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List of works by Suse Broyde

4-hydroxyequilenin-adenine lesions in DNA duplexes: stereochemistry, damage site, and structure

scientific article published on January 2007

5-Formylcytosine mediated DNA-protein cross-links block DNA replication and induce mutations in human cells

5-Formylcytosine mediated DNA-protein cross-links block DNA replication and induce mutations in human cells

scientific article published on 01 July 2018

5-Formylcytosine-induced DNA-peptide cross-links reduce transcription efficiency, but do not cause transcription errors in human cells

scientific article published on 09 October 2019

A Bulky DNA Lesion Derived from a Highly Potent Polycyclic Aromatic Tumorigen Stabilizes Nucleosome Core Particle Structure ⬇️

scientific article published on October 28, 2010

A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4).

scientific article

A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.

scientific article

Absolute configurations of DNA lesions determined by comparisons of experimental ECD and ORD spectra with DFT calculations

scientific article (publication date: 2009)

Absolute configurations of spiroiminodihydantoin and allantoin stereoisomers: comparison of computed and measured electronic circular dichroism spectra

scientific article

Accommodation of a 1S-(-)-benzo[c]phenanthrenyl-N6-dA adduct in the Y-family Dpo4 DNA polymerase active site: structural insights through molecular dynamics simulations

scientific article published on March 2005

Accommodation of an N-(deoxyguanosin-8-yl)-2-acetylaminofluorene adduct in the active site of human DNA polymerase iota: Hoogsteen or Watson-Crick base pairing?

scientific article published on January 2009

Accurate representation of B-DNA double helical structure with implicit solvent and counterions

scientific article

Adenine–DNA Adducts Derived from the Highly Tumorigenic Dibenzo[a,l]pyrene Are Resistant to Nucleotide Excision Repair while Guanine Adducts Are Not ⬇️

scientific article published on April 24, 2013

Altering DNA polymerase incorporation fidelity by distorting the dNTP binding pocket with a bulky carcinogen-damaged template.

scientific article

Assignment of absolute configurations of the enantiomeric spiroiminodihydantoin nucleobases by experimental and computational optical rotatory dispersion methods

scientific article published on 01 July 2006

Base Flipping Free Energy Profiles for Damaged and Undamaged DNA ⬇️

scientific article published on December 20, 2010

Base Sequence Context Effects on Nucleotide Excision Repair ⬇️

scientific article published on August 23, 2010

Bypass of DNA-Protein Cross-links Conjugated to the 7-Deazaguanine Position of DNA by Translesion Synthesis Polymerases

scientific article published on 12 September 2016

Comparative mutagenesis of the C8-guanine adducts of 1-nitropyrene and 1,6- and 1,8-dinitropyrene in a CpG repeat sequence. A slipped frameshift intermediate model for dinucleotide deletion

scientific article published on 17 September 2002

Conformational analysis of a 4-hydroxyequilenin Guanine adduct using density functional theory

scientific article

Conformational properties of equilenin-DNA adducts: stereoisomer and base effects

scientific article published on 17 April 2008

Conformational searches elucidate effects of stereochemistry on structures of deoxyadenosine covalently bound to tumorigenic metabolites of benzo[C] phenanthrene.

scientific article

Conformations of stereoisomeric base adducts to 4-hydroxyequilenin

scientific article

Correction: Resistance to Nucleotide Excision Repair of Bulky Guanine Adducts Opposite Abasic Sites in DNA Duplexes and Relationships between Structure and Function

scientific article published on 29 October 2015

DNA Cytosine Methylation: Structural and Thermodynamic Characterization of the Epigenetic Marking Mechanism ⬇️

scientific article published on April 12, 2013

DNA adduct structure-function relationships: comparing solution with polymerase structures.

scientific article published on 04 December 2007

DNA adducts from a tumorigenic metabolite of benzo[a]pyrene block human RNA polymerase II elongation in a sequence- and stereochemistry-dependent manner

scientific article

DNA damage, mutagenesis, and DNA repair.

scientific article published on 27 December 2010

DNA repair: How to accurately bypass damage

scientific article published on June 2010

Deformations of promoter DNA bound to carcinogens help interpret effects on TATA-element structure and activity

scientific article

Determination of absolute configurations of 4-hydroxyequilenin-cytosine and -adenine adducts by optical rotatory dispersion, electronic circular dichroism, density functional theory calculations, and mass spectrometry.

