Suse Broyde, Ph.D. - Publications

Affiliations: 
Biology New York University, New York, NY, United States 
Area:
mutagenesis and carcinogenesis
Website:
http://broyde.nyu.edu/

219 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Ji S, Park D, Kropachev K, Kolbanovskiy M, Fu I, Broyde S, Essawy M, Geacintov NE, Tretyakova NY. 5-Formylcytosine-induced DNA-peptide cross-links reduce transcription efficiency, but do not do cause transcription errors in human cells. The Journal of Biological Chemistry. PMID 31597704 DOI: 10.1074/jbc.RA119.009834  0.92
2019 Ji S, Thomforde J, Rogers C, Fu I, Broyde S, Tretyakova NY. Transcriptional Bypass of DNA-protein and DNA-peptide Conjugates by T7 RNA Polymerase. Acs Chemical Biology. PMID 31573793 DOI: 10.1021/acschembio.9b00365  0.52
2019 Paul D, Mu H, Zhao H, Ouerfelli O, Jeffrey PD, Broyde S, Min JH. Structure and mechanism of pyrimidine-pyrimidone (6-4) photoproduct recognition by the Rad4/XPC nucleotide excision repair complex. Nucleic Acids Research. PMID 31106376 DOI: 10.1093/nar/gkz359  0.76
2018 Shafirovich V, Kolbanovskiy M, Kropachev K, Liu Z, Cai Y, Terzidis MA, Masi A, Chatgilialoglu C, Amin S, Dadali A, Broyde S, Geacintov NE. Nucleotide Excision Repair and Impact of Site-Specific 5',8-Cyclopurine and Bulky DNA Lesions on the Physical Properties of Nucleosomes. Biochemistry. PMID 30570250 DOI: 10.1021/acs.biochem.8b01066  0.92
2018 Fu I, Smith DJ, Broyde S. Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome. Dna Repair. PMID 30522887 DOI: 10.1016/j.dnarep.2018.11.012  0.52
2018 Mu H, Zhang Y, Geacintov NE, Broyde S. Lesion sensing during initial binding by yeast XPC/Rad4: toward predicting resistance to nucleotide excision repair. Chemical Research in Toxicology. PMID 30284444 DOI: 10.1021/acs.chemrestox.8b00231  0.92
2018 Ji S, Fu I, Naldiga S, Shao H, Basu AK, Broyde S, Tretyakova NY. 5-Formylcytosine mediated DNA-protein cross-links block DNA replication and induce mutations in human cells. Nucleic Acids Research. PMID 30184121 DOI: 10.1093/nar/gky809  0.52
2018 Mu H, Geacintov NE, Broyde S, Yeo JE, Schärer OD. Molecular basis for damage recognition and verification by XPC-RAD23B and TFIIH in nucleotide excision repair. Dna Repair. PMID 30174301 DOI: 10.1016/j.dnarep.2018.08.005  0.92
2018 Ji S, Fu I, Naldiga S, Shao H, Basu AK, Broyde S, Tretyakova NY. 5-Formylcytosine mediated DNA-protein cross-links block DNA replication and induce mutations in human cells. Nucleic Acids Research. PMID 29905846 DOI: 10.1093/nar/gky444  0.52
2018 Cai Y, Fu I, Geacintov NE, Zhang Y, Broyde S. 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. Dna Repair. 65: 73-78. PMID 29631253 DOI: 10.1016/j.dnarep.2018.02.009  0.92
2017 Chakraborty S, Steinbach PJ, Paul D, Mu H, Broyde S, Min JH, Ansari A. Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex. Nucleic Acids Research. PMID 29267981 DOI: 10.1093/nar/gkx1216  0.76
2017 Geacintov NE, Broyde S. Repair-Resistant DNA Lesions. Chemical Research in Toxicology. PMID 28750166 DOI: 10.1021/acs.chemrestox.7b00128  0.92
2017 Kolbanovskiy M, Chowdhury MA, Nadkarni A, Broyde S, Geacintov NE, Scicchitano DA, Shafirovich V. The Non-Bulky DNA Lesions Spiroiminodihydantoin and 5-Guanidinohydantoin Significantly Block Human RNA Polymerase II Elongation in vitro. Biochemistry. PMID 28514164 DOI: 10.1021/acs.biochem.7b00295  0.92
2017 Mu H, Geacintov NE, Min JH, Zhang Y, Broyde S. The 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. Chemical Research in Toxicology. PMID 28460163 DOI: 10.1021/acs.chemrestox.7b00074  0.92
2017 Fu I, Cai Y, Geacintov NE, Zhang Y, Broyde S. Nucleosome histone tail conformation and dynamics: impacts of lysine acetylation and a nearby minor groove benzo[a]pyrene-derived lesion. Biochemistry. PMID 28304160 DOI: 10.1021/acs.biochem.6b01208  0.92
2016 Wickramaratne S, Ji S, Mukherjee S, Su Y, Pence MG, Lior-Hoffmann L, Fu I, Broyde S, Guengerich FP, Distefano M, Scharer OD, Sham YY, Tretyakova N. Bypass of DNA-Protein Cross-links Conjugated to the 7-Deazaguanine Position of DNA by Translesion Synthesis Polymerases. The Journal of Biological Chemistry. PMID 27621316 DOI: 10.1074/jbc.M116.745257  0.76
2015 Fu I, Cai Y, Zhang Y, Geacintov NE, Broyde S. Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study. Biochemistry. PMID 26709619 DOI: 10.1021/acs.biochem.5b01166  1
2015 Liu Z, Ding S, Kropachev K, Jia L, Amin S, Broyde S, Geacintov NE. Correction: Resistance to Nucleotide Excision Repair of Bulky Guanine Adducts Opposite Abasic Sites in DNA Duplexes and Relationships between Structure and Function. Plos One. 10: e0142068. PMID 26512721 DOI: 10.1371/journal.pone.0142068  1
2015 Perera L, Freudenthal BD, Beard WA, Shock DD, Pedersen LG, Wilson SH. Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse. Proceedings of the National Academy of Sciences of the United States of America. 112: E5228-36. PMID 26351676 DOI: 10.1073/pnas.1511207112  1
2015 Liu Z, Ding S, Kropachev K, Lei J, Amin S, Broyde S, Geacintov NE. Resistance to Nucleotide Excision Repair of Bulky Guanine Adducts Opposite Abasic Sites in DNA Duplexes and Relationships between Structure and Function. Plos One. 10: e0137124. PMID 26340000 DOI: 10.1371/journal.pone.0137124  0.92
2015 Mu H, Geacintov NE, Zhang Y, Broyde S. Recognition of Damaged DNA for Nucleotide Excision Repair: A Correlated Motion Mechanism with a Mismatched cis-syn Thymine Dimer Lesion. Biochemistry. 54: 5263-7. PMID 26270861 DOI: 10.1021/acs.biochem.5b00840  1
2015 Koch SC, Kuper J, Gasteiger KL, Simon N, Strasser R, Eisen D, Geiger S, Schneider S, Kisker C, Carell T. Structural insights into the recognition of cisplatin and AAF-dG lesion by Rad14 (XPA). Proceedings of the National Academy of Sciences of the United States of America. PMID 26100901 DOI: 10.1073/pnas.1508509112  1
