FIND

researchers

DISCOVER

relevant articles

PROMOTE

your research

now for free

Suse Broyde

Research Profile

Chemicals & Drugs

Concepts & Ideas

Phenomena

Co-author Network

Publications

TOP 3
Jin Yang; Yingkai Zhang; Lee Lior-Hoffmann; Shenglong Wang; Suse Broyde
DNA Cytosine methylation: structural and thermodynamic characterization of the epigenetic marking mechanism.
Yijin Tang; Shantu Amin; Suse Broyde; Yuqin Cai; Shuang Ding; Donald M Jerina; Chin H Lin; Zhi Liu; Fabian A Rodriguez; Jane M Sayer; Nicholas E Geacintov
Nuclear magnetic resonance solution structure of an N(2)-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: intercalation from the minor groove with ruptured Watson-Crick base pairing.
Hong Mu; Lihua Wang; Lu Zhang; Nicholas E Geacintov; Alexander Kolbanovskiy; Marina Kolbanovskiy; Konstantin Kropachev; Suse Broyde
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.

Register for free to view:

Visualized networks:

See your personal network in
sophisticated graphical views

GeoTargeted Searches:

Locate experts around the world
and connect with global collaborators

Research Profiles:

See the research activity
of experts around the globe

Geonetwork of Suse Broyde (preview)

Cities where this author has publications
Cities where co-authors of this author have publications

