SUSE B BROYDE

Summary

Affiliation: New York University
Country: USA

Publications

  1. pmc Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase
    Pingna Xu
    Department of Biology, New York University, New York, NY, USA
    Nucleic Acids Res 35:4275-88. 2007
  2. pmc The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions
    Lei Jia
    Department of Biology and Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
    Nucleic Acids Res 36:6571-84. 2008
  3. pmc 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
    Ling Zhang
    Department of Chemistry, New York University, New York, NY, USA
    Nucleic Acids Res 34:3326-37. 2006
  4. pmc 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
    Kerry Donny-Clark
    Department of Biology, New York University, New York, NY 10003, USA
    Nucleic Acids Res 37:7095-109. 2009
  5. pmc 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)
    Lihua Wang
    Biology Department, New York University, New York, NY 10003, USA
    Nucleic Acids Res 34:785-95. 2006
  6. pmc Structural, energetic and dynamic properties of guanine(C8)-thymine(N3) cross-links in DNA provide insights on susceptibility to nucleotide excision repair
    Shuang Ding
    Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
    Nucleic Acids Res 40:2506-17. 2012
  7. pmc 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
    Hong Mu
    Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
    Nucleic Acids Res 40:9675-90. 2012
  8. ncbi request reprint DNA adduct structure-function relationships: comparing solution with polymerase structures
    Suse Broyde
    Department of Biology, New York University, New York NY 10003, USA
    Chem Res Toxicol 21:45-52. 2008
  9. pmc Lesion processing: high-fidelity versus lesion-bypass DNA polymerases
    Suse Broyde
    Department of Biology, New York University, 100 Washington Square East, 1009 Silver Center, New York, NY 10003, USA
    Trends Biochem Sci 33:209-19. 2008
  10. pmc Differential nucleotide excision repair susceptibility of bulky DNA adducts in different sequence contexts: hierarchies of recognition signals
    Yuqin Cai
    Department of Chemistry, New York University, New York, NY 10003, USA
    J Mol Biol 385:30-44. 2009

Collaborators

  • Nicholas Geacintov
  • Dinshaw Patel
  • Min Wu
  • DAVID SCICCHITANO
  • V Shafirovich
  • Ling Zhang
  • JUDY BOLTON
  • S H Wilson
  • Yuan Cheng
  • Robert Shapiro
  • F Guengerich
  • S Frank Yan
  • D O Zharkov
  • BENOIT contact ROUX
  • W K Olson
  • Shuang Ding
  • Lihua Wang
  • Yuqin Cai
  • Lei Jia
  • Konstantin Kropachev
  • Alexander Kolbanovskiy
  • Olga Rechkoblit
  • Alexandra Dimitri
  • Pingna Xu
  • Rebecca A Perlow-Poehnelt
  • Rebecca A Perlow
  • Linjing Yang
  • Kerry Donny-Clark
  • Shantu Amin
  • Na Zhang
  • Lucy Malinina
  • Lida Oum
  • Brian E Hingerty
  • Tamar Schlick
  • Alexander Kolbanovskii
  • Hong Mu
  • Marina Kolbanovskiy
  • Marina Kolbanovskii
  • Yijin Tang
  • Alexander Durandin
  • Yingkai Zhang
  • Fabián A Rodríguez
  • Chin Lin
  • Ilya Likhterov
  • Qing Zhang
  • Thomas M Schinecker
  • William A Beard
  • Svetlana A Durandina
  • Zhi Liu
  • Rong Xu
  • Adam Schwaid
  • Yuan Cho Lee
  • Conor Crean
  • Bennett Van Houten
  • Anant Shastry
  • Vladimir A Kuzmin
  • Yang Liu
  • Fabian Rodríguez
  • Angela K Goodenough
  • Richard B van Breemen
  • John A Burns
  • Yan Wang
  • Xinyun Yu
  • Po Hu
  • Lorena S Beese
  • Vitaly Kuryavyi
  • Aleksandr Kolbanovskiy
  • Xuanwei Huang
  • Arthur P Grollman
  • A R Srinivasan
  • William Beard

