly replicated DNA can be removed by DNA mismatch repair. In this review, we consider evidence supporting the hypothesis that the second mechanism, proofreading, can operate in two different ways. Primer terminal mismatches made by either Pol δ or Pol ε can be 'intrinsically' proofread. This mechanism occurs by direct transfer of a misinserted base made at the polymerase active site to the exonuclease active site that is located a short distance away. Intrinsic proofreading allows mismatch excision without intervening enzyme dissociation. Alternatively, considerable evidence suggests that mismatches made by any of the three replicases can also be proofread by 'extrinsic' proofreading by Pol δ. Extrinsic proofreading occurs when a mismatch made by any of the three replicases is initially abandoned, thereby allowing the exonuclease active site of Pol δ to bind directly to and remove the mismatch before replication continues. Here we review the evidence that extrinsic proofreading significantly enhances the fidelity of nuclear DNA replication, and we then briefly consider the implications of this process for evolution and disease.
MeSH term(s)	DNA ; DNA Polymerase II/metabolism ; DNA Polymerase III/metabolism ; DNA Replication ; Exonucleases/metabolism
Chemical Substances	DNA (9007-49-2) ; DNA Polymerase II (EC 2.7.7.7) ; DNA Polymerase III (EC 2.7.7.7) ; Exonucleases (EC 3.1.-)
Language	English
Publishing date	2022-07-04
Publishing country	Netherlands
Document type	Journal Article ; Review ; Research Support, N.I.H., Intramural
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2022.103369
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Article ; Online: A simple but profound mutation in mouse DNA polymerase ε drives tumorigenesis.

Kunkel, Thomas A

The Journal of clinical investigation

2018 Volume 128, Issue 9, Page(s) 3754–3756

Abstract: Over 40 years ago, Loeb and colleagues proposed that errors in DNA replication produce a mutator phenotype that is involved in generating the multiple mutations required for tumor development. In this issue of the JCI, Li, Castrillon, and colleagues ... ...

Abstract	Over 40 years ago, Loeb and colleagues proposed that errors in DNA replication produce a mutator phenotype that is involved in generating the multiple mutations required for tumor development. In this issue of the JCI, Li, Castrillon, and colleagues describe a mouse model containing a single base change in the gene encoding replicative DNA polymerase ε (POLE) that mimics the "ultramutator" phenotype recently reported in many human tumors. Their seminal accomplishment validates Loeb's hypothesis and the use of mutational signatures to understand the origins and potentially the treatment of human tumors, and it offers an exciting opportunity to further explore the mechanisms responsible for normal DNA replication fidelity and their perturbations.
MeSH term(s)	Animals ; Carcinogenesis ; Cell Transformation, Neoplastic ; DNA Polymerase II/genetics ; DNA Replication ; Humans ; Mice ; Mutation ; Neoplasms
Chemical Substances	DNA Polymerase II (EC 2.7.7.7)
Language	English
Publishing date	2018-08-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Comment
ZDB-ID	3067-3
ISSN	1558-8238 ; 0021-9738
ISSN (online)	1558-8238
ISSN	0021-9738
DOI	10.1172/JCI123021
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Article ; Online: Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair.

Lujan, Scott Alexander / Kunkel, Thomas A

Cells

2021 Volume 10, Issue 5

Abstract: We describe the contribution of DNA mismatch repair (MMR) to the stability of the eukaryotic nuclear genome as determined by whole-genome sequencing. To date, wild-type nuclear genome mutation rates are known for over 40 eukaryotic species, while ... ...

Abstract	We describe the contribution of DNA mismatch repair (MMR) to the stability of the eukaryotic nuclear genome as determined by whole-genome sequencing. To date, wild-type nuclear genome mutation rates are known for over 40 eukaryotic species, while measurements in mismatch repair-defective organisms are fewer in number and are concentrated on
MeSH term(s)	Cell Nucleus/genetics ; DNA Damage ; DNA Mismatch Repair ; DNA Mutational Analysis ; Genomic Instability ; Humans ; Mutation Rate ; Whole Genome Sequencing
Language	English
Publishing date	2021-05-17
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells10051224
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Article ; Online: Celebrating DNA's Repair Crew.