Flash Player Required

All Publications

2013: Jin Yang; Yingkai Zhang; Lee Lior-Hoffmann; Shenglong Wang; Suse Broyde
DNA Cytosine methylation: structural and thermodynamic characterization of the epigenetic marking mechanism.
Biochemistry 2013;52(16):2828-38.
2012: Yijin Tang; Shantu Amin; Suse Broyde; Yuqin Cai; Shuang Ding; Donald M Jerina; Chin H Lin; Zhi Liu; Fabian A Rodriguez; Jane M Sayer; Nicholas E Geacintov
Nuclear magnetic resonance solution structure of an N(2)-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: intercalation from the minor groove with ruptured Watson-Crick base pairing.
Biochemistry 2012;51(48):9751-62.
2012: Hong Mu; Lihua Wang; Lu Zhang; Nicholas E Geacintov; Alexander Kolbanovskiy; Marina Kolbanovskiy; Konstantin Kropachev; Suse Broyde
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.
Nucleic acids research 2012;40(19):9675-90.
2012: Lee Lior-Hoffmann; Lihua Wang; Shenglong Wang; Suse Broyde; Nicholas E Geacintov; Yingkai Zhang
Preferred WMSA catalytic mechanism of the nucleotidyl transfer reaction in human DNA polymerase κ elucidates error-free bypass of a bulky DNA lesion.
Nucleic acids research 2012;40(18):9193-205.
2012: Shuang Ding; Svetlana A Durandina; Suse Broyde; Yuqin Cai; Marina Kolbanovskiy; Konstantin Kropachev; Zhi Liu; Vladimir Shafirovich; Nicholas E Geacintov
Structural, energetic and dynamic properties of guanine(C8)-thymine(N3) cross-links in DNA provide insights on susceptibility to nucleotide excision repair.
Nucleic acids research 2012;40(6):2506-17.
2012: Yuqin Cai; Nicholas E Geacintov; Suse Broyde
Nucleotide excision repair efficiencies of bulky carcinogen-DNA adducts are governed by a balance between stabilizing and destabilizing interactions.
Biochemistry 2012;51(7):1486-99.
2011: Dara A Reeves; Shantu Amin; Suse Broyde; Yuqin Cai; Ying Chen; Shuang Ding; Alexander Kolbanovskiy; Marina Kolbanovskiy; Konstantin Kropachev; Jacek Krzeminski; Hong Mu; Dinshaw J Patel; Nicholas E Geacintov
Resistance of bulky DNA lesions to nucleotide excision repair can result from extensive aromatic lesion-base stacking interactions.
Nucleic acids research 2011;39(20):8752-64.
2011: Yang Liu; Dara Reeves; Bennett Van Houten; Alexander Kolbanovskiy; Marina Kolbanovskiy; Konstantin Kropachev; Judy L Bolton; Suse Broyde; Yuqin Cai; Shuang Ding; Nicholas E Geacintov
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.
DNA repair 2011;10(7):684-96.
2011: Yuqin Cai; Shuang Ding; Nicholas E Geacintov; Suse Broyde
Intercalative conformations of the 14R (+)- and 14S (-)-trans-anti-DB[a,l]P-N⁶-dA adducts: molecular modeling and MD simulations.
Chemical research in toxicology 2011;24(4):522-31.
2010: Yuqin Cai; Lihua Wang; Shuang Ding; Adam Schwaid; Nicholas E Geacintov; Suse Broyde
A bulky DNA lesion derived from a highly potent polycyclic aromatic tumorigen stabilizes nucleosome core particle structure.
Biochemistry 2010;49(46):9943-5.
2010: Suse Broyde; Dinshaw J Patel
DNA repair: How to accurately bypass damage.
Nature 2010;465(7301):1023-4.
2010: Yuqin Cai; Konstantin Kropachev; Rong Xu; Yijin Tang; Marina Kolbanovskii; Alexander Kolbanovskii; Shantu Amin; Dinshaw J Patel; Suse Broyde; Nicholas E Geacintov
Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion.
Journal of molecular biology 2010;399(3):397-409.
2010: Olga Rechkoblit; Alexander Kolbanovskiy; Lucy Malinina; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4.
Nature structural & molecular biology 2010;17(3):379-88.
2010: Ashis Basu; Suse Broyde; Shigenori Iwai; Caroline Kisker
DNA damage, mutagenesis, and DNA repair.
Journal of nucleic acids 2010;2010():182894.
2010: Yuqin Cai; Dinshaw J Patel; Suse Broyde; Nicholas E Geacintov
Base sequence context effects on nucleotide excision repair.
Journal of nucleic acids 2010;2010():.
2009: Kerry Donny-Clark; Suse Broyde
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.
Nucleic acids research 2009;37(21):7095-109.
2009: Lei Jia; Konstantin Kropachev; Shuang Ding; Bennett Van Houten; Nicholas E Geacintov; Suse Broyde
Exploring damage recognition models in prokaryotic nucleotide excision repair with a benzo[a]pyrene-derived lesion in UvrB.
Biochemistry 2009;48(38):8948-57.
2009: Na Zhang; Shuang Ding; Alexander Kolbanovskiy; Anant Shastry; Vladimir A Kuzmin; Judy L Bolton; Dinshaw J Patel; Suse Broyde; Nicholas E Geacintov
NMR and computational studies of stereoisomeric equine estrogen-derived DNA cytidine adducts in oligonucleotide duplexes: opposite orientations of diastereomeric forms.
Biochemistry 2009;48(30):7098-109.
2009: Lihua Wang; Suse Broyde; Yingkai Zhang
Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase.
Journal of molecular biology 2009;389(4):787-96.
2009: Pingna Xu; Lida Oum; Yuan-Cho Lee; Nicholas E Geacintov; Suse Broyde
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.
Biochemistry 2009;48(22):4677-90.
2009: Shuang Ding; Lei Jia; Alexander Durandin; Conor Crean; Alexander Kolbanovskiy; Vladimir Shafirovich; Suse Broyde; Nicholas E Geacintov
Absolute configurations of spiroiminodihydantoin and allantoin stereoisomers: comparison of computed and measured electronic circular dichroism spectra.