Detail Information

Publications61

  1. pmc Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase
    Pingna Xu
    Department of Biology, New York University, New York, NY, USA
    Nucleic Acids Res 35:4275-88. 2007
    ..In vivo, a switch to a potentially error-prone bypass polymerase likely dominates translesion bypass...
  2. pmc The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions
    Lei Jia
    Department of Biology and Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
    Nucleic Acids Res 36:6571-84. 2008
    ..Absence of the N-clasp in Dpo4 explains the error-prone processing of the same lesion by this enzyme. Thus, our studies elucidate structure-function relationships in the fidelity of lesion bypass...
  3. pmc 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
    Ling Zhang
    Department of Chemistry, New York University, New York, NY, USA
    Nucleic Acids Res 34:3326-37. 2006
    ..2006), PLoS Biol., 4, e11). However, N2-dG adducts, which can reside on the minor groove side, appear to cause less hindrance when in this position...
  4. pmc 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
    Kerry Donny-Clark
    Department of Biology, New York University, New York, NY 10003, USA
    Nucleic Acids Res 37:7095-109. 2009
    ..With syn dA*, there is also an opportunity for increased misincorporation of dGTP. These results expand our understanding of the versatility and flexibility of polymerase iota and its lesion bypass functions in humans...
  5. pmc 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)
    Lihua Wang
    Biology Department, New York University, New York, NY 10003, USA
    Nucleic Acids Res 34:785-95. 2006
    ..Possible relevance of our new major groove structure for AAF-dG to other polymerases, lesion repair and solution conformations are discussed...
  6. pmc Structural, energetic and dynamic properties of guanine(C8)-thymine(N3) cross-links in DNA provide insights on susceptibility to nucleotide excision repair
    Shuang Ding
    Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
    Nucleic Acids Res 40:2506-17. 2012
    ..Our combined experimental and computational studies provide structural and thermodynamic understanding of the features of the damaged duplexes that produce the most robust NER response...
  7. pmc 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
    Hong Mu
    Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
    Nucleic Acids Res 40:9675-90. 2012
    ..Overall, the greater NER efficiencies are correlated with greater extents of base sequence-dependent local untwisting and minor groove opening together with weaker stacking interactions...
  8. ncbi request reprint DNA adduct structure-function relationships: comparing solution with polymerase structures
    Suse Broyde
    Department of Biology, New York University, New York NY 10003, USA
    Chem Res Toxicol 21:45-52. 2008
    ..While the polymerase interactions can on occasion override the solution preferences, intrinsic adduct conformations favored in solution are often manifested within polymerases and likely play a significant role in lesion processing...
  9. pmc Lesion processing: high-fidelity versus lesion-bypass DNA polymerases
    Suse Broyde
    Department of Biology, New York University, 100 Washington Square East, 1009 Silver Center, New York, NY 10003, USA
    Trends Biochem Sci 33:209-19. 2008
    ....
  10. pmc Differential nucleotide excision repair susceptibility of bulky DNA adducts in different sequence contexts: hierarchies of recognition signals
    Yuqin Cai
    Department of Chemistry, New York University, New York, NY 10003, USA
    J Mol Biol 385:30-44. 2009
    ..Furthermore, combinations of several locally destabilizing features in the hierarchy, consistent with a multipartite model, may provide a relatively strong recognition signal...
  11. ncbi request reprint Extending the understanding of mutagenicity: structural insights into primer-extension past a benzo[a]pyrene diol epoxide-DNA adduct
    Rebecca A Perlow
    Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
    J Mol Biol 327:797-818. 2003
    ..These studies reveal in molecular detail the kinds of specific structural interactions that determine the function of a processive DNA polymerase when challenged by a bulky DNA adduct...
  12. ncbi request reprint Conformational searches elucidate effects of stereochemistry on structures of deoxyadenosine covalently bound to tumorigenic metabolites of benzo[C] phenanthrene
    Min Wu
    Department of Chemistry, New York University, New York, NY 10003, USA
    Front Biosci 9:2807-18. 2004
    ....
  13. pmc 4-hydroxyequilenin-adenine lesions in DNA duplexes: stereochemistry, damage site, and structure
    Shuang Ding
    Department of Chemistry and Department of Biology, New York University, 100 Washington Square East, New York, New York 10003
    Biochemistry 46:182-91. 2007
