Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase β

A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition

(2019) Mallory R Smith et al.   NUCLEIC ACIDS RESEARCH

Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase β

(2018) Myong-Chul Koag et al.   BIOCHEMICAL JOURNAL

The nature of the DNA substrate influences pre-catalytic conformational changes of DNA polymerase β

(2018) Ji Huang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2017) Matilde Clarissa Malfatti et al.   NUCLEIC ACIDS RESEARCH

A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family

(2017) Jordi Carreras-Puigvert et al.   Nature Communications

Polder maps: improving OMIT maps by excluding bulk solvent

(2017) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase η

(2016) Yan Su et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Self-Activated Mechanism for Nucleic Acid Polymerization Catalyzed by DNA/RNA Polymerases

(2016) Vito Genna et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism

(2016) Vinod K. Batra et al.   STRUCTURE

Formation and Repair of Mismatches Containing Ribonucleotides and Oxidized Bases at Repeated DNA Sequences

(2015) Piera Cilli et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Replicative DNA Polymerase δ but Not ε Proofreads Errors in Cis and in Trans

(2015) Carrie L. Flood et al.   PLoS Genetics

Structure and Mechanism of DNA Polymerase β

(2014) William A. Beard et al.   BIOCHEMISTRY

Cellular Levels of 8-Oxoguanine in either DNA or the Nucleotide Pool Play Pivotal Roles in Carcinogenesis and Survival of Cancer Cells

(2014) Yusaku Nakabeppu   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Fluorescence Resonance Energy Transfer Studies of DNA Polymerase β

(2014) Jamie B. Towle-Weicksel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide

(2014) Bret D. Freudenthal et al.   NATURE

ATP insertion opposite 8-oxo-deoxyguanosine by Pol4 mediates error-free tolerance in Schizosaccharomyces pombe

(2014) Guillermo Sastre-Moreno et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Catherine J. Potenski et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Heather Ordonez et al.   NUCLEIC ACIDS RESEARCH

The E295K Cancer Variant of Human Polymerase β Favors the Mismatch Conformational Pathway during Nucleotide Selection

(2013) Brian E. Eckenroth et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DNA Base Damage by Reactive Oxygen Species, Oxidizing Agents, and UV Radiation

(2013) J. Cadet et al.   Cold Spring Harbor Perspectives in Biology

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

(2012) Martin A.M. Reijns et al.   CELL

Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase δ

(2012) Anders R. Clausen et al.   DNA REPAIR

Human DNA Polymerase ϵ Is Able to Efficiently Extend from Multiple Consecutive Ribonucleotides

(2012) A. Yasemin Göksenin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DNA damage by reactive species: Mechanisms, mutation and repair

(2012) N R Jena   JOURNAL OF BIOSCIENCES

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly

(2012) Bret D. Freudenthal et al.   STRUCTURE

Molecular Insights into DNA Polymerase Deterrents for Ribonucleotide Insertion

(2011) Nisha A. Cavanaugh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

DNA Polymerase β Ribonucleotide Discrimination

(2010) Nisha A. Cavanaugh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DNA polymerase structure-based insight on the mutagenic properties of 8-oxoguanine

(2010) William A. Beard et al.   MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS

Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases

(2010) S. A. Nick McElhinny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of oxidized guanosine 5′-triphosphate as a viable inhibitor of soluble guanylyl cyclase

(2009) Celeste Bolin et al.   FREE RADICAL BIOLOGY AND MEDICINE

A Novel Mechanism of Sugar Selection Utilized by a Human X-Family DNA Polymerase

(2009) Jessica A. Brown et al.   JOURNAL OF MOLECULAR BIOLOGY

Hydroxyl radical oxidation of guanosine 5′-triphosphate (GTP): requirement for a GTP–Cu(II) complex

(2009) Giselle Cerchiaro et al.   REDOX REPORT

The Involvement of DNA-Damage and -Repair Defects in Neurological Dysfunction

(2008) Avanti Kulkarni et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Role of Induced Fit in Enzyme Specificity: A Molecular Forward/Reverse Switch

(2008) Kenneth A. Johnson   JOURNAL OF BIOLOGICAL CHEMISTRY

Structures of DNA Polymerase β with Active-Site Mismatches Suggest a Transient Abasic Site Intermediate during Misincorporation

(2008) Vinod K. Batra et al.   MOLECULAR CELL

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

(2008) Xiang-Jun Lu et al.   Nature Protocols