Chemical research in toxicology 2009;22(6):1189-93.
2009: Olga Rechkoblit; Lucy Malinina; Yuan Cheng; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases.
Structure (London, England : 1993) 2009;17(5):725-36.
2009: Konstantin Kropachev; Marina Kolbanovskii; Yuqin Cai; Fabian Rodríguez; Alexander Kolbanovskii; Yang Liu; Lu Zhang; Shantu Amin; Dinshaw J Patel; Suse Broyde; Nicholas E Geacintov
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 of molecular biology 2009;386(5):1193-203.
2009: Kerry Donny-Clark; Robert Shapiro; Suse Broyde
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?
Biochemistry 2009;48(1):7-18.
2009: Yuqin Cai; Dinshaw J Patel; Nicholas E Geacintov; Suse Broyde
Differential nucleotide excision repair susceptibility of bulky DNA adducts in different sequence contexts: hierarchies of recognition signals.
Journal of molecular biology 2009;385(1):30-44.
2009: Shuang Ding; Alexander Kolbanovskiy; Alexander Durandin; Conor Crean; Vladimir Shafirovich; Suse Broyde; Nicholas E Geacintov
Absolute configurations of DNA lesions determined by comparisons of experimental ECD and ORD spectra with DFT calculations.
Chirality 2009;21 Suppl 1():E231-41.
2008: Lei Jia; Nicholas E Geacintov; Suse Broyde
The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions.
Nucleic acids research 2008;36(20):6571-84.
2008: Alexandra Dimitri; John A Burns; Suse Broyde; David A Scicchitano
Transcription elongation past O6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase.
Nucleic acids research 2008;36(20):6459-71.
2008: Shuang Ding; Yan Wang; Alexander Kolbanovskiy; Alexander Durandin; Judy L Bolton; Richard B Van Breemen; Suse Broyde; Nicholas E Geacintov
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.
Chemical research in toxicology 2008;21(9):1739-48.
2008: Alexandra Dimitri; Lei Jia; Vladimir Shafirovich; Nicholas E Geacintov; Suse Broyde; David A Scicchitano
Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase.
DNA repair 2008;7(8):1276-88.
2008: Shuang Ding; Robert Shapiro; Yuqin Cai; Nicholas E Geacintov; Suse Broyde
Conformational properties of equilenin-DNA adducts: stereoisomer and base effects.
Chemical research in toxicology 2008;21(5):1064-73.
2008: Suse Broyde; Lihua Wang; Olga Rechkoblit; Nicholas E Geacintov; Dinshaw J Patel
Lesion processing: high-fidelity versus lesion-bypass DNA polymerases.
Trends in biochemical sciences 2008;33(5):209-19.
2008: Pingna Xu; Lida Oum; Nicholas E Geacintov; Suse Broyde
Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase: a 5'-slippage mechanism.
Biochemistry 2008;47(9):2701-9.
2008: Alexandra Dimitri; Angela K Goodenough; F Peter Guengerich; Suse Broyde; David A Scicchitano
Transcription processing at 1,N2-ethenoguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase.
Journal of molecular biology 2008;375(2):353-66.
2008: Suse Broyde; Lihua Wang; Ling Zhang; Olga Rechkoblit; Nicholas E Geacintov; Dinshaw J Patel
DNA adduct structure-function relationships: comparing solution with polymerase structures.
Chemical research in toxicology 2008;21(1):45-52.
2007: Yuqin Cai; Dinshaw J Patel; Nicholas E Geacintov; Suse Broyde
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 of molecular biology 2007;374(2):292-305.
2007: VINCENT MOCQUET; Konstantin Kropachev; Marina Kolbanovskiy; Alexander Kolbanovskiy; Angels Tapias; Yuqin Cai; Suse Broyde; Nicholas E Geacintov; Jean-Marc Egly
The human DNA repair factor XPC-HR23B distinguishes stereoisomeric benzo[a]pyrenyl-DNA lesions.
The EMBO journal 2007;26(12):2923-32.
2007: Lei Jia; Vladimir Shafirovich; Nicholas E Geacintov; Suse Broyde
Lesion specificity in the base excision repair enzyme hNeil1: modeling and dynamics studies.
Biochemistry 2007;46(18):5305-14.
2007: Lihua Wang; Xinyun Yu; Po Hu; Suse Broyde; Yingkai Zhang
A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.
Journal of the American Chemical Society 2007;129(15):4731-7.
2007: Rebecca A Perlow-Poehnelt; Ilya Likhterov; Lihua Wang; David A Scicchitano; Nicholas E Geacintov; Suse Broyde
Increased flexibility enhances misincorporation: temperature effects on nucleotide incorporation opposite a bulky carcinogen-DNA adduct by a Y-family DNA polymerase.
The Journal of biological chemistry 2007;282(2):1397-408.
2007: Shuang Ding; Robert Shapiro; Nicholas E Geacintov; Suse Broyde
4-hydroxyequilenin-adenine lesions in DNA duplexes: stereochemistry, damage site, and structure.
Biochemistry 2007;46(1):182-91.
2007: Pingna Xu; Lida Oum; Lorena S Beese; Nicholas E Geacintov; Suse Broyde
Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase.
Nucleic acids research 2007;35(13):4275-88.
2007: Fabián A Rodríguez; Yuqin Cai; Chin Lin; Yijin Tang; Alexander Kolbanovskiy; Shantu Amin; Dinshaw J Patel; Suse Broyde; Nicholas E Geacintov
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.
Nucleic acids research 2007;35(5):1555-68.
2006: Alexander Durandin; Lei Jia; Conor Crean; Alexander Kolbanovskiy; Shuang Ding; Vladimir Shafirovich; Suse Broyde; Nicholas E Geacintov