2015 Cai Y, Kropachev K, Terzidis MA, Masi A, Chatgilialoglu C, Geacintov NE, Broyde S. Differences in the access of lesions to the nucleotide excision repair machinery in nucleosomes. Biochemistry. PMID 26091016 DOI: 10.1021/acs.biochem.5b00564  1
2014 Lior-Hoffmann L, Ding S, Geacintov NE, Zhang Y, Broyde S. Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity. Biochemistry. 53: 5683-91. PMID 25148552 DOI: 10.1021/bi5007964  1
2014 Lee YC, Cai Y, Mu H, Broyde S, Amin S, Chen X, Min JH, Geacintov NE. The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: is there a correlation? Dna Repair. 19: 55-63. PMID 24784728 DOI: 10.1016/j.dnarep.2014.03.026  1
2014 Rodríguez FA, Liu Z, Lin CH, Ding S, Cai Y, Kolbanovskiy A, Kolbanovskiy M, Amin S, Broyde S, Geacintov NE. Nuclear magnetic resonance studies of an N2-guanine adduct derived from the tumorigen dibenzo[a,l]pyrene in DNA: impact of adduct stereochemistry, size, and local DNA sequence on solution conformations. Biochemistry. 53: 1827-41. PMID 24617538 DOI: 10.1021/bi4017044  1
2014 Kropachev K, Ding S, Terzidis MA, Masi A, Liu Z, Cai Y, Kolbanovskiy M, Chatgilialoglu C, Broyde S, Geacintov NE, Shafirovich V. Structural basis for the recognition of diastereomeric 5',8-cyclo-2'-deoxypurine lesions by the human nucleotide excision repair system. Nucleic Acids Research. 42: 5020-32. PMID 24615810 DOI: 10.1093/nar/gku162  1
2014 Cai Y, Geacintov NE, Broyde S. Ribonucleotides as nucleotide excision repair substrates. Dna Repair. 13: 55-60. PMID 24290807 DOI: 10.1016/j.dnarep.2013.10.010  1
2013 Mu H, Kropachev K, Chen Y, Zhang H, Cai Y, Geacintov NE, Broyde S. Role of structural and energetic factors in regulating repair of a bulky DNA lesion with different opposite partner bases. Biochemistry. 52: 5517-21. PMID 23902560 DOI: 10.1021/bi4009177  1
2013 Cai Y, Zheng H, Ding S, Kropachev K, Schwaid AG, Tang Y, Mu H, Wang S, Geacintov NE, Zhang Y, Broyde S. Free energy profiles of base flipping in intercalative polycyclic aromatic hydrocarbon-damaged DNA duplexes: energetic and structural relationships to nucleotide excision repair susceptibility. Chemical Research in Toxicology. 26: 1115-25. PMID 23758590 DOI: 10.1021/tx400156a  1
2013 Kropachev K, Kolbanovskiy M, Liu Z, Cai Y, Zhang L, Schwaid AG, Kolbanovskiy A, Ding S, Amin S, Broyde S, Geacintov NE. Adenine-DNA adducts derived from the highly tumorigenic Dibenzo[a,l]pyrene are resistant to nucleotide excision repair while guanine adducts are not. Chemical Research in Toxicology. 26: 783-93. PMID 23570232 DOI: 10.1021/tx400080k  1
2013 Yang J, Lior-Hoffmann L, Wang S, Zhang Y, Broyde S. DNA cytosine methylation: structural and thermodynamic characterization of the epigenetic marking mechanism. Biochemistry. 52: 2828-38. PMID 23528166 DOI: 10.1021/bi400163k  1
2012 Tang Y, Liu Z, Ding S, Lin CH, Cai Y, Rodriguez FA, Sayer JM, Jerina DM, Amin S, Broyde S, Geacintov NE. 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. 51: 9751-62. PMID 23121427 DOI: 10.1021/bi3013577  1
2012 Mu H, Kropachev K, Wang L, Zhang L, Kolbanovskiy A, Kolbanovskiy M, Geacintov NE, Broyde S. 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. 40: 9675-90. PMID 22904073 DOI: 10.1093/nar/gks788  1
2012 Lior-Hoffmann L, Wang L, Wang S, Geacintov NE, Broyde S, Zhang Y. 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. 40: 9193-205. PMID 22772988 DOI: 10.1093/nar/gks653  1
2012 Cai Y, Geacintov NE, Broyde S. Nucleotide excision repair efficiencies of bulky carcinogen-DNA adducts are governed by a balance between stabilizing and destabilizing interactions. Biochemistry. 51: 1486-99. PMID 22242833 DOI: 10.1021/bi201794x  1
2012 Ding S, Kropachev K, Cai Y, Kolbanovskiy M, Durandina SA, Liu Z, Shafirovich V, Broyde S, Geacintov NE. 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. 40: 2506-17. PMID 22135299 DOI: 10.1093/nar/gkr1087  1
2011 Reeves DA, Mu H, Kropachev K, Cai Y, Ding S, Kolbanovskiy A, Kolbanovskiy M, Chen Y, Krzeminski J, Amin S, Patel DJ, Broyde S, Geacintov NE. Resistance of bulky DNA lesions to nucleotide excision repair can result from extensive aromatic lesion-base stacking interactions. Nucleic Acids Research. 39: 8752-64. PMID 21764772 DOI: 10.1093/nar/gkr537  1
2011 Liu Y, Reeves D, Kropachev K, Cai Y, Ding S, Kolbanovskiy M, Kolbanovskiy A, Bolton JL, Broyde S, Van Houten B, Geacintov NE. 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. 10: 684-96. PMID 21741328 DOI: 10.1016/j.dnarep.2011.04.020  1
2011 Cai Y, Ding S, Geacintov NE, Broyde S. 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. 24: 522-31. PMID 21361377 DOI: 10.1021/tx1004002  1
2011 Broyde S, Wang L, Cai Y, Jia L, Shapiro R, Patel DJ, Geacintov NE. Covalent polycyclic aromatic hydrocarbon-DNA adducts: Carcinogenicity, structure, and function Current Cancer Research. 6: 181-207. DOI: 10.1007/978-1-61737-995-6_9  1
2010 Basu A, Broyde S, Iwai S, Kisker C. DNA damage, mutagenesis, and DNA repair. Journal of Nucleic Acids. 2010: 182894. PMID 21234397 DOI: 10.4061/2010/182894  1
2010 Zheng H, Cai Y, Ding S, Tang Y, Kropachev K, Zhou Y, Wang L, Wang S, Geacintov NE, Zhang Y, Broyde S. Base flipping free energy profiles for damaged and undamaged DNA. Chemical Research in Toxicology. 23: 1868-70. PMID 21090780 DOI: 10.1021/tx1003613  1
2010 Cai Y, Wang L, Ding S, Schwaid A, Geacintov NE, Broyde S. A bulky DNA lesion derived from a highly potent polycyclic aromatic tumorigen stabilizes nucleosome core particle structure. Biochemistry. 49: 9943-5. PMID 20964331 DOI: 10.1021/bi101560y  1
2010 Cai Y, Patel DJ, Broyde S, Geacintov NE. Base sequence context effects on nucleotide excision repair. Journal of Nucleic Acids. 2010. PMID 20871811 DOI: 10.4061/2010/174252  1
2010 Broyde S, Patel DJ. DNA repair: How to accurately bypass damage. Nature. 465: 1023-4. PMID 20577203 DOI: 10.1038/4651023a  1