    ..These characteristics may manifest themselves in terms of differential nucleotide excision repair susceptibilities and mutagenic activities of the 4-OHEN-A and C adducts...
  14. doi request reprint Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases
    Olga Rechkoblit
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Structure 17:725-36. 2009
    ..Because of homology between Dpo4 and Pol eta, such a dynamic screening mechanism might be utilized by Dpo4 and Pol eta to regulate error-free versus error-prone bypass of oxoG and other lesions...
  15. ncbi request reprint 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
    Na Zhang
    Program in Cellular Biochemistry and Biophysics, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    J Mol Biol 346:951-65. 2005
    ..Such conformational differences in methylated and unmethylated CpG sequences may be significant because of potential alterations in the cellular processing of the [BP]G adducts by DNA transcription, replication, and repair enzymes...
  16. pmc Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion
    Olga Rechkoblit
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    PLoS Biol 4:e11. 2006
    ....
  17. ncbi request reprint Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery
    Nicholas E Geacintov
    Chemistry Department, New York University, New York, NY 10003 5180, USA
    Biopolymers 65:202-10. 2002
    ..These structural effects correlate with the differential NER susceptibilities and stem from the intrinsically distinct shapes of the fjord and bay region PAH diol epoxide-N(6)-adenine adducts...
  18. pmc Relating repair susceptibility of carcinogen-damaged DNA with structural distortion and thermodynamic stability
    Min Wu
    Department of Chemistry, New York University, New York, NY 10003, USA
    Nucleic Acids Res 30:3422-32. 2002
    ..These differences are due to the different intrinsic topologies of the rigid, planar bay region adducts versus the twisted, sterically hindered fjord region adducts...
  19. ncbi request reprint DNA adducts from a tumorigenic metabolite of benzo[a]pyrene block human RNA polymerase II elongation in a sequence- and stereochemistry-dependent manner
    Rebecca A Perlow
    Department of Biology, New York University, 100 Washington Square East, Mail Code 5181, New York 10003, USA
    J Mol Biol 321:29-47. 2002
    ..It is likely that these differences between the behaviors of T7RNAP and human RNAPII are a result of the structural characteristics of the enzymes' active sites, a hypothesis that is explored in light of their known crystal structures...
  20. pmc Exploring damage recognition models in prokaryotic nucleotide excision repair with a benzo[a]pyrene-derived lesion in UvrB
    Lei Jia
    Department of Biology, New York University, 100 Washington Square East, Room 1009, New York, New York 10003, USA
    Biochemistry 48:8948-57. 2009
    ....
  21. ncbi request reprint Increased flexibility enhances misincorporation: temperature effects on nucleotide incorporation opposite a bulky carcinogen-DNA adduct by a Y-family DNA polymerase
    Rebecca A Perlow-Poehnelt
    Department of Biology, New York University, New York, New York 10003, USA
    J Biol Chem 282:1397-408. 2007
    ..The observed temperature effect suggests that conformational flexibility plays a role in nucleotide incorporation and bypass fidelity opposite (+)-ta-[BP]G by Dpo4...
  22. ncbi request reprint 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
    Yuqin Cai
    Department of Chemistry, New York University, New York, NY 10003, USA
    J Mol Biol 374:292-305. 2007
    ....
  23. ncbi request reprint Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se
    Linjing Yang
    Department of Chemistry and Courant, Institute of Mathematical Sciences, New York University and the Howard Hughes Medical Institute, 251 Mercer Street, New York, New York 10012, USA
    J Mol Biol 317:651-71. 2002
    ..These results suggest new lines of experimentation in the study of polymerase mechanisms (e.g. enzyme mutants), which should provide further insights into mechanisms of error discrimination and DNA synthesis fidelity...
  24. pmc A bulky DNA lesion derived from a highly potent polycyclic aromatic tumorigen stabilizes nucleosome core particle structure
    Yuqin Cai
    Department of Biology, New York University, New York, New York 10003, United States
    Biochemistry 49:9943-5. 2010
    ..These findings suggest that such lesions should be as resistant to NER in the nucleosome environment as they are in free DNA...
  25. ncbi request reprint Deformations of promoter DNA bound to carcinogens help interpret effects on TATA-element structure and activity
    Qing Zhang
    Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and the Howard Hughes Medical Institute, 251 Mercer Street, New York, NY 10012, USA
    Philos Transact A Math Phys Eng Sci 362:1479-96. 2004