Assignment of absolute configurations of the enantiomeric spiroiminodihydantoin nucleobases by experimental and computational optical rotatory dispersion methods.
Chemical research in toxicology 2006;19(7):908-13.
2006: Lei Jia; Vladimir Shafirovich; Robert Shapiro; Nicholas E Geacintov; Suse Broyde
Flexible 5-guanidino-4-nitroimidazole DNA lesions: structures and thermodynamics.
Biochemistry 2006;45(21):6644-55.
2006: Ling Zhang; Olga Rechkoblit; Lihua Wang; Dinshaw J Patel; Robert Shapiro; Suse Broyde
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.
Nucleic acids research 2006;34(11):3326-37.
2006: Lihua Wang; Suse Broyde
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).
Nucleic acids research 2006;34(3):785-95.
2006: Olga Rechkoblit; Lucy Malinina; Yuan Cheng; Vitaly Kuryavyi; Suse Broyde; Nicholas E Geacintov; Dinshaw J Patel
Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion.
PLoS biology 2006;4(1):e11.
2005: Shuang Ding; Robert Shapiro; Nicholas E Geacintov; Suse Broyde
Equilenin-derived DNA adducts to cytosine in DNA duplexes: structures and thermodynamics.
Biochemistry 2005;44(44):14565-76.
2005: Lei Jia; Vladimir Shafirovich; Robert Shapiro; Nicholas E Geacintov; Suse Broyde
Structural and thermodynamic features of spiroiminodihydantoin damaged DNA duplexes.
Biochemistry 2005;44(40):13342-53.
2005: Ling Zhang; Robert Shapiro; Suse Broyde
Molecular dynamics of a food carcinogen-DNA adduct in a replicative DNA polymerase suggest hindered nucleotide incorporation and extension.
Chemical research in toxicology 2005;18(9):1347-63.
2005: Lei Jia; Vladimir Shafirovich; Robert Shapiro; Nicholas E Geacintov; Suse Broyde
Spiroiminodihydantoin lesions derived from guanine oxidation: structures, energetics, and functional implications.
Biochemistry 2005;44(16):6043-51.
2005: Na Zhang; Chin Lin; Xuanwei Huang; Alexander Kolbanovskiy; Brian E Hingerty; Shantu Amin; Suse Broyde; Nicholas E Geacintov; Dinshaw J Patel
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.
Journal of molecular biology 2005;346(4):951-65.
2005: Lihua Wang; Min Wu; Shi Fang Yan; Dinshaw J Patel; Nicholas E Geacintov; Suse Broyde
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.
Chemical research in toxicology 2005;18(3):441-56.
2004: Rebecca A Perlow-Poehnelt; Dmitry O Zharkov; Arthur P Grollman; Suse Broyde
Substrate discrimination by formamidopyrimidine-DNA glycosylase: distinguishing interactions within the active site.
Biochemistry 2004;43(51):16092-105.
2004: Min Wu; Shi Fang Yan; Jian Tan; Dinshaw J Patel; Nicholas E Geacintov; Suse Broyde
Conformational searches elucidate effects of stereochemistry on structures of deoxyadenosine covalently bound to tumorigenic metabolites of benzo[C] phenanthrene.
Frontiers in bioscience : a journal and virtual library 2004;9():2807-18.
2004: Rebecca A Perlow-Poehnelt; Ilya Likhterov; David A Scicchitano; Nicholas E Geacintov; Suse Broyde
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.
The Journal of biological chemistry 2004;279(35):36951-61.
2004: Qing Zhang; Suse Broyde; Tamar Schlick
Deformations of promoter DNA bound to carcinogens help interpret effects on TATA-element structure and activity.
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 2004;362(1820):1479-96.
2004: Shi Fang Yan; Min Wu; Nicholas E Geacintov; Suse Broyde
Altering DNA polymerase incorporation fidelity by distorting the dNTP binding pocket with a bulky carcinogen-damaged template.
Biochemistry 2004;43(24):7750-65.
2004: Linjing Yang; William A Beard; Samuel H Wilson; Suse Broyde; Tamar Schlick
Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses.
Biophysical journal 2004;86(6):3392-408.
2004: Lihua Wang; Brian E Hingerty; Robert Shapiro; Suse Broyde
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.
Chemical research in toxicology 2004;17(3):311-24.
2004: Elena I Zaika; Rebecca A Perlow; Eileen Matz; Suse Broyde; Rotem Sertchook; Arthur P Grollman; Dmitry O Zharkov
Substrate discrimination by formamidopyrimidine-DNA glycosylase: a mutational analysis.
The Journal of biological chemistry 2004;279(6):4849-61.
2003: Lisa A Peterson; Choua C Vu; Brian E Hingerty; Suse Broyde; Monique Cosman
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.
Biochemistry 2003;42(45):13134-44.
2003: Thomas M Schinecker; Rebecca A Perlow; Suse Broyde; Nicholas E Geacintov; David A Scicchitano
Human RNA polymerase II is partially blocked by DNA adducts derived from tumorigenic benzo[c]phenanthrene diol epoxides: relating biological consequences to conformational preferences.
Nucleic acids research 2003;31(20):6004-15.
2003: Shuang Ding; Robert Shapiro; Nicholas E Geacintov; Suse Broyde
Conformations of stereoisomeric base adducts to 4-hydroxyequilenin.
Chemical research in toxicology 2003;16(6):695-707.
2003: Rebecca A Perlow; Suse Broyde
Extending the understanding of mutagenicity: structural insights into primer-extension past a benzo[a]pyrene diol epoxide-DNA adduct.
Journal of molecular biology 2003;327(4):797-818.
2003: Shixiang Yan; Min Wu; Dinshaw J Patel; Nicholas E Geacintov; Suse Broyde