2010 Cai Y, Kropachev K, Xu R, Tang Y, Kolbanovskii M, Kolbanovskii A, Amin S, Patel DJ, Broyde S, Geacintov NE. Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion. Journal of Molecular Biology. 399: 397-409. PMID 20399214 DOI: 10.1016/j.jmb.2010.04.004  1
2010 Rechkoblit O, Kolbanovskiy A, Malinina L, Geacintov NE, Broyde S, Patel DJ. Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4. Nature Structural & Molecular Biology. 17: 379-88. PMID 20154704 DOI: 10.1038/nsmb.1771  1
2010 Broyde S, Wang L, Patel DJ, Geacintov NE. Elucidating Structure-Function Relationships in Bulky DNA Lesions: From Solution Structures to Polymerases The Chemical Biology of Dna Damage. 331-352. DOI: 10.1002/9783527630110.ch14  1
2010 Cai Y, Kropachev K, Kolbanovskiy M, Kolbanovskiy A, Broyde S, Patel DJ, Geacintov NE. Recognition and Removal of Bulky DNA Lesions by the Nucleotide Excision Repair System The Chemical Biology of Dna Damage. 261-298. DOI: 10.1002/9783527630110.ch12  1
2010 Geacintov NE, Broyde S. Introduction and Perspectives on the Chemistry and Biology of DNA Damage The Chemical Biology of Dna Damage. 1-20. DOI: 10.1002/9783527630110.ch1  1
2010 Geacintov NE, Broyde S. The Chemical Biology of DNA Damage The Chemical Biology of Dna Damage. 1-449. DOI: 10.1002/9783527630110  1
2009 Ding S, Kolbanovskiy A, Durandin A, Crean C, Shafirovich V, Broyde S, Geacintov NE. Absolute configurations of DNA lesions determined by comparisons of experimental ECD and ORD spectra with DFT calculations. Chirality. 21: E231-41. PMID 19937959 DOI: 10.1002/chir.20804  1
2009 Donny-Clark K, Broyde S. 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. 37: 7095-109. PMID 19767609 DOI: 10.1093/nar/gkp745  1
2009 Jia L, Kropachev K, Ding S, Van Houten B, Geacintov NE, Broyde S. Exploring damage recognition models in prokaryotic nucleotide excision repair with a benzo[a]pyrene-derived lesion in UvrB. Biochemistry. 48: 8948-57. PMID 19681599 DOI: 10.1021/bi9010072  1
2009 Zhang N, Ding S, Kolbanovskiy A, Shastry A, Kuzmin VA, Bolton JL, Patel DJ, Broyde S, Geacintov NE. NMR and computational studies of stereoisomeric equine estrogen-derived DNA cytidine adducts in oligonucleotide duplexes: opposite orientations of diastereomeric forms. Biochemistry. 48: 7098-109. PMID 19527068 DOI: 10.1021/bi9006429  1
2009 Ding S, Jia L, Durandin A, Crean C, Kolbanovskiy A, Shafirovich V, Broyde S, Geacintov NE. Absolute configurations of spiroiminodihydantoin and allantoin stereoisomers: comparison of computed and measured electronic circular dichroism spectra. Chemical Research in Toxicology. 22: 1189-93. PMID 19485408 DOI: 10.1021/tx900107q  1
2009 Rechkoblit O, Malinina L, Cheng Y, Geacintov NE, Broyde S, Patel DJ. Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases. Structure (London, England : 1993). 17: 725-36. PMID 19446528 DOI: 10.1016/j.str.2009.03.011  1
2009 Wang L, Broyde S, Zhang Y. 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. 389: 787-96. PMID 19389406 DOI: 10.1016/j.jmb.2009.04.029  1
2009 Xu P, Oum L, Lee YC, Geacintov NE, Broyde S. 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. 48: 4677-90. PMID 19364137 DOI: 10.1021/bi802363f  1
2009 Kropachev K, Kolbanovskii M, Cai Y, Rodríguez F, Kolbanovskii A, Liu Y, Zhang L, Amin S, Patel D, Broyde S, Geacintov NE. 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. 386: 1193-203. PMID 19162041 DOI: 10.1016/j.jmb.2008.12.082  1
2009 Donny-Clark K, Shapiro R, Broyde S. 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. 48: 7-18. PMID 19072536 DOI: 10.1021/bi801283d  1
2009 Cai Y, Patel DJ, Geacintov NE, Broyde S. Differential nucleotide excision repair susceptibility of bulky DNA adducts in different sequence contexts: hierarchies of recognition signals. Journal of Molecular Biology. 385: 30-44. PMID 18948114 DOI: 10.1016/j.jmb.2008.09.087  1
2008 Jia L, Geacintov NE, Broyde S. 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. 36: 6571-84. PMID 18931375 DOI: 10.1093/nar/gkn719  1
2008 Dimitri A, Burns JA, Broyde S, Scicchitano DA. Transcription elongation past O6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase. Nucleic Acids Research. 36: 6459-71. PMID 18854351 DOI: 10.1093/nar/gkn657  1
2008 Ding S, Wang Y, Kolbanovskiy A, Durandin A, Bolton JL, van Breemen RB, Broyde S, Geacintov NE. 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. 21: 1739-48. PMID 18680315 DOI: 10.1021/tx800095f  1
2008 Dimitri A, Jia L, Shafirovich V, Geacintov NE, Broyde S, Scicchitano DA. Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase. Dna Repair. 7: 1276-88. PMID 18555749 DOI: 10.1016/j.dnarep.2008.04.007  1
2008 Ding S, Shapiro R, Cai Y, Geacintov NE, Broyde S. Conformational properties of equilenin-DNA adducts: stereoisomer and base effects. Chemical Research in Toxicology. 21: 1064-73. PMID 18416538 DOI: 10.1021/tx800010u  1
2008 Broyde S, Wang L, Rechkoblit O, Geacintov NE, Patel DJ. Lesion processing: high-fidelity versus lesion-bypass DNA polymerases. Trends in Biochemical Sciences. 33: 209-19. PMID 18407502 DOI: 10.1016/j.tibs.2008.02.004  1
2008 Xu P, Oum L, Geacintov NE, Broyde S. Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase: a 5'-slippage mechanism. Biochemistry. 47: 2701-9. PMID 18260644 DOI: 10.1021/bi701839q  1
2008 Broyde S, Wang L, Zhang L, Rechkoblit O, Geacintov NE, Patel DJ. DNA adduct structure-function relationships: comparing solution with polymerase structures. Chemical Research in Toxicology. 21: 45-52. PMID 18052109 DOI: 10.1021/tx700193x  1
2008 Dimitri A, Goodenough AK, Guengerich FP, Broyde S, Scicchitano DA. Transcription processing at 1,N2-ethenoguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase. Journal of Molecular Biology. 375: 353-66. PMID 18022639 DOI: 10.1016/j.jmb.2007.10.057  1
2007 Cai Y, Patel DJ, Geacintov NE, Broyde S. 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. 374: 292-305. PMID 17942115 DOI: 10.1016/j.jmb.2007.09.034  1