Kunkel, Thomas A

Cell

2015 Volume 163, Issue 6, Page(s) 1301–1303

Abstract: This year, the Nobel Prize in Chemistry has been awarded to Tomas Lindahl, Aziz Sancar, and Paul Modrich for their seminal studies of the mechanisms by which cells from bacteria to man repair DNA damage that is generated by normal cellular metabolism and ...

Abstract	This year, the Nobel Prize in Chemistry has been awarded to Tomas Lindahl, Aziz Sancar, and Paul Modrich for their seminal studies of the mechanisms by which cells from bacteria to man repair DNA damage that is generated by normal cellular metabolism and stress from the environment. These studies beautifully illustrate the remarkable power of DNA repair to influence life from evolution through disease susceptibility.
MeSH term(s)	Bacteria/metabolism ; Chemistry/history ; DNA/chemistry ; DNA Damage ; DNA Repair ; Eukaryota/metabolism ; History, 21st Century ; Humans ; Nobel Prize
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2015-12-03
Publishing country	United States
Document type	Biography ; Historical Article ; Journal Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2015.11.028
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Article ; Online: Mitochondrial DNA Enrichment for Sensitive Next-Generation Sequencing.

Wu, Shilan / Longley, Matthew J / Lujan, Scott A / Kunkel, Thomas A / Copeland, William C

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2615, Page(s) 427–441

Abstract: Mitochondrial DNA (mtDNA) encodes components essential for cellular respiration. Low levels of point mutations and deletions accumulate in mtDNA during normal aging. However, improper maintenance of mtDNA results in mitochondrial diseases, stemming from ... ...

Abstract	Mitochondrial DNA (mtDNA) encodes components essential for cellular respiration. Low levels of point mutations and deletions accumulate in mtDNA during normal aging. However, improper maintenance of mtDNA results in mitochondrial diseases, stemming from progressive loss of mitochondrial function through the accelerated formation of deletions and mutations in mtDNA. To better understand the molecular mechanisms underlying the creation and propagation of mtDNA deletions, we developed the LostArc next-generation DNA sequencing pipeline to detect and quantify rare mtDNA species in small tissue samples. LostArc procedures are designed to minimize PCR amplification of mtDNA and instead achieve enrichment of mtDNA by selective destruction of nuclear DNA. This approach leads to cost-effective, high-depth sequencing of mtDNA with a sensitivity sufficient to identify one mtDNA deletion per million mtDNA circles. Here, we describe detailed protocols for isolation of genomic DNA from mouse tissues, enrichment of mtDNA through enzymatic destruction of linear nuclear DNA, and preparation of libraries for unbiased next-generation sequencing of mtDNA.
MeSH term(s)	Mice ; Animals ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Mitochondrial Diseases/genetics ; Point Mutation ; High-Throughput Nucleotide Sequencing/methods
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2023-02-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2922-2_28
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Article ; Online: DNA polymerase λ Loop1 variant yields unexpected gain-of-function capabilities in nonhomologous end-joining.

Kaminski, Andrea M / Chiruvella, Kishore K / Ramsden, Dale A / Bebenek, Katarzyna / Kunkel, Thomas A / Pedersen, Lars C

DNA repair

2024 Volume 136, Page(s) 103645

Abstract: DNA polymerases lambda (Polλ) and mu (Polμ) are X-Family polymerases that participate in DNA double-strand break (DSB) repair by the nonhomologous end-joining pathway (NHEJ). Both polymerases direct synthesis from one DSB end, using template derived from ...

Abstract	DNA polymerases lambda (Polλ) and mu (Polμ) are X-Family polymerases that participate in DNA double-strand break (DSB) repair by the nonhomologous end-joining pathway (NHEJ). Both polymerases direct synthesis from one DSB end, using template derived from a second DSB end. In this way, they promote the NHEJ ligation step and minimize the sequence loss normally associated with this pathway. The two polymerases differ in cognate substrate, as Polλ is preferred when synthesis must be primed from a base-paired DSB end, while Polμ is required when synthesis must be primed from an unpaired DSB end. We generated a Polλ variant (Polλ
MeSH term(s)	DNA-Directed DNA Polymerase/metabolism ; Gain of Function Mutation ; DNA Polymerase beta/metabolism ; DNA Repair ; DNA/metabolism ; DNA End-Joining Repair
Chemical Substances	DNA polymerase beta2 (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; DNA Polymerase beta (EC 2.7.7.7) ; DNA (9007-49-2)
Language	English
Publishing date	2024-02-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2024.103645
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Article ; Online: Structural Insights into the Specificity of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Family X DNA Polymerases.