Simulating structural and thermodynamic properties of carcinogen-damaged DNA.
Biophysical journal 2003;84(4):2137-48.
2003: Shixiang Yan; Min Wu; Tonko Buterin; Hanspeter Naegeli; Nicholas E Geacintov; Suse Broyde
Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[a]pyrene diol epoxide-adenine adducts.
Biochemistry 2003;42(8):2339-54.
2002: Pablo Hilario; Shixiang Yan; Brian E Hingerty; Suse Broyde; Ashis K Basu
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.
The Journal of biological chemistry 2002;277(47):45068-74.
2002: Nicholas E Geacintov; Suse Broyde; Tonko Buterin; Hanspeter Naegeli; Min Wu; Shixiang Yan; Dinshaw J Patel
Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery.
Biopolymers 2002;65(3):202-10.
2002: Rebecca A Perlow; Suse Broyde
Toward understanding the mutagenicity of an environmental carcinogen: structural insights into nucleotide incorporation preferences.
Journal of molecular biology 2002;322(2):291-309.
2002: Linjing Yang; William A Beard; Samuel Wilson; Benoit Roux; Suse Broyde; Tamar Schlick
Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus.
Journal of molecular biology 2002;321(3):459-78.
2002: Rebecca A Perlow; Alexander Kolbanovskii; Brian E Hingerty; Nicholas E Geacintov; Suse Broyde; David A Scicchitano
DNA adducts from a tumorigenic metabolite of benzo[a]pyrene block human RNA polymerase II elongation in a sequence- and stereochemistry-dependent manner.
Journal of molecular biology 2002;321(1):29-47.
2002: Min Wu; Shixiang Yan; Dinshaw J Patel; Nicholas E Geacintov; Suse Broyde
Relating repair susceptibility of carcinogen-damaged DNA with structural distortion and thermodynamic stability.
Nucleic acids research 2002;30(15):3422-32.
2002: Lihua Wang; Brian E Hingerty; A R Srinivasan; Wilma K Olson; Suse Broyde
Accurate representation of B-DNA double helical structure with implicit solvent and counterions.
Biophysical journal 2002;83(1):382-406.
2002: Shixiang Yan; Min Wu; Shuang Ding; Nicholas E Geacintov; Suse Broyde
Conformational analysis of a 4-hydroxyequilenin Guanine adduct using density functional theory.
Chemical research in toxicology 2002;15(5):648-53.
2002: Linjing Yang; William A Beard; Samuel H Wilson; Suse Broyde; Tamar Schlick
Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se.
Journal of molecular biology 2002;317(5):651-71.
2001: Min Wu; Shixiang Yan; Dinshaw J Patel; Nicholas E Geacintov; Suse Broyde
Cyclohexene ring and Fjord region twist inversion in stereoisomeric DNA adducts of enantiomeric benzo[c]phenanthrene diol epoxides.
Chemical research in toxicology 2001;14(12):1629-42.
2001: Qian Ruan; Ping Zhuang; S Li; Rebecca A Perlow; A R Srinivasan; Xiang-Jun Lu; Suse Broyde; Wilma K Olson; Nicholas E Geacintov
Base sequence effects in bending induced by bulky carcinogen-DNA adducts: experimental and computational analysis.
Biochemistry 2001;40(35):10458-72.
2001: Sherry Yan; R Shapiro; Nicholas E Geacintov; Suse Broyde
Stereochemical, structural, and thermodynamic origins of stability differences between stereoisomeric benzo[a]pyrene diol epoxide deoxyadenosine adducts in a DNA mutational hot spot sequence.
Journal of the American Chemical Society 2001;123(29):7054-66.
2001: Karen Brown; Brian E Hingerty; E A Guenther; Viswanathan V Krishnan; Suse Broyde; Kenneth W Turteltaub; Monique Cosman
Solution structure of the 2-amino-1- methyl-6-phenylimidazo[4,5-b]pyridine C8-deoxyguanosine adduct in duplex DNA.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(15):8507-12.
2001: Rebecca A Perlow; Suse Broyde
Evading the proofreading machinery of a replicative DNA polymerase: induction of a mutation by an environmental carcinogen.
Journal of molecular biology 2001;309(2):519-36.
2001: J Gauvin; Suse Broyde; Robert Shapiro
The food mutagen 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline: a conformational analysis of its major DNA adduct and comparison with the 2-amino-3-methylimidazo[4,5-f]quinoline adduct.
Chemical research in toxicology 2001;14(5):476-82.
2001: C H Lin; X Huang; A Kolbanovskii; Brian E Hingerty; Shantu Amin; Suse Broyde; Nicholas E Geacintov; Dinshaw J Patel
Molecular topology of polycyclic aromatic carcinogens determines DNA adduct conformation: a link to tumorigenic activity.
Journal of molecular biology 2001;306(5):1059-80.
2000: S Shimotakahara; Andrey Gorin; Alexander Kolbanovskiy; A Kettani; Brian E Hingerty; Shantu Amin; Suse Broyde; Nicholas E Geacintov; Dinshaw J Patel
Accomodation of S-cis-tamoxifen-N(2)-guanine adduct within a bent and widened DNA minor groove.
Journal of molecular biology 2000;302(2):377-93.
2000: J Tan; Nicholas E Geacintov; Suse Broyde
Conformational determinants of structures in stereoisomeric cis-opened anti-benzo[a]pyrene diol epoxide adducts to adenine in DNA.
Chemical research in toxicology 2000;13(9):811-22.
1999: X Wu; Robert Shapiro; Suse Broyde
Conformational analysis of the major DNA adduct derived from the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline.
Chemical research in toxicology 1999;12(10):895-905.
1999: Xiaoling kang; Andrey Gorin; Brian E Hingerty; Suse Broyde; Dinshaw J Patel