2007 Xu P, Oum L, Beese LS, Geacintov NE, Broyde S. Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase. Nucleic Acids Research. 35: 4275-88. PMID 17576677 DOI: 10.1093/nar/gkm416  1
2007 Mocquet V, Kropachev K, Kolbanovskiy M, Kolbanovskiy A, Tapias A, Cai Y, Broyde S, Geacintov NE, Egly JM. The human DNA repair factor XPC-HR23B distinguishes stereoisomeric benzo[a]pyrenyl-DNA lesions. The Embo Journal. 26: 2923-32. PMID 17525733 DOI: 10.1038/sj.emboj.7601730  1
2007 Jia L, Shafirovich V, Geacintov NE, Broyde S. Lesion specificity in the base excision repair enzyme hNeil1: modeling and dynamics studies. Biochemistry. 46: 5305-14. PMID 17432829 DOI: 10.1021/bi062269m  1
2007 Wang L, Yu X, Hu P, Broyde S, Zhang Y. A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV. Journal of the American Chemical Society. 129: 4731-7. PMID 17375926 DOI: 10.1021/ja068821c  1
2007 Rodríguez FA, Cai Y, Lin C, Tang Y, Kolbanovskiy A, Amin S, Patel DJ, Broyde S, Geacintov NE. 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. 35: 1555-68. PMID 17287290 DOI: 10.1093/nar/gkm022  1
2007 Ding S, Shapiro R, Geacintov NE, Broyde S. 4-hydroxyequilenin-adenine lesions in DNA duplexes: stereochemistry, damage site, and structure. Biochemistry. 46: 182-91. PMID 17198388 DOI: 10.1021/bi061652o  1
2007 Perlow-Poehnelt RA, Likhterov I, Wang L, Scicchitano DA, Geacintov NE, Broyde S. 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. 282: 1397-408. PMID 17090533 DOI: 10.1074/jbc.M606769200  1
2006 Durandin A, Jia L, Crean C, Kolbanovskiy A, Ding S, Shafirovich V, Broyde S, Geacintov NE. Assignment of absolute configurations of the enantiomeric spiroiminodihydantoin nucleobases by experimental and computational optical rotatory dispersion methods. Chemical Research in Toxicology. 19: 908-13. PMID 16841958 DOI: 10.1021/tx060078e  1
2006 Zhang L, Rechkoblit O, Wang L, Patel DJ, Shapiro R, Broyde S. 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. 34: 3326-37. PMID 16820532 DOI: 10.1093/nar/gkl425  1
2006 Jia L, Shafirovich V, Shapiro R, Geacintov NE, Broyde S. Flexible 5-guanidino-4-nitroimidazole DNA lesions: structures and thermodynamics. Biochemistry. 45: 6644-55. PMID 16716075 DOI: 10.1021/bi0601757  1
2006 Wang L, Broyde S. 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. 34: 785-95. PMID 16452300 DOI: 10.1093/nar/gkj479  1
2006 Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ. Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion. Plos Biology. 4: e11. PMID 16379496 DOI: 10.1371/journal.pbio.0040011  1
2005 Ding S, Shapiro R, Geacintov NE, Broyde S. Equilenin-derived DNA adducts to cytosine in DNA duplexes: structures and thermodynamics. Biochemistry. 44: 14565-76. PMID 16262256 DOI: 10.1021/bi051090t  1
2005 Jia L, Shafirovich V, Shapiro R, Geacintov NE, Broyde S. Structural and thermodynamic features of spiroiminodihydantoin damaged DNA duplexes. Biochemistry. 44: 13342-53. PMID 16201759 DOI: 10.1021/bi050790v  1
2005 Zhang L, Shapiro R, Broyde S. Molecular dynamics of a food carcinogen-DNA adduct in a replicative DNA polymerase suggest hindered nucleotide incorporation and extension. Chemical Research in Toxicology. 18: 1347-63. PMID 16167826 DOI: 10.1021/tx050132b  1
2005 Jia L, Shafirovich V, Shapiro R, Geacintov NE, Broyde S. Spiroiminodihydantoin lesions derived from guanine oxidation: structures, energetics, and functional implications. Biochemistry. 44: 6043-51. PMID 15835893 DOI: 10.1021/bi0473657  1
2005 Wang L, Wu M, Yan SF, Patel DJ, Geacintov NE, Broyde S. 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. 18: 441-56. PMID 15777084 DOI: 10.1021/tx049786v  1
2005 Zhang N, Lin C, Huang X, Kolbanovskiy A, Hingerty BE, Amin S, Broyde S, Geacintov NE, Patel DJ. 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. 346: 951-65. PMID 15701509 DOI: 10.1016/j.jmb.2004.12.027  1
2004 Perlow-Poehnelt RA, Zharkov DO, Grollman AP, Broyde S. Substrate discrimination by formamidopyrimidine-DNA glycosylase: distinguishing interactions within the active site. Biochemistry. 43: 16092-105. PMID 15610004 DOI: 10.1021/bi048747f  1
2004 Wu M, Yan SF, Tan J, Patel DJ, Geacintov NE, Broyde S. 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. 9: 2807-18. PMID 15353316  1
2004 Zhang Q, Broyde S, Schlick T. 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. 362: 1479-96. PMID 15306462 DOI: 10.1098/rsta.2004.1386  1
2004 Perlow-Poehnelt RA, Likhterov I, Scicchitano DA, Geacintov NE, Broyde S. 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. 279: 36951-61. PMID 15210693 DOI: 10.1074/jbc.M404332200  1
2004 Yan SF, Wu M, Geacintov NE, Broyde S. Altering DNA polymerase incorporation fidelity by distorting the dNTP binding pocket with a bulky carcinogen-damaged template. Biochemistry. 43: 7750-65. PMID 15196018 DOI: 10.1021/bi0499516  1
2004 Yang L, Beard WA, Wilson SH, Broyde S, Schlick T. Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses. Biophysical Journal. 86: 3392-408. PMID 15189842 DOI: 10.1529/biophysj.103.036012  1
2004 Wang L, Hingerty BE, Shapiro R, Broyde S. 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. 17: 311-24. PMID 15025501 DOI: 10.1021/tx034218l  1
2004 Zaika EI, Perlow RA, Matz E, Broyde S, Gilboa R, Grollman AP, Zharkov DO. Substrate discrimination by formamidopyrimidine-DNA glycosylase: a mutational analysis. The Journal of Biological Chemistry. 279: 4849-61. PMID 14607836 DOI: 10.1074/jbc.M310262200  1
2003 Peterson LA, Vu C, Hingerty BE, Broyde S, Cosman M. 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. 42: 13134-44. PMID 14609323 DOI: 10.1021/bi035217v  1
2003 Schinecker TM, Perlow RA, Broyde S, Geacintov NE, Scicchitano DA. 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. 31: 6004-15. PMID 14530448 DOI: 10.1093/nar/gkg771  1
2003 Ding S, Shapiro R, Geacintov NE, Broyde S. Conformations of stereoisomeric base adducts to 4-hydroxyequilenin. Chemical Research in Toxicology. 16: 695-707. PMID 12807352 DOI: 10.1021/tx0340246  1