Kaminski, Andrea M / Kunkel, Thomas A / Pedersen, Lars C / Bebenek, Katarzyna

Genes

2021 Volume 13, Issue 1

Abstract: 8-oxo-guanine (8OG) is a common base lesion, generated by reactive oxygen species, which has been associated with human diseases such as cancer, aging-related neurodegenerative disorders and atherosclerosis. 8OG is highly mutagenic, due to its dual- ... ...

Abstract	8-oxo-guanine (8OG) is a common base lesion, generated by reactive oxygen species, which has been associated with human diseases such as cancer, aging-related neurodegenerative disorders and atherosclerosis. 8OG is highly mutagenic, due to its dual-coding potential it can pair both with adenine or cytidine. Therefore, it creates a challenge for DNA polymerases striving to correctly replicate and/or repair genomic or mitochondrial DNA. Numerous structural studies provide insights into the mechanistic basis of the specificity of 8OG bypass by DNA polymerases from different families. Here, we focus on how repair polymerases from Family X (Pols β, λ and µ) engage DNA substrates containing the oxidized guanine. We review structures of binary and ternary complexes for the three polymerases, which represent distinct steps in their catalytic cycles-the binding of the DNA substrate and the incoming nucleotide, followed by its insertion and extension. At each of these steps, the polymerase may favor or exclude the correct C or incorrect A, affecting the final outcome, which varies depending on the enzyme.
MeSH term(s)	8-Hydroxy-2'-Deoxyguanosine/metabolism ; Catalytic Domain/genetics ; DNA/genetics ; DNA/metabolism ; DNA Repair/genetics ; DNA Replication/genetics ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Humans
Chemical Substances	8-Hydroxy-2'-Deoxyguanosine (88847-89-6) ; DNA (9007-49-2) ; DNA polymerase X (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2021-12-22
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13010015
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Article ; Online: Ribonucleotide incorporation into DNA during DNA replication and its consequences.

Zhou, Zhi-Xiong / Williams, Jessica S / Lujan, Scott A / Kunkel, Thomas A

Critical reviews in biochemistry and molecular biology

2021 Volume 56, Issue 1, Page(s) 109–124

Abstract: Ribonucleotides are the most abundant non-canonical nucleotides in the genome. Their vast presence and influence over genome biology is becoming increasingly appreciated. Here we review the recent progress made in understanding their genomic presence, ... ...

Abstract	Ribonucleotides are the most abundant non-canonical nucleotides in the genome. Their vast presence and influence over genome biology is becoming increasingly appreciated. Here we review the recent progress made in understanding their genomic presence, incorporation characteristics and usefulness as biomarkers for polymerase enzymology. We also discuss ribonucleotide processing, the genetic consequences of unrepaired ribonucleotides in DNA and evidence supporting the significance of their transient presence in the nuclear genome.
MeSH term(s)	Animals ; Biomarkers/metabolism ; Cell Nucleus/metabolism ; DNA/genetics ; DNA/metabolism ; DNA Repair/genetics ; DNA Replication/genetics ; DNA-Directed DNA Polymerase/metabolism ; Genome, Mitochondrial ; Genomic Instability ; Humans ; Ribonucleotides/genetics ; Ribonucleotides/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism
Chemical Substances	Biomarkers ; Ribonucleotides ; DNA (9007-49-2) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2021-01-18
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	1000977-2
ISSN	1549-7798 ; 1381-3455 ; 1040-9238
ISSN (online)	1549-7798
ISSN	1381-3455 ; 1040-9238
DOI	10.1080/10409238.2020.1869175
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