Solution structures of aminofluorene [AF]-stacked conformers of the syn [AF]-C8-dG adduct positioned opposite dC or dA at a template-primer junction.
Biochemistry 1999;38(33):10855-70.
1999: Xiaoling kang; Andrey Gorin; R Krishnasamy; Brian E Hingerty; Ashis K Basu; Suse Broyde; Dinshaw J Patel
Solution structure of the N-(deoxyguanosin-8-yl)-1-aminopyrene ([AP]dG) adduct opposite dA in a DNA duplex.
Biochemistry 1999;38(33):10843-54.
1999: B Mao; Xiaoling kang; Andrey Gorin; J Chen; Brian E Hingerty; Shantu Amin; Suse Broyde; Nicholas E Geacintov; Dinshaw J Patel
Solution structure of the (+)-cis-anti-benzo[a]pyrene-dA ([BP]dA) adduct opposite dT in a DNA duplex.
Biochemistry 1999;38(33):10831-42.
1999: X M Xie; Nicholas E Geacintov; Suse Broyde
Origins of conformational differences between cis and trans DNA adducts derived from enantiomeric anti-benzo[a]pyrene diol epoxides.
Chemical research in toxicology 1999;12(7):597-609.
1999: X M Xie; Nicholas E Geacintov; Suse Broyde
Stereochemical origin of opposite orientations in DNA adducts derived from enantiomeric anti-benzo[a]pyrene diol epoxides with different tumorigenic potentials.
Biochemistry 1999;38(10):2956-68.
1998: D Roy; Brian E Hingerty; Robert Shapiro; Suse Broyde
A slipped replication intermediate model is stabilized by the syn orientation of N-2-aminofluorene- and N-2-(acetyl)aminofluorene-modified guanine at a mutational hotspot.
Chemical research in toxicology 1998;11(11):1301-11.
1998: Dinshaw J Patel; B Mao; Z Gu; Brian E Hingerty; Andrey Gorin; Ashis K Basu; Suse Broyde
Nuclear magnetic resonance solution structures of covalent aromatic amine-DNA adducts and their mutagenic relevance.
Chemical research in toxicology 1998;11(5):391-407.
1998: Robert Shapiro; S Ellis; Brian E Hingerty; Suse Broyde
Effect of ring size on conformations of aromatic amine-DNA adducts: the aniline-C8 guanine adduct resides in the B-DNA major groove.
Chemical research in toxicology 1998;11(4):335-41.
1998: Sheo B Singh; W A Beard; Brian E Hingerty; S H Wilson; Suse Broyde
Interactions between DNA polymerase beta and the major covalent adduct of the carcinogen (+)-anti-benzo[a]pyrene diol epoxide with DNA at a primer-template junction.
Biochemistry 1998;37(3):878-84.
1998: B Mao; Brian E Hingerty; Suse Broyde; Dinshaw J Patel
Solution structure of the aminofluorene [AF]-external conformer of the anti-[AF]-C8-dG adduct opposite dC in a DNA duplex.
Biochemistry 1998;37(1):95-106.
1998: B Mao; Brian E Hingerty; Suse Broyde; Dinshaw J Patel
Solution structure of the aminofluorene [AF]-intercalated conformer of the syn-[AF]-C8-dG adduct opposite dC in a DNA duplex.
Biochemistry 1998;37(1):81-94.
1997: B Mao; Xiaoling kang; Andrey Gorin; Brian E Hingerty; Suse Broyde; Dinshaw J Patel
Solution structure of the aminofluorene-stacked conformer of the syn [AF]-C8-dG adduct positioned at a template-primer junction.
Biochemistry 1997;36(47):14491-501.
1997: B Mao; Andrey Gorin; Xiaoling kang; Brian E Hingerty; Suse Broyde; Dinshaw J Patel
Solution structure of the aminofluorene-intercalated conformer of the syn [AF]-C8-dG adduct opposite a--2 deletion site in the NarI hot spot sequence context.
Biochemistry 1997;36(47):14479-90.
1997: B Feng; Andrey Gorin; Alexander Kolbanovskiy; Brian E Hingerty; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
Solution conformation of the (-)-trans-anti-[BP]dG adduct opposite a deletion site in a DNA duplex: intercalation of the covalently attached benzo[a]pyrene into the helix with base displacement of the modified deoxyguanosine into the minor groove.
Biochemistry 1997;36(45):13780-90.
1997: B Feng; Andrey Gorin; Brian E Hingerty; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
Structural alignment of the (+)-trans-anti-benzo[a]pyrene-dG adduct positioned opposite dC at a DNA template-primer junction.
Biochemistry 1997;36(45):13769-79.
1997: R Grad; Robert Shapiro; Brian E Hingerty; Suse Broyde
A molecular mechanics and dynamics study of the minor adduct between DNA and the carcinogen 2-(acetylamino)fluorene (dG-N2-AAF).
Chemical research in toxicology 1997;10(10):1123-32.
1997: Nicholas E Geacintov; Monique Cosman; Brian E Hingerty; Shantu Amin; Suse Broyde; Dinshaw J Patel
NMR solution structures of stereoisometric covalent polycyclic aromatic carcinogen-DNA adduct: principles, patterns, and diversity.
Chemical research in toxicology 1997;10(2):111-46.
1996: B Mao; R R Vyas; Brian E Hingerty; Suse Broyde; Ashis K Basu; Dinshaw J Patel
Solution conformation of the N-(deoxyguanosin-8-yl)-1-aminopyrene ([AP]dG) adduct opposite dC in a DNA duplex.
Biochemistry 1996;35(39):12659-70.
1996: M Cosman; Brian E Hingerty; N Luneva; Shantu Amin; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
Solution conformation of the (-)-cis-anti-benzo[a]pyrenyl-dG adduct opposite dC in a DNA duplex: intercalation of the covalently attached BP ring into the helix with base displacement of the modified deoxyguanosine into the major groove.
Biochemistry 1996;35(30):9850-63.