2003 Yan S, Wu M, Patel DJ, Geacintov NE, Broyde S. Simulating structural and thermodynamic properties of carcinogen-damaged DNA. Biophysical Journal. 84: 2137-48. PMID 12668423 DOI: 10.1016/S0006-3495(03)75020-6  1
2003 Perlow RA, Broyde S. Extending the understanding of mutagenicity: structural insights into primer-extension past a benzo[a]pyrene diol epoxide-DNA adduct. Journal of Molecular Biology. 327: 797-818. PMID 12654264 DOI: 10.1016/S0022-2836(03)00187-6  1
2003 Yan S, Wu M, Buterin T, Naegeli H, Geacintov NE, Broyde S. Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[a]pyrene diol epoxide-adenine adducts. Biochemistry. 42: 2339-54. PMID 12600201 DOI: 10.1021/bi0270081  1
2002 Hilario P, Yan S, Hingerty BE, Broyde S, Basu AK. 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. 277: 45068-74. PMID 12239219 DOI: 10.1074/jbc.M208103200  1
2002 Geacintov NE, Broyde S, Buterin T, Naegeli H, Wu M, Yan S, Patel DJ. Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery. Biopolymers. 65: 202-10. PMID 12228925 DOI: 10.1002/bip.10239  1
2002 Perlow RA, Broyde S. Toward understanding the mutagenicity of an environmental carcinogen: structural insights into nucleotide incorporation preferences. Journal of Molecular Biology. 322: 291-309. PMID 12217692 DOI: 10.1016/S0022-2836(02)00751-9  1
2002 Yang L, Beard W, Wilson S, Roux B, Broyde S, Schlick T. Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus. Journal of Molecular Biology. 321: 459-78. PMID 12162959 DOI: 10.1016/S0022-2836(02)00617-4  1
2002 Wu M, Yan S, Patel DJ, Geacintov NE, Broyde S. Relating repair susceptibility of carcinogen-damaged DNA with structural distortion and thermodynamic stability. Nucleic Acids Research. 30: 3422-32. PMID 12140327  1
2002 Perlow RA, Kolbanovskii A, Hingerty BE, Geacintov NE, Broyde S, Scicchitano DA. 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. 321: 29-47. PMID 12139931 DOI: 10.1016/S0022-2836(02)00593-4  1
2002 Wang L, Hingerty BE, Srinivasan AR, Olson WK, Broyde S. Accurate representation of B-DNA double helical structure with implicit solvent and counterions. Biophysical Journal. 83: 382-406. PMID 12080128 DOI: 10.1016/S0006-3495(02)75177-1  1
2002 Yan S, Wu M, Ding S, Geacintov NE, Broyde S. Conformational analysis of a 4-hydroxyequilenin Guanine adduct using density functional theory. Chemical Research in Toxicology. 15: 648-53. PMID 12018985 DOI: 10.1021/tx0101797  1
2002 Yang L, Beard WA, Wilson SH, Broyde S, Schlick T. Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. Journal of Molecular Biology. 317: 651-71. PMID 11955015 DOI: 10.1006/jmbi.2002.5450  1
2001 Wu M, Yan S, Patel DJ, Geacintov NE, Broyde S. Cyclohexene ring and Fjord region twist inversion in stereoisomeric DNA adducts of enantiomeric benzo[c]phenanthrene diol epoxides. Chemical Research in Toxicology. 14: 1629-42. PMID 11743746 DOI: 10.1021/tx010152n  1
2001 Ruan Q, Zhuang P, Li S, Perlow R, Srinivasan AR, Lu XJ, Broyde S, Olson WK, Geacintov NE. Base sequence effects in bending induced by bulky carcinogen-DNA adducts: experimental and computational analysis. Biochemistry. 40: 10458-72. PMID 11523987 DOI: 10.1021/bi002643x  1
2001 Yan S, Shapiro R, Geacintov NE, Broyde S. 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. 123: 7054-66. PMID 11459484 DOI: 10.1021/ja0043035  1
2001 Brown K, Hingerty BE, Guenther EA, Krishnan VV, Broyde S, Turteltaub KW, Cosman M. 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. 98: 8507-12. PMID 11438709 DOI: 10.1073/pnas.151251898  1
2001 Perlow RA, Broyde S. Evading the proofreading machinery of a replicative DNA polymerase: induction of a mutation by an environmental carcinogen. Journal of Molecular Biology. 309: 519-36. PMID 11371169 DOI: 10.1006/jmbi.2001.4674  1
2001 Gauvin J, Broyde S, Shapiro R. 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. 14: 476-82. PMID 11368544 DOI: 10.1021/tx000144r  1
2001 Lin CH, Huang X, Kolbanovskii A, Hingerty BE, Amin S, Broyde S, Geacintov NE, Patel DJ. Molecular topology of polycyclic aromatic carcinogens determines DNA adduct conformation: a link to tumorigenic activity. Journal of Molecular Biology. 306: 1059-80. PMID 11237618 DOI: 10.1006/jmbi.2001.4425  1
2000 Tan J, Geacintov NE, Broyde S. Conformational determinants of structures in stereoisomeric cis-opened anti-benzo[a]pyrene diol epoxide adducts to adenine in DNA. Chemical Research in Toxicology. 13: 811-22. PMID 10995253 DOI: 10.1021/tx000094q  1
2000 Shimotakahara S, Gorin A, Kolbanovskiy A, Kettani A, Hingerty BE, Amin S, Broyde S, Geacintov N, Patel DJ. Accomodation of S-cis-tamoxifen-N(2)-guanine adduct within a bent and widened DNA minor groove. Journal of Molecular Biology. 302: 377-93. PMID 10970740 DOI: 10.1006/jmbi.2000.4071  1
2000 Tan J, Geacintov NE, Broyde S. Principles governing conformations in stereoisomeric adducts of Bay region benzo[a]pyrene diol epoxides to adenine in DNA: Steric and hydrophobic effects are dominant Journal of the American Chemical Society. 122: 3021-3032. DOI: 10.1021/ja993624h  1
1999 Wu X, Shapiro R, Broyde S. Conformational analysis of the major DNA adduct derived from the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline. Chemical Research in Toxicology. 12: 895-905. PMID 10525264 DOI: 10.1021/tx990108w  1
1999 Gu Z, Gorin A, Hingerty BE, Broyde S, Patel DJ. 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. 38: 10855-70. PMID 10451382 DOI: 10.1021/bi991266p  1
1999 Gu Z, Gorin A, Krishnasamy R, Hingerty BE, Basu AK, Broyde S, Patel DJ. Solution structure of the N-(deoxyguanosin-8-yl)-1-aminopyrene ([AP]dG) adduct opposite dA in a DNA duplex. Biochemistry. 38: 10843-54. PMID 10451381 DOI: 10.1021/bi9912138  1
1999 Mao B, Gu Z, Gorin A, Chen J, Hingerty BE, Amin S, Broyde S, Geacintov NE, Patel DJ. Solution structure of the (+)-cis-anti-benzo[a]pyrene-dA ([BP]dA) adduct opposite dT in a DNA duplex. Biochemistry. 38: 10831-42. PMID 10451380 DOI: 10.1021/bi991212f  1