scientific article published on 05 August 2008

Differences in the Access of Lesions to the Nucleotide Excision Repair Machinery in Nucleosomes

scientific article published on 30 June 2015

Differential nucleotide excision repair susceptibility of bulky DNA adducts in different sequence contexts: hierarchies of recognition signals

scientific article

Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion

scientific article

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

scientific article published on 19 September 2007

Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex

scientific article published on 18 December 2017

Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study ⬇️

scientific article

Equilenin-derived DNA adducts to cytosine in DNA duplexes: structures and thermodynamics

scientific article published in November 2005

Exocyclic amino groups of flanking guanines govern sequence-dependent adduct conformations and local structural distortions for minor groove-aligned benzo[a]pyrenyl-guanine lesions in a GG mutation hotspot context

scientific article published on 7 February 2007

Exploring damage recognition models in prokaryotic nucleotide excision repair with a benzo[a]pyrene-derived lesion in UvrB

scientific article

Extending the understanding of mutagenicity: structural insights into primer-extension past a benzo[a]pyrene diol epoxide-DNA adduct

scientific article published in April 2003

Flexible 5-guanidino-4-nitroimidazole DNA lesions: structures and thermodynamics

scientific article published on May 2006

Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase

scientific article published on 18 June 2007

Free Energy Profiles of Base Flipping in Intercalative Polycyclic Aromatic Hydrocarbon-Damaged DNA Duplexes: Energetic and Structural Relationships to Nucleotide Excision Repair Susceptibility ⬇️

scientific article published on 02 July 2013

Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses.

scientific article

Human RNA polymerase II is partially blocked by DNA adducts derived from tumorigenic benzo[c]phenanthrene diol epoxides: relating biological consequences to conformational preferences ⬇️

scientific article published on October 15, 2003

Impact of Conformational Heterogeneity of OxoG Lesions and Their Pairing Partners on Bypass Fidelity by Y Family Polymerases

scientific article

Impact of DNA sequences in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex

scientific article published on 17 January 2020

Increased flexibility enhances misincorporation: temperature effects on nucleotide incorporation opposite a bulky carcinogen-DNA adduct by a Y-family DNA polymerase

scientific article published on 6 November 2006

Influence of local sequence context on damaged base conformation in human DNA polymerase iota: molecular dynamics studies of nucleotide incorporation opposite a benzo[a]pyrene-derived adenine lesion

scientific article

Intercalative Conformations of the 14R (+)- and 14S (−)-trans-anti-DB[a,l]P-N6-dA Adducts: Molecular Modeling and MD Simulations ⬇️

scientific article published on February 28, 2011

Lesion processing: high-fidelity versus lesion-bypass DNA polymerases

scientific article published on 11 April 2008

Lesion sensing during initial binding by yeast XPC/Rad4: toward predicting resistance to nucleotide excision repair

scientific article published on 22 October 2018

Lesion specificity in the base excision repair enzyme hNeil1: modeling and dynamics studies

scientific article published on 14 April 2007

Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein

scientific article published in 2021

Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus

scientific article

Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4

scientific article

Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement

scientific article

Molecular basis for damage recognition and verification by XPC-RAD23B and TFIIH in nucleotide excision repair

scientific article published on 23 August 2018

Molecular dynamics of a food carcinogen-DNA adduct in a replicative DNA polymerase suggest hindered nucleotide incorporation and extension

scientific article published in September 2005

Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies

scientific article published on 4 July 2006

NMR and computational studies of stereoisomeric equine estrogen-derived DNA cytidine adducts in oligonucleotide duplexes: opposite orientations of diastereomeric forms

scientific article

Nuclear Magnetic Resonance Solution Structure of an N2-Guanine DNA Adduct Derived from the Potent Tumorigen Dibenzo[a,l]pyrene: Intercalation from the Minor Groove with Ruptured Watson–Crick Base Pairing ⬇️

scientific article published on November 15, 2012

Nuclear Magnetic Resonance Studies of an N 2 -Guanine Adduct Derived from the Tumorigen Dibenzo[ a , l ]pyrene in DNA: Impact of Adduct Stereochemistry, Size, and Local DNA Sequence on Solution Conformations

scientific article

Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion

scientific article

Nucleotide Excision Repair Efficiencies of Bulky Carcinogen–DNA Adducts Are Governed by a Balance between Stabilizing and Destabilizing Interactions ⬇️

scientific article (publication date: 21 February 2012)

Nucleotide Excision Repair Lesion-Recognition Protein Rad4 Captures a Pre-Flipped Partner Base in a Benzo[a]pyrene-Derived DNA Lesion: How Structure Impacts the Binding Pathway

scientific article

Nucleotide Excision Repair and Impact of Site-Specific 5',8-Cyclopurine and Bulky DNA Lesions on the Physical Properties of Nucleosomes

scientific article published on 07 January 2019

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 ⬇️

scientific article published on August 16, 2012

Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase: a 5'-slippage mechanism

scientific article published on 9 February 2008

Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se.