1996: S J Nolan; R R Vyas; Brian E Hingerty; S Ellis; Suse Broyde; R Shapiro; Ashis K Basu
Solution properties and computational analysis of an oligodeoxynucleotide containing N-(deoxyguanosin-8-yl)-1-aminopyrene.
Carcinogenesis 1996;17(1):133-44.
1995: B Mao; Brian E Hingerty; Suse Broyde; Dinshaw J Patel
Solution conformation of [AF]dG opposite a -2 deletion site in a DNA duplex: intercalation of the covalently attached aminofluorene ring into the helix with base displacement of the C8-modified syn guanine and adjacent unpaired 3'-adenine into the major groove.
Biochemistry 1995;34(51):16641-53.
1995: M Cosman; Brian E Hingerty; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
Structural alignments of (+)- and (-)-trans-anti-benzo[a]pyrene-dG adducts positioned at a DNA template-primer junction.
Biochemistry 1995;34(46):15334-50.
1995: M Cosman; R Xu; Brian E Hingerty; Shantu Amin; R G Harvey; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
Solution conformation of the (-)-trans-anti-5-methylchrysene-dG adduct opposite dC in a DNA duplex: DNA bending associated with wedging of the methyl group of 5-methylchrysene to the 3'-side of the modification site.
Biochemistry 1995;34(18):6247-60.
1995: B Mao; M Cosman; Brian E Hingerty; Suse Broyde; Dinshaw J Patel
Solution conformation of [AF]dG opposite a -1 deletion site in a DNA duplex: intercalation of the covalently attached aminofluorene ring into the helix with base displacement of the C8-modified Syn guanine into the major groove.
Biochemistry 1995;34(18):6226-38.
1995: P Abuaf; Brian E Hingerty; Suse Broyde; D Grunberger
Solution conformation of the N-(deoxyguanosin-8-yl)aminofluorene adduct opposite deoxyinosine and deoxyguanosine in DNA by NMR and computational characterization.
Chemical research in toxicology 1995;8(3):369-78.
1995: M Cosman; A Laryea; R Fiala; Brian E Hingerty; Shantu Amin; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
Solution conformation of the (-)-trans-anti-benzo[c]phenanthrene-dA ([BPh]dA) adduct opposite dT in a DNA duplex: intercalation of the covalently attached benzo[c]phenanthrenyl ring to the 3'-side of the adduct site and comparison with the (+)-trans-anti-[BPh]dA opposite dT stereoisomer.
Biochemistry 1995;34(4):1295-307.
1995: Robert Shapiro; S Ellis; Brian E Hingerty; Suse Broyde
Major and minor groove conformations of DNA trimers modified on guanine or adenine by 4-aminobiphenyl: adenine adducts favor the minor groove.
Chemical research in toxicology 1995;8(1):117-27.
1994: M Cosman; R Fiala; Brian E Hingerty; Shantu Amin; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
Solution conformation of the (+)-cis-anti-[BP]dG adduct opposite a deletion site in a DNA duplex: intercalation of the covalently attached benzo[a]pyrene into the helix with base displacement of the modified deoxyguanosine into the minor groove.
Biochemistry 1994;33(38):11518-27.
1994: M Cosman; R Fiala; Brian E Hingerty; Shantu Amin; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
Solution conformation of the (+)-trans-anti-[BP]dG adduct opposite a deletion site in a DNA duplex: intercalation of the covalently attached benzo[a]pyrene into the helix with base displacement of the modified deoxyguanosine into the major groove.
Biochemistry 1994;33(38):11507-17.
1994: S B Singh; B Li; B E Hingerty; R Shapiro; Suse Broyde
Molecular dynamics simulation of a tumorigenic benzo[a]pyrene metabolite bound to DNA at a single strand-double strand junction.
Annals of the New York Academy of Sciences 1994;726():57-70.
1994: Robert Shapiro; D Sidawi; Y S Miao; Brian E Hingerty; K E Schmidt; J Moskowitz; Suse Broyde
Conformation of amine-modified DNA: 2-aminofluorene- and 2-(acetylamino)fluorene-modified deoxydinucleoside monophosphates with all possible nearest neighbors. A comparison of search and optimization methods.
Chemical research in toxicology 1994;7(2):239-53.
1994: A M Carothers; W Yuan; Brian E Hingerty; Suse Broyde; D Grunberger; E G Snyderwine
Mutation and repair induced by the carcinogen 2-(hydroxyamino)-1-methyl-6-phenylimidazo[4,5-b]pyridine (N-OH-PhIP) in the dihydrofolate reductase gene of Chinese hamster ovary cells and conformational modeling of the dG-C8-PhIP adduct in DNA.
Chemical research in toxicology 1994;7(2):209-18.
1993: M Cosman; R Fiala; Brian E Hingerty; A Laryea; H Lee; R G Harvey; Shantu Amin; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
Solution conformation of the (+)-trans-anti-[BPh]dA adduct opposite dT in a DNA duplex: intercalation of the covalently attached benzo[c]phenanthrene to the 5'-side of the adduct site without disruption of the modified base pair.
Biochemistry 1993;32(46):12488-97.
1993: M Cosman; Carlos de los Santos; R Fiala; Brian E Hingerty; V Ibanez; E Luna; R Harvey; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
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.
Biochemistry 1993;32(16):4145-55.
1993: S F O'Handley; D G Sanford; R Xu; C C Lester; B E Hingerty; Suse Broyde; T R Krugh
Structural characterization of an N-acetyl-2-aminofluorene (AAF) modified DNA oligomer by NMR, energy minimization, and molecular dynamics.