1999 Xie XM, Geacintov NE, Broyde S. Origins of conformational differences between cis and trans DNA adducts derived from enantiomeric anti-benzo[a]pyrene diol epoxides. Chemical Research in Toxicology. 12: 597-609. PMID 10409399 DOI: 10.1021/tx990021a  1
1999 Xie XM, Geacintov NE, Broyde S. Stereochemical origin of opposite orientations in DNA adducts derived from enantiomeric anti-benzo[a]pyrene diol epoxides with different tumorigenic potentials. Biochemistry. 38: 2956-68. PMID 10074348 DOI: 10.1021/bi9825605  1
1999 Broyde S, Hingerty BE. Effective Computational Strategies for Determining Structures of Carcinogen-Damaged DNA Journal of Computational Physics. 151: 313-332. DOI: 10.1006/jcph.1998.6172  1
1998 Roy D, Hingerty BE, Shapiro R, Broyde S. 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. 11: 1301-11. PMID 9815190 DOI: 10.1021/tx980106w  1
1998 Patel DJ, Mao B, Gu Z, Hingerty BE, Gorin A, Basu AK, Broyde S. Nuclear magnetic resonance solution structures of covalent aromatic amine-DNA adducts and their mutagenic relevance. Chemical Research in Toxicology. 11: 391-407. PMID 9585469 DOI: 10.1021/tx9702143  1
1998 Shapiro R, Ellis S, Hingerty BE, Broyde S. 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. 11: 335-41. PMID 9548804 DOI: 10.1021/tx970211q  1
1998 Singh SB, Beard WA, Hingerty BE, Wilson SH, Broyde S. 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. 37: 878-84. PMID 9454577 DOI: 10.1021/bi9720639  1
1998 Mao B, Hingerty BE, Broyde S, Patel DJ. Solution structure of the aminofluorene [AF]-external conformer of the anti-[AF]-C8-dG adduct opposite dC in a DNA duplex. Biochemistry. 37: 95-106. PMID 9425029 DOI: 10.1021/bi972258g  1
1998 Mao B, Hingerty BE, Broyde S, Patel DJ. Solution structure of the aminofluorene [AF]-intercalated conformer of the syn-[AF]-C8-dG adduct opposite dC in a DNA duplex. Biochemistry. 37: 81-94. PMID 9425028 DOI: 10.1021/bi972257o  1
1997 Mao B, Gu Z, Gorin A, Hingerty BE, Broyde S, Patel DJ. Solution structure of the aminofluorene-stacked conformer of the syn [AF]-C8-dG adduct positioned at a template-primer junction. Biochemistry. 36: 14491-501. PMID 9398168 DOI: 10.1021/bi972206r  1
1997 Mao B, Gorin A, Gu Z, Hingerty BE, Broyde S, Patel DJ. 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. 36: 14479-90. PMID 9398167 DOI: 10.1021/bi972205z  1
1997 Feng B, Gorin A, Kolbanovskiy A, Hingerty BE, Geacintov NE, Broyde S, Patel DJ. 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. 36: 13780-90. PMID 9374854 DOI: 10.1021/bi970070r  1
1997 Feng B, Gorin A, Hingerty BE, Geacintov NE, Broyde S, Patel DJ. Structural alignment of the (+)-trans-anti-benzo[a]pyrene-dG adduct positioned opposite dC at a DNA template-primer junction. Biochemistry. 36: 13769-79. PMID 9374853 DOI: 10.1021/bi970069s  1
1997 Grad R, Shapiro R, Hingerty BE, Broyde S. 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. 10: 1123-32. PMID 9348435 DOI: 10.1021/tx970092e  1
1997 Geacintov NE, Cosman M, Hingerty BE, Amin S, Broyde S, Patel DJ. NMR solution structures of stereoisometric covalent polycyclic aromatic carcinogen-DNA adduct: principles, patterns, and diversity. Chemical Research in Toxicology. 10: 111-46. PMID 9049424 DOI: 10.1021/tx9601418  1
1996 Mao B, Vyas RR, Hingerty BE, Broyde S, Basu AK, Patel DJ. Solution conformation of the N-(deoxyguanosin-8-yl)-1-aminopyrene ([AP]dG) adduct opposite dC in a DNA duplex. Biochemistry. 35: 12659-70. PMID 8841109 DOI: 10.1021/bi961078o  1
1996 Broyde S. Setting the stage for predicting RNA thermodynamic properties and their structural components. Biophysical Journal. 70: 1571-2. PMID 8785315 DOI: 10.1016/S0006-3495(96)79722-9  1
1996 Cosman M, Hingerty BE, Luneva N, Amin S, Geacintov NE, Broyde S, Patel DJ. 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. 35: 9850-63. PMID 8703959 DOI: 10.1021/bi9605346  1
1996 Nolan SJ, Vyas RR, Hingerty BE, Ellis S, Broyde S, Shapiro R, Basu AK. Solution properties and computational analysis of an oligodeoxynucleotide containing N-(deoxyguanosin-8-yl)-1-aminopyrene. Carcinogenesis. 17: 133-44. PMID 8565123 DOI: 10.1093/carcin/17.1.133  1
1996 Cosman M, Hingerty BE, Amin S, Broyde S, Geacintov NE, Patel DJ. NMR solution structures of adducts derived from the binding of polycyclic aromatic diol epoxides to DNA Polycyclic Aromatic Compounds. 10: 153-160.  1
1995 Mao B, Hingerty BE, Broyde S, Patel DJ. 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. 34: 16641-53. PMID 8527437  1
1995 Cosman M, Laryea A, Fiala R, Hingerty BE, Amin S, Geacintov NE, Broyde S, Patel DJ. 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. 34: 1295-307. PMID 7827077  0.92
1995 Cosman M, Xu R, Hingerty BE, Amin S, Harvey RG, Geacintov NE, Broyde S, Patel DJ. 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. 34: 6247-60. PMID 7742330  0.92
1995 Mao B, Cosman M, Hingerty BE, Broyde S, Patel DJ. 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. 34: 6226-38. PMID 7742328  0.76
1995 Shapiro R, Ellis S, Hingerty BE, Broyde S. 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. 8: 117-27. PMID 7703355  1
1995 Abuaf P, Hingerty BE, Broyde S, Grunberger D. 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. 8: 369-78. PMID 7578923  1
1995 Cosman M, Hingerty BE, Geacintov NE, Broyde S, Patel DJ. Structural alignments of (+)- and (-)-trans-anti-benzo[a]pyrene-dG adducts positioned at a DNA template-primer junction. Biochemistry. 34: 15334-50. PMID 7578150 DOI: 10.1021/bi00046a043  1
1995 Hingerty BE, Broyde S. The molecular mechanics program DUPLEX: Computing structures of carcinogen modified DNA by surveying the potential energy surface Molecular Engineering. 5: 219-227. DOI: 10.1007/BF00999590  1
1994 Shapiro R, Sidawi D, Miao YS, Hingerty BE, Schmidt KE, Moskowitz J, Broyde S. 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. 7: 239-53. PMID 8199314  1