    ..The unravelled structures and interactions thus reveal the effect of different adduct locations on TATA-TBP complex formation and suggest how transcription initiation may be affected by the presence of a bulky BP...
  26. ncbi request reprint Role of base sequence context in conformational equilibria and nucleotide excision repair of benzo[a]pyrene diol epoxide-adenine adducts
    Shixiang Yan
    Department of Chemistry, New York University, New York, New York 10003, USA
    Biochemistry 42:2339-54. 2003
    ..Such sequence specific differential repair could contribute to the existence of mutational hotspots and thereby contribute to the complexity of cancer initiation...
  27. pmc Accurate representation of B-DNA double helical structure with implicit solvent and counterions
    Lihua Wang
    Biology Department, New York University, New York, New York 10003, USA
    Biophys J 83:382-406. 2002
    ....
  28. pmc Simulating structural and thermodynamic properties of carcinogen-damaged DNA
    Shixiang Yan
    Department of Chemistry, New York University, New York, NY 10003, USA
    Biophys J 84:2137-48. 2003
    ..The structural and thermodynamic features of these stereoisomeric adducts are also discussed in relation to their reported low susceptibilities to nucleotide excision repair...
  29. ncbi request reprint 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
    Rebecca A Perlow-Poehnelt
    Department of Biology, New York University, New York, NY 10003, USA
    J Biol Chem 279:36951-61. 2004
    ....
  30. pmc Absolute configurations of DNA lesions determined by comparisons of experimental ECD and ORD spectra with DFT calculations
    Shuang Ding
    Department of Biology, New York University, New York, USA
    Chirality 21:E231-41. 2009
    ..Establishing the stereochemistry of DNA lesions is highly useful for understanding their biological impact, especially when sufficient amounts of material are not available for other methods of structural characterization...
  31. ncbi request reprint Toward understanding the mutagenicity of an environmental carcinogen: structural insights into nucleotide incorporation preferences
    Rebecca A Perlow
    Department of Biology, New York University, New York, NY 10003, USA
    J Mol Biol 322:291-309. 2002
    ..Structural rationalization of the incorporation preference opposite (+)-trans-anti-[BP]-N(2)-dG by T7 DNA polymerase contributes to providing a molecular explanation for mutations caused by this carcinogen-DNA adduct in a model system...
  32. ncbi request reprint Molecular dynamics of a food carcinogen-DNA adduct in a replicative DNA polymerase suggest hindered nucleotide incorporation and extension
    Ling Zhang
    Department of Chemistry, New York University, New York, New York 10003, USA
    Chem Res Toxicol 18:1347-63. 2005
    ..Polymerase stalling would be the more common outcome and in vivo could lead to switch to an error-prone bypass polymerase...
  33. ncbi request reprint Structural and thermodynamic features of spiroiminodihydantoin damaged DNA duplexes
    Lei Jia
    Department of Chemistry, New York University, New York, New York 10003, USA
    Biochemistry 44:13342-53. 2005
    ..The structural characteristics may relate to observed mutagenic properties of the Sp stereoisomers, including possible stereoisomer-dependent differences...
  34. pmc 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?
    Kerry Donny-Clark
    Department of Biology and Chemistry, New York University, New York, New York 10003, USA
    Biochemistry 48:7-18. 2009
    ..This suggests the possibility of an expanded role for poliota in lesion bypass...
  35. pmc 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
    Konstantin Kropachev
    Department of Chemistry, New York University, New York, NY 10003, USA
    J Mol Biol 386:1193-203. 2009
    ..These results demonstrate that the identical lesion can be repaired with markedly variable efficiency in different local sequence contexts that differentially alter the structural features of the DNA duplex around the lesion site...
  36. pmc 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
    Pingna Xu
    Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, New York 10003, USA
    Biochemistry 48:4677-90. 2009
    ....
  37. pmc Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion
    Yuqin Cai
    Department of Biology, New York University, New York, NY 10003, USA
    J Mol Biol 399:397-409. 2010
    ....
  38. pmc NMR and computational studies of stereoisomeric equine estrogen-derived DNA cytidine adducts in oligonucleotide duplexes: opposite orientations of diastereomeric forms
    Na Zhang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Biochemistry 48:7098-109. 2009
    ..These differences in stereoisomeric adduct conformations may play a role in the processing of these lesions in cellular environments...
  39. ncbi request reprint Equilenin-derived DNA adducts to cytosine in DNA duplexes: structures and thermodynamics
    Shuang Ding
    Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, USA
