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Impact of DNA sequences on DNA ?opening? by the Rad4/XPC nucleotide excision repair complex

Journal Article · · DNA Repair

Research Organization:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Organization:
DOE - Office Of Science; National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI ID:
1820451
Journal Information:
DNA Repair, Vol. 107
Country of Publication:
United States
Language:
ENGLISH

References (105)

Photobiological Origins of the Field of Genomic Maintenance journal December 2015
UV-Induced DNA Damage and Mutagenesis in Chromatin journal November 2016
Nucleotide Excision Repair in Eukaryotes journal October 2013
Molecular Mechanisms of Mammalian Global Genome Nucleotide Excision Repair journal February 2006
DNA Damage and Associated DNA Repair Defects in Disease and Premature Aging journal August 2019
Xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome: A complex genotype–phenotype relationship journal April 2007
Differential Nucleotide Excision Repair Susceptibility of Bulky DNA Adducts in Different Sequence Contexts: Hierarchies of Recognition Signals journal January 2009
The Sequence Dependence of Human Nucleotide Excision Repair Efficiencies of Benzo[a]pyrene-derived DNA Lesions: Insights into the Structural Factors that Favor Dual Incisions journal March 2009
Probing for DNA damage with β-hairpins: Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro journal July 2011
Adenine–DNA Adducts Derived from the Highly Tumorigenic Dibenzo[ a , l ]pyrene Are Resistant to Nucleotide Excision Repair while Guanine Adducts Are Not journal April 2013
Dynamics of a Benzo[a]pyrene-derived Guanine DNA Lesion in TGT and CGC Sequence Contexts: Enhanced Mobility in TGT Explains Conformational Heterogeneity, Flexible Bending, and Greater Susceptibility to Nucleotide Excision Repair journal November 2007
Lesion Sensing during Initial Binding by Yeast XPC/Rad4: Toward Predicting Resistance to Nucleotide Excision Repair journal October 2018
A multistep damage recognition mechanism for global genomic nucleotide excision repair journal March 2001
Repair-Resistant DNA Lesions journal July 2017
The DNA damage response to transcription stress journal September 2019
Functional regulation of the DNA damage-recognition factor DDB2 by ubiquitination and interaction with xeroderma pigmentosum group C protein journal January 2015
DNA damage detection in nucleosomes involves DNA register shifting journal May 2019
Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair journal July 2012
Recognition of DNA damage by the Rad4 nucleotide excision repair protein journal September 2007
Structure and mechanism of pyrimidine–pyrimidone (6-4) photoproduct recognition by the Rad4/XPC nucleotide excision repair complex journal May 2019
Recognition of DNA Adducts by Human Nucleotide Excision Repair: EVIDENCE FOR A THERMODYNAMIC PROBING MECHANISM journal October 1996
Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery journal September 2002
DNA Quality Control by Conformational Readout on the Undamaged Strand of the Double Helix journal August 2005
DNA repair triggered by sensors of helical dynamics journal November 2007
Kinetic gating mechanism of DNA damage recognition by Rad4/XPC journal January 2015
Tethering-facilitated DNA ‘opening’ and complementary roles of β-hairpin motifs in the Rad4/XPC DNA damage sensor protein journal October 2020
Twist-open mechanism of DNA damage recognition by the Rad4/XPC nucleotide excision repair complex journal March 2016
Single-Molecule Imaging Reveals that Rad4 Employs a Dynamic DNA Damage Recognition Process journal October 2016
A Compendium of Mutational Signatures of Environmental Agents journal May 2019
Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex journal December 2017
[20] Processing of X-ray diffraction data collected in oscillation mode book January 1997
Overview of the CCP 4 suite and current developments journal March 2011
Features and development of Coot journal March 2010
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix journal October 2019
Filtering artifacts from lifetime distributions when maximizing entropy using a bootstrapped model journal August 2012
Analysis of Kinetics Using a Hybrid Maximum-Entropy/Nonlinear-Least-Squares Method: Application to Protein Folding journal April 2002
Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein journal January 2021
FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids journal September 2012
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes journal September 1998
Bending and Torsional Flexibility of G/C-rich Sequences as Determined by Cyclization Assays journal December 1995
AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein–Protein Interaction Interfaces journal July 2015
Distant Neighbor Base Sequence Context Effects in Human Nucleotide Excision Repair of a Benzo[a]pyrene-derived DNA Lesion journal June 2010
Nucleotide excision repair of 2-acetylaminofluorene- and 2-aminofluorene-(C8)-guanine adducts: molecular dynamics simulations elucidate how lesion structure and base sequence context impact repair efficiencies journal August 2012
Stable binding of human XPC complex to irradiated DNA confers strong discrimination for damaged sites 1 1Edited by M. Yaniv journal July 2000
The XPC−HR23B Complex Displays High Affinity and Specificity for Damaged DNA in a True-Equilibrium Fluorescence Assay journal May 2002
Diversity of the damage recognition step in the global genomic nucleotide excision repair in vitro journal April 2001
Overproduction, Purification, and Characterization of the XPC Subunit of the Human DNA Repair Excision Nuclease journal August 1996
Biochemical and Structural Domain Analysis of Xeroderma Pigmentosum Complementation Group C Protein journal December 2006
Pre-Steady-State Binding of Damaged DNA by XPC−hHR23B Reveals a Kinetic Mechanism for Damage Discrimination journal February 2006
Structural, energetic and dynamic properties of guanine(C8)–thymine(N3) cross-links in DNA provide insights on susceptibility to nucleotide excision repair journal November 2011