1994 Carothers AM, Yuan W, Hingerty BE, Broyde S, Grunberger D, Snyderwine EG. 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. 7: 209-18. PMID 8199311  1
1994 Singh SB, Li B, Hingerty BE, Shapiro R, Broyde S. 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. 726: 57-70. PMID 8092708  1
1994 Cosman M, Fiala R, Hingerty BE, Amin S, Geacintov NE, Broyde S, Patel DJ. 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. 33: 11518-27. PMID 7918365  0.92
1994 Cosman M, Fiala R, Hingerty BE, Amin S, Geacintov NE, Broyde S, Patel DJ. 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. 33: 11507-17. PMID 7918364  0.92
1993 Cosman M, de los Santos C, Fiala R, Hingerty BE, Ibanez V, Luna E, Harvey R, Geacintov NE, Broyde S, Patel DJ. 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. 32: 4145-55. PMID 8476845  1
1993 O'Handley SF, Sanford DG, Xu R, Lester CC, Hingerty BE, Broyde S, Krugh TR. Structural characterization of an N-acetyl-2-aminofluorene (AAF) modified DNA oligomer by NMR, energy minimization, and molecular dynamics. Biochemistry. 32: 2481-97. PMID 8448107  0.36
1993 Cosman M, Fiala R, Hingerty BE, Laryea A, Lee H, Harvey RG, Amin S, Geacintov NE, Broyde S, Patel D. 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. 32: 12488-97. PMID 8241140  1
1992 de los Santos C, Cosman M, Hingerty BE, Ibanez V, Margulis LA, Geacintov NE, Broyde S, Patel DJ. 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. 31: 5245-52. PMID 1606148  1
1992 Cosman M, de los Santos C, Fiala R, Hingerty BE, Singh SB, Ibanez V, Margulis LA, Live D, Geacintov NE, Broyde S. 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. 89: 1914-8. PMID 1311854  1
1991 Singh SB, Hingerty BE, Singh UC, Greenberg JP, Geacintov NE, Broyde S. 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. 51: 3482-92. PMID 1905197  1
1990 Norman D, Live D, Sastry M, Lipman R, Hingerty BE, Tomasz M, Broyde S, Patel DJ. 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. 29: 2861-75. PMID 2346750  1
1989 Norman D, Abuaf P, Hingerty BE, Live D, Grunberger D, Broyde S, Patel DJ. 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. 28: 7462-76. PMID 2819081  1
1989 Hingerty BE, Figueroa S, Hayden TL, Broyde S. Prediction of DNA structure from sequence: a build-up technique. Biopolymers. 28: 1195-222. PMID 2775836 DOI: 10.1002/bip.360280703  1
1989 Shapiro R, Hingerty BE, Broyde S. Minor-groove binding models for acetylaminofluorene modified DNA. Journal of Biomolecular Structure & Dynamics. 7: 493-513. PMID 2627297 DOI: 10.1080/07391102.1989.10508506  0.68
1988 Jacobson MD, Shapiro R, Underwood GR, Broyde S, Verna L, Hingerty BE. Synthesis and conformation of a dinucleoside monophosphate modified by aniline. Chemical Research in Toxicology. 1: 152-9. PMID 2979725  1
1987 Broyde S, Hingerty BE. Visualization of an AAF induced frameshift mutation: molecular views of base displacement in B-DNA from minimized potential energy calculations. Nucleic Acids Research. 15: 6539-52. PMID 3627997 DOI: 10.1093/nar/15.16.6539  1
1987 Hingerty BE, Broyde S. Conformations of DNA modified by carcinogenic aromatic amines: 2-Aminofluorene and 2-acetylaminofluorene energy-refined tetramer models Annals of the New York Academy of Sciences. 494: 407-411.  1
1986 Shapiro R, Underwood GR, Zawadzka H, Broyde S, Hingerty BE. Conformation of d(CpG) modified by the carcinogen 4-aminobiphenyl: a combined experimental and theoretical analysis. Biochemistry. 25: 2198-205. PMID 3707942  1
1986 Hingerty BE, Broyde S. Energy minimized structures of carcinogen-DNA adducts: 2-acetylaminofluorene and 2-aminofluorene. Journal of Biomolecular Structure & Dynamics. 4: 365-72. PMID 3271449 DOI: 10.1080/07391102.1986.10506355  0.36
1986 Broyde S, Hingerty BE. Conformations of DNA modified by the carcinogen 4-aminobiphenyl Annals of the New York Academy of Sciences. 86-89.  1
1985 Hingerty BE, Broyde S. Carcinogen-base stacking and base-base stacking in dCpdG modified by (+) and (-) anti-BPDE. Biopolymers. 24: 2279-99. PMID 4092090 DOI: 10.1002/bip.360241209  1
1985 Broyde S, Hingerty BE, Srinivasan AR. Influence of the carcinogen 4-aminobiphenyl on DNA conformation. Carcinogenesis. 6: 719-25. PMID 4006057 DOI: 10.1093/carcin/6.5.719  1
1985 Broyde S, Hingerty B. Conformations of DNA adducts with polycyclic aromatic carcinogens. Progress in Clinical and Biological Research. 172: 153-71. PMID 3991669  1
1985 Broyde S, Hingerty B. Base displacement in AAF-modified Z-DNA. Carcinogenesis. 6: 151-4. PMID 3967335 DOI: 10.1093/carcin/6.1.151  1
1984 Neidle S, Kuroda R, Broyde S, Hingerty BE, Levine RA, Miller DW, Evans FE. 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. 12: 8219-33. PMID 6504698 DOI: 10.1093/nar/12.21.8219  1
1984 Broyde S, Hingerty B. Mutagenicity of polycyclic aromatic hydrocarbons and amines: A conformational hypothesis Annals of the New York Academy of Sciences. 119-122.  1
1983 Hingerty B, Broyde S. AAF linked to the guanine amino group: a B-Z junction. Nucleic Acids Research. 11: 3241-54. PMID 6856457 DOI: 10.1093/nar/11.10.3241  1
1983 Broyde S, Hingerty B. Conformation of 2-aminofluorene-modified DNA. Biopolymers. 22: 2423-41. PMID 6652225 DOI: 10.1002/bip.360221109  1
1983 Broyde S, Hingerty B. An internal fluorene model for iodo-N-2-acetylaminofluorene modified DNA. Chemico-Biological Interactions. 47: 69-78. PMID 6640786 DOI: 10.1016/0009-2797(83)90148-5  1
1983 Hingerty B, Broyde S. A conformational analysis of the (+) anti BPDE adduct to the guanine amino group of dCpdG. Journal of Biomolecular Structure & Dynamics. 1: 905-12. PMID 6443880 DOI: 10.1080/07391102.1983.10507492  1
1982 Hingerty B, Broyde S. Conformation of the deoxydinucleoside monophosphate dCpdG modified at carbon 8 of guanine with 2-(acetylamino)fluorene. Biochemistry. 21: 3243-52. PMID 7104322  1