Biochemistry 1993;32(10):2481-97.
1992: Carlos de los Santos; M Cosman; Brian E Hingerty; V Ibanez; L A Margulis; Nicholas E Geacintov; Suse Broyde; Dinshaw J Patel
Influence of benzo[a]pyrene diol epoxide chirality on solution conformations of DNA covalent adducts: the (-)-trans-anti-[BP]G.C adduct structure and comparison with the (+)-trans-anti-[BP]G.C enantiomer.
Biochemistry 1992;31(23):5245-52.
1992: M Cosman; Carlos de los Santos; R Fiala; Brian E Hingerty; Sheo B Singh; V Ibanez; L A Margulis; D Live; Nicholas E Geacintov; Suse Broyde
Solution conformation of the major adduct between the carcinogen (+)-anti-benzo[a]pyrene diol epoxide and DNA.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(5):1914-8.
1991: Sheo B Singh; Brian E Hingerty; U C Singh; J P Greenberg; Nicholas E Geacintov; Suse Broyde
Structures of the (+)- and (-)-trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo(a)pyre ne adducts to guanine-N2 in a duplex dodecamer.
Cancer research 1991;51(13):3482-92.
1990: David G Norman; D Live; M Sastry; R Lipman; Brian E Hingerty; Maria Tomasz; Suse Broyde; Dinshaw J Patel
NMR and computational characterization of mitomycin cross-linked to adjacent deoxyguanosines in the minor groove of the d(T-A-C-G-T-A).d(T-A-C-G-T-A) duplex.
Biochemistry 1990;29(11):2861-75.
1989: Robert Shapiro; Brian E Hingerty; Suse Broyde
Minor-groove binding models for acetylaminofluorene modified DNA.
Journal of biomolecular structure & dynamics 1989;7(3):493-513.
1989: David G Norman; P Abuaf; Brian E Hingerty; D Live; D Grunberger; Suse Broyde; Dinshaw J Patel
NMR and computational characterization of the N-(deoxyguanosin-8-yl)aminofluorene adduct [(AF)G] opposite adenosine in DNA: (AF)G[syn].A[anti] pair formation and its pH dependence.
Biochemistry 1989;28(18):7462-76.
1989: B E Hingerty; S Figueroa; T L Hayden; Suse Broyde
Prediction of DNA structure from sequence: a build-up technique.
Biopolymers 1989;28(7):1195-222.
1988: M D Jacobson; Robert Shapiro; G R Underwood; Suse Broyde; L Verna; Brian E Hingerty
Synthesis and conformation of a dinucleoside monophosphate modified by aniline.
Chemical research in toxicology 1988;1(3):152-9.
1987: Suse Broyde; B E Hingerty
Visualization of an AAF induced frameshift mutation: molecular views of base displacement in B-DNA from minimized potential energy calculations.
Nucleic acids research 1987;15(16):6539-52.
1986: B E Hingerty; Suse Broyde
Energy minimized structures of carcinogen-DNA adducts: 2-acetylaminofluorene and 2-aminofluorene.
Journal of biomolecular structure & dynamics 1986;4(3):365-72.
1986: Robert Shapiro; G R Underwood; H Zawadzka; Suse Broyde; Brian E Hingerty
Conformation of d(CpG) modified by the carcinogen 4-aminobiphenyl: a combined experimental and theoretical analysis.
Biochemistry 1986;25(8):2198-205.
1985: B E Hingerty; Suse Broyde
Carcinogen-base stacking and base-base stacking in dCpdG modified by (+) and (-) anti-BPDE.
Biopolymers 1985;24(12):2279-99.
1985: Suse Broyde; B E Hingerty; A R Srinivasan
Influence of the carcinogen 4-aminobiphenyl on DNA conformation.
Carcinogenesis 1985;6(5):719-25.
1985: Suse Broyde; B Hingerty
Conformations of DNA adducts with polycyclic aromatic carcinogens.
Progress in clinical and biological research 1985;172A():153-71.
1985: Suse Broyde; B Hingerty
Base displacement in AAF-modified Z-DNA.
Carcinogenesis 1985;6(1):151-4.
1984: S Neidle; R Kuroda; Suse Broyde; B E Hingerty; R A Levine; D W Miller; F E Evans
Studies on the conformation and dynamics of the C8-substituted guanine adduct of the carcinogen acetylaminofluorene; model for a possible Z-DNA modified structure.
Nucleic acids research 1984;12(21):8219-33.
1983: B Hingerty; Suse Broyde
A conformational analysis of the (+) anti BPDE adduct to the guanine amino group of dCpdG.
Journal of biomolecular structure & dynamics 1983;1(4):905-12.
1983: Suse Broyde; B Hingerty
Conformation of 2-aminofluorene-modified DNA.
Biopolymers 1983;22(11):2423-41.
1983: Suse Broyde; B Hingerty
An internal fluorene model for iodo-N-2-acetylaminofluorene modified DNA.
Chemico-biological interactions 1983;47(1):69-78.
1983: B Hingerty; Suse Broyde
AAF linked to the guanine amino group: a B-Z junction.
Nucleic acids research 1983;11(10):3241-54.
1982: B Hingerty; Suse Broyde
Conformation of the deoxydinucleoside monophosphate dCpdG modified at carbon 8 of guanine with 2-(acetylamino)fluorene.
Biochemistry 1982;21(13):3243-52.
1982: B E Hingerty; Suse Broyde; W K Olson
The poly(rU) coil: a minimum-energy model that matches experimental observations.
Biopolymers 1982;21(6):1167-88.
1982: Suse Broyde; B E Hingerty
DNA backbone conformation in AAF modified dCpdG: variable conformational modes of achieving base displacement.
Chemico-biological interactions 1982;40(1):113-9.
1981: Regina Santella; D Grunberger; Suse Broyde; B E Hingerty
Z-DNA conformation of N-2-acetylaminofluorene modified poly(dG-dC).poly(dG-dC) determined by reactivity with anti cytidine antibodies and minimized potential energy calculations.
Nucleic acids research 1981;9(20):5459-67.