scientific article published on April 2002

Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase

scientific article

Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion

scientific article

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 ⬇️

scientific article published on July 8, 2011

Recognition of Damaged DNA for Nucleotide Excision Repair: A Correlated Motion Mechanism with a Mismatched cis-syn Thymine Dimer Lesion

scientific article

Relating repair susceptibility of carcinogen-damaged DNA with structural distortion and thermodynamic stability

scientific article

Repair-Resistant DNA Lesions

scientific article published on 27 July 2017

Resistance of bulky DNA lesions to nucleotide excision repair can result from extensive aromatic lesion–base stacking interactions ⬇️

scientific article published on July 15, 2011

Resistance to Nucleotide Excision Repair of Bulky Guanine Adducts Opposite Abasic Sites in DNA Duplexes and Relationships between Structure and Function

scientific article published on 4 September 2015

Ribonucleotides as nucleotide excision repair substrates

scientific article

Role of Structural and Energetic Factors in Regulating Repair of a Bulky DNA Lesion with Different Opposite Partner Bases ⬇️

scientific article published on 05 August 2013

Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[a]pyrene diol epoxide-adenine adducts

scientific article published in March 2003

Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome

scientific article published on 29 November 2018

Simulating structural and thermodynamic properties of carcinogen-damaged DNA.

scientific article

Solution conformation of the (+)-cis-anti-[BP]dG adduct in a DNA duplex: intercalation of the covalently attached benzo[a]pyrenyl ring into the helix and displacement of the modified deoxyguanosine

scientific article published in April 1993

Solution conformation of the major adduct between the carcinogen (+)-anti-benzo[a]pyrene diol epoxide and DNA ⬇️

scientific article published on March 1, 1992

Solution structure of an O6-[4-oxo-4-(3-pyridyl)butyl]guanine adduct in an 11 mer DNA duplex: evidence for formation of a base triplex

scientific article

Spiroiminodihydantoin lesions derived from guanine oxidation: structures, energetics, and functional implications

scientific article published in April 2005

Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion

scientific article

Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity

scientific article

Structural and stereoisomer effects of model estrogen quinone-derived DNA adducts: N6-(2-hydroxyestron-6(alpha,beta)-yl)-2'-deoxyadenosine and N2-(2-hydroxyestron-6(alpha,beta)-yl)-2'-deoxyguanosine

scientific article published in March 2004

Structural and thermodynamic features of spiroiminodihydantoin damaged DNA duplexes

scientific article

Structural basis for the recognition of diastereomeric 5',8-cyclo-2'-deoxypurine lesions by the human nucleotide excision repair system

scientific article

Structural characterization of an N-acetyl-2-aminofluorene (AAF) modified DNA oligomer by NMR, energy minimization, and molecular dynamics

scientific article published on 01 March 1993

Structural, energetic and dynamic properties of guanine(C8)-thymine(N3) cross-links in DNA provide insights on susceptibility to nucleotide excision repair

scientific article published in December 2011

Structure and mechanism of pyrimidine-pyrimidone (6-4) photoproduct recognition by the Rad4/XPC nucleotide excision repair complex

scientific article published on 01 July 2019

Substrate discrimination by formamidopyrimidine-DNA glycosylase: a mutational analysis

scientific article

Substrate discrimination by formamidopyrimidine-DNA glycosylase: distinguishing interactions within the active site

scientific article published in December 2004

Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognition

scientific article published on 8 March 2018

Tethering-facilitated DNA 'opening' and complementary roles of β-hairpin motifs in the Rad4/XPC DNA damage sensor protein

scientific article published on 29 October 2020

The DNA damage-sensing NER repair factor XPC-RAD23B does not recognize bulky DNA lesions with a missing nucleotide opposite the lesion

scientific article published on 01 October 2020

The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions

scientific article (publication date: November 2008)

The Nonbulky DNA Lesions Spiroiminodihydantoin and 5-Guanidinohydantoin Significantly Block Human RNA Polymerase II Elongation in Vitro

scientific article published on 17 May 2017

The human DNA repair factor XPC-HR23B distinguishes stereoisomeric benzo[a]pyrenyl-DNA lesions

scientific article (publication date: 20 June 2007)

The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: is there a correlation?

scientific article

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

scientific article published on 08 January 2009

The spacious active site of a Y-family DNA polymerase facilitates promiscuous nucleotide incorporation opposite a bulky carcinogen-DNA adduct: elucidating the structure-function relationship through experimental and computational approaches

scientific article

Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery

scientific article

Toward understanding the mutagenicity of an environmental carcinogen: structural insights into nucleotide incorporation preferences

scientific article published in September 2002

Transcription elongation past O6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase

scientific article published on 14 October 2008

Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase

scientific article published on 13 June 2008

Transcription processing at 1,N2-ethenoguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase

scientific article published on 30 October 2007

Transcriptional Bypass of DNA-Protein and DNA-Peptide Conjugates by T7 RNA Polymerase

scientific article published on 21 October 2019

Variable impact of conformationally distinct DNA lesions on nucleosome structure and dynamics: Implications for nucleotide excision repair

scientific article published on 28 December 2019

Visualizing sequence-governed nucleotide selectivities and mutagenic consequences through a replicative cycle: processing of a bulky carcinogen N2-dG lesion in a Y-family DNA polymerase

scientific article

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