1982 Broyde S, Hingerty BE. DNA backbone conformation in AAF modified dCpdG: variable conformational modes of achieving base displacement. Chemico-Biological Interactions. 40: 113-9. PMID 7074712 DOI: 10.1016/0009-2797(82)90032-1  1
1982 Hingerty BE, Broyde SB, Olson WK. The poly(rU) coil: a minimum-energy model that matches experimental observations. Biopolymers. 21: 1167-88. PMID 6178444 DOI: 10.1002/bip.360210612  1
1981 Santella RM, Grunberger D, Broyde S, Hingerty BE. 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. 9: 5459-67. PMID 7301595 DOI: 10.1093/nar/9.20.5459  1
1979 Broyde S, Hingerty B. Conformational origin of the pyrimidine (3'-5') purine base sequence preference for intercalation into RNAs. Biopolymers. 18: 2905-10. PMID 508906 DOI: 10.1002/bip.1979.360181117  1
1979 Broyde S, Hingerty B. The influence of terminal 3', 5' phosphates on conformations of dApdA. Nucleic Acids Research. 6: 2165-78. PMID 461185 DOI: 10.1093/nar/6.6.2165  1
1978 Hingerty B, Broyde S. A model for the single stranded random coil form of polydeoxyadenylic acid from minimum energy conformations of the dimeric subunit. Nucleic Acids Research. 5: 3249-60. PMID 704355 DOI: 10.1093/nar/5.9.3249  1
1978 Broyde S, Hingerty B. 'A' forms of RNAs in single strands, duplexes and RNA-DNA hybrids. Nucleic Acids Research. 5: 2729-41. PMID 693318 DOI: 10.1093/nar/5.8.2729  1
1978 Hingerty B, Broyde S. Helix geometry of single stranded DNA 'A' and 'B' forms from minimum energy conformations of dimeric subunits Nucleic Acids Research. 5: 127-137. PMID 643603 DOI: 10.1093/nar/5.1.127  1
1978 Broyde S, Wartell RM, Stellman SD, Hingerty B. Minimum energy conformations of DNA dimeric subunits: Potential energy calculations for dGpdC, dApdA, dCpdC, dGpdG, and dTpdT Biopolymers. 17: 1485-1506.  1
1976 Stellman SD, Broyde SB, Wartell RM. Influence of ribose 2'-O-methylation on GpC conformation by classical potential energy calculations. Biopolymers. 15: 1951-64. PMID 963238 DOI: 10.1002/bip.1976.360151007  1
1975 Hingerty B, Subramanian E, Stellman SD, Broyde SB, Sato T, Langridge R. Structure of guanylyl-3',5'-cytidine monophosphate. II. Description of the molecular and crystal structure of the calcium derivative in space group P2(1). Biopolymers. 14: 227-36. PMID 1174655 DOI: 10.1002/bip.1975.360140116  1
1975 Broyde SB, Wartell RM, Stellman SD, Hingerty B, Langridge R. Classical potential energy calculations for ApA, CpC, GpG, and UpU. The influence of the bases on RNA subunit conformations. Biopolymers. 14: 1597-1613. PMID 1156657 DOI: 10.1002/bip.1975.360140805  1
1975 Stellman SD, Hingerty B, Broyde S, Langridge R. Conformation of a rare nucleoside in the anti codon loop of tRNAs: potential energy calculations for 2' O methyl cytidine Biopolymers. 14: 2049-2060.  1
1975 Broyde SB, Stellman SD, Wartell RM. The A and B conformations of DNA and RNA subunits. Potential energy calculations for dGpdC Biopolymers. 14: 2625-2637.  1
1974 Broyde SB, Stellman SD, Hingerty B, Langridge R. Conformational stability in dinucleoside phosphate crystals. Semiempirical potential energy calculations for uridylyl-3'-5'-adenosine monophosphate (UpA) and guanylyl-3',5'-cytidine monophosphate (GpC). Biopolymers. 13: 1243-59. PMID 4851147 DOI: 10.1002/bip.1974.360130615  1
1973 Stellman SD, Hingerty B, Broyde SB, Subramanian E, Sato T, LaNGRIDGE R. Letter: Conformation of guanosine cytidine 3',5'-monophosphate (GpC). Macromolecules. 6: 652-3. PMID 4805365  1
1973 Stellman SD, Hingerty B, Broyde SB, Subramanian E, Sato T, Langridge R. Structure of guanosine-3',5'-cytidine monophosphate. I. Semi-empirical potential energy calculations and model-building. Biopolymers. 12: 2731-50. PMID 4782550 DOI: 10.1002/bip.1973.360121208  1
1971 Broyde SB. Stop reacting and debate the issue [3] Chemical and Engineering News. 49: 3-4.  1
1971 Strauss G, Broyde SB, Kurucsev T. Concentration quenching of proflavine hydrochloride in dry films of sodium deoxyribonucleate and poly (vinyl alcohol) Journal of Physical Chemistry. 75: 2727-2733.  1
1969 Aghion J, Broyde SB, Brody SS. Surface reactions of chlorophyll a monolayers at a water-air interface. Photochemistry and complex formation Biochemistry. 8: 3120-3126.  1
1968 Brody SS, Broyde SB. Low Temperature Absorption Spectra of Chlorophyll a in Polar and Nonpolar Solvents Biophysical Journal. 8: 1511-1533. PMID 5713456 DOI: 10.1016/S0006-3495(68)86570-1  1
1968 Brody M, Broyde SB, Yeh CC, Brody SS. Chlorophyll-sensitized oxidation-reduction reactions of hemin in pyridine Biochemistry. 7: 3007-3015.  1
1968 Broyde SB, Brody SS, Brody M. Absorption difference spectroscopy of chlorophyll a in ethanol solution Bba - Bioenergetics. 153: 183-187.  1
1967 Broyde SB, Brody SS. Emission spectra of chlorophyll-a in polar and nonpolar solvents The Journal of Chemical Physics. 46: 3334-3340.  1
1966 Broyde SB, Brody SS. Spectral Studies of a Chlorophyll Pigment with Fluorescence Maximum at 698 mμ Biophysical Journal. 6: 353-366. PMID 5962283 DOI: 10.1016/S0006-3495(66)86661-4  1
1965 Broyde SB, Brody SS. Preparation of a colloidal form of chlorophyll a from concentrated solution Bba - Biophysics Including Photosynthesis. 94: 586-588. PMID 14314370  1
1965 Broyde SB, Brody SS. F698: A pigment found in preparations of chlorophyll Biochemical and Biophysical Research Communications. 19: 444-451.  1
1964 Oster G, Broyde SB, Bellin JS. Spectral properties of chlorophyllin a Journal of the American Chemical Society. 86: 1309-1313.  1
1964 Oster G, Bellin JS, Broyde SB. Photochemical properties of chlorophyllin a Journal of the American Chemical Society. 86: 1313-1318.  1
1963 Brody SS, Broyde SB. A Low-temperature emission band from dilute solutions of pure chlorophyll a [19] Nature. 199: 1097-1098. PMID 14066950 DOI: 10.1038/1991097a0  1
1961 Oster G, Broyde SB. Photochemical properties of water-soluble chlorophyll Nature. 192: 132-133. PMID 14482583 DOI: 10.1038/192132a0  1
Show low-probability matches.