Base Sequence Context Effects on Nucleotide Excision Repair journal January 2010
The Solution Structure of DNA Duplex-Decamer Containing the (6-4) Photoproduct of Thymidylyl(3'5')Thymidine by NMR and Relaxation Matrix Refinement journal March 1995
CONTRASTING STRUCTURAL IMPACTS INDUCED BY cis-syn CYCLOBUTANE DIMER AND (6–4) ADDUCT IN DNA DUPLEX DECAMERS: IMPLICATION IN MUTAGENESIS AND REPAIR ACTIVITY journal July 1995
Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates journal February 2017
Conformational changes in the oligonucleotide duples d(GCGTTGCG). d (CGCAACGC) induced by formation of a cis-syn thymine dimer. A two-dimensional NMR study journal January 1987
Solution-state structure of a DNA dodecamer duplex containing a Cis-Syn thymine cyclobutane dimer, the major UV photoproduct of DNA journal October 1998
Site-specific effect of thymine dimer formation on dAn.dTn tract bending and its biological implications. journal October 1991
Crystal structure of a DNA decamer containing a cis-syn thymine dimer journal November 2002
Thermodynamic and base-pairing studies of matched and mismatched DNA dodecamer duplexes containing cis-syn, (6-4) and Dewar photoproducts of TT journal August 1998
The In Situ Repair Kinetics of Epidermal Thymine Dimers and 6-4 Photoproducts in Human Skin Types I and II journal June 1996
Nucleotide excision repair by dual incisions in plants journal April 2016
Nucleotide Excision Repair Efficiencies of Bulky Carcinogen–DNA Adducts Are Governed by a Balance between Stabilizing and Destabilizing Interactions journal February 2012
Dissociation Dynamics of XPC-RAD23B from Damaged DNA Is a Determining Factor of NER Efficiency journal June 2016
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA journal November 2009
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA journal September 2014
Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution journal July 2016
Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution journal May 2015
Single-nucleotide resolution dynamic repair maps of UV damage in Saccharomyces cerevisiae genome journal March 2018
Super hotspots and super coldspots in the repair of UV-induced DNA damage in the human genome journal January 2021
Cisplatin DNA damage and repair maps of the human genome at single-nucleotide resolution journal September 2016
Differential damage and repair of DNA-adducts induced by anti-cancer drug cisplatin across mouse organs journal January 2019
The involvement of nucleotide excision repair proteins in the removal of oxidative DNA damage journal October 2020
Xeroderma pigmentosum group C protein interacts physically and functionally with thymine DNA glycosylase journal January 2003
Stimulation of DNA Glycosylase Activities by XPC Protein Complex: Roles of Protein-Protein Interactions journal January 2010
Regulation of DNA demethylation by the XPC DNA repair complex in somatic and pluripotent stem cells journal April 2017
Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells journal April 2015
Architecture of the human XPC DNA repair and stem cell coactivator complex journal November 2015
A DNA Repair Complex Functions as an Oct4/Sox2 Coactivator in Embryonic Stem Cells journal September 2011
NER Factors Are Recruited to Active Promoters and Facilitate Chromatin Modification for Transcription in the Absence of Exogenous Genotoxic Attack journal April 2010
Nucleotide Excision Repair and Transcriptional Regulation: TFIIH and Beyond journal June 2016
XPC is an RNA polymerase II cofactor recruiting ATAC to promoters by interacting with E2F1 journal July 2018
UV induced ubiquitination of the yeast Rad4–Rad23 complex promotes survival by regulating cellular dNTP pools journal July 2015
Genome-Wide Analysis of the Effects of Location and Number of Stress Response Elements on Gene Expression in Saccharomyces cerevisiae journal November 2008
Stress-controlled transcription factors, stress-induced genes and stress tolerance in budding yeast journal October 2000
The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: Is there a correlation? journal July 2014
DNA bending by the human damage recognition complex XPC–HR23B journal March 2003
Fluorescence Correlation Spectroscopy of the Binding of Nucleotide Excision Repair Protein XPC-hHr23B with DNA Substrates journal June 2008
The human DNA ends proteome uncovers an unexpected entanglement of functional pathways journal February 2016
Structural basis of TFIIH activation for nucleotide excision repair journal June 2019
Single-molecule visualization reveals the damage search mechanism for the human NER protein XPC-RAD23B journal August 2019
Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA) journal June 2015
Single molecule analysis reveals monomeric XPA bends DNA and undergoes episodic linear diffusion during damage search journal March 2020
Single-molecule analysis reveals two separate DNA-binding domains in the Escherichia coli UvrA dimer journal February 2009
Role of the two ATPase domains of Escherichia coli UvrA in binding non-bulky DNA lesions and interaction with UvrB journal November 2010
Mechanism of MutS Searching for DNA Mismatches and Signaling Repair journal December 2008
Determination of protein-DNA binding constants and specificities from statistical analyses of single molecules: MutS-DNA interactions journal July 2005
DNA bending and unbending by MutS govern mismatch recognition and specificity journal November 2003
Studying protein-DNA interactions using atomic force microscopy journal January 2018
Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates journal April 2014
Cooperative cluster formation, DNA bending and base-flipping by O 6 -alkylguanine-DNA alkyltransferase journal June 2012
Kinetic Mechanism for the Excision of Hypoxanthine by Escherichia coli AlkA and Evidence for Binding to DNA Ends journal April 2011
A comprehensive catalogue of somatic mutations from a human cancer genome journal December 2009
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures journal September 2003
Error estimates on averages of correlated data journal July 1989
Free energy simulations: Use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence journal February 2004