    Biochemistry 44:14565-76. 2005
    ..The unusual structures and the stereochemical effects underlie their biological processing as miscoding DNA lesions whose mutagenic properties may contribute to breast cancer...
  40. ncbi request reprint Spiroiminodihydantoin lesions derived from guanine oxidation: structures, energetics, and functional implications
    Lei Jia
    Department of Chemistry, New York University, New York, New York 10003, USA
    Biochemistry 44:6043-51. 2005
    ..In addition, stereoisomer-specific differences indicate the possibility that their processing by cellular replication and repair enzymes may be differentially affected by their absolute configuration...
  41. pmc 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
    Fabián A Rodríguez
    Department of Chemistry, New York University, New York, NY, USA
    Nucleic Acids Res 35:1555-68. 2007
    ..The minor groove width opens near the lesion in both cases, but more for 5'- ... CGG*C.... Differential sequence-dependent removal rates of this lesion result and may contribute to the mutation hotspot phenomenon...
  42. pmc Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase
    Lihua Wang
    Biology Department, New York University, New York, NY 10003, USA
    J Mol Biol 389:787-96. 2009
    ..These unifying features are likely requisite elements for nucleotidyl transfer reactions...
  43. ncbi request reprint 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
    Lihua Wang
    Department of Biololgy, New York University, New York, New York 10003, USA
    Chem Res Toxicol 18:441-56. 2005
    ..Furthermore, these models suggest how error-prone translesion synthesis by Y-family polymerases might produce mutations that may play a role in the initiation of cancer...
  44. pmc Flexible 5-guanidino-4-nitroimidazole DNA lesions: structures and thermodynamics
    Lei Jia
    Department of Chemistry, New York University, New York, New York 10003, USA
    Biochemistry 45:6644-55. 2006
    ..However, hydrogen bonding interactions between NI and partner G or A are also found, which would be compatible with the observed mismatches...
  45. ncbi request reprint Substrate discrimination by formamidopyrimidine-DNA glycosylase: distinguishing interactions within the active site
    Rebecca A Perlow-Poehnelt
    Department of Biology, New York University, 100 Washington Square East, Room 1009M, New York, New York 10003, USA
    Biochemistry 43:16092-105. 2004
    ....
  46. ncbi request reprint Conformations of stereoisomeric base adducts to 4-hydroxyequilenin
    Shuang Ding
    Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, USA
    Chem Res Toxicol 16:695-707. 2003
    ..Such opposite orientations could cause stereoisomer pairs of lesions to respond differently to DNA replication and repair enzymes...
  47. pmc Transcription elongation past O6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase
    Alexandra Dimitri
    Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003, USA
    Nucleic Acids Res 36:6459-71. 2008
    ..In addition, the partial blockage of RNA polymerase II suggests that transcription-coupled DNA repair could play an auxiliary role in the clearance of this lesion...
  48. pmc A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV
    Lihua Wang
    Biology and Chemistry Departments, New York University, New York, NY 10003, USA
    J Am Chem Soc 129:4731-7. 2007
    ..This WMSA mechanism takes specific advantage of the unique structural features of this low-fidelity lesion-bypass Y-family polymerase, which has a more spacious and solvent-exposed active site than replicative and repair polymerases...
  49. pmc Lesion specificity in the base excision repair enzyme hNeil1: modeling and dynamics studies
    Lei Jia
    Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, New York 10003, USA
    Biochemistry 46:5305-14. 2007
    ....
  50. ncbi request reprint Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase: a 5'-slippage mechanism
    Pingna Xu
    Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York City, New York 10003, USA
    Biochemistry 47:2701-9. 2008
    ..In addition, the dATP can be misincorporated opposite the adduct. The 5'-slippage pattern may be generally facilitated in cases where the base 3' to the lesion is the same as the adducted base...
  51. ncbi request reprint Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus
    Linjing Yang
    Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and the Howard Hughes Medical Institute, 251 Mercer Street, 10012, New York, NY, USA
    J Mol Biol 321:459-78. 2002
    ....
  52. pmc Transcription processing at 1,N2-ethenoguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase
    Alexandra Dimitri
    Department of Biology, New York University, New York, NY 10003, USA
    J Mol Biol 375:353-66. 2008
    ..Thus, our data suggest that this repair pathway is likely engaged in the clearance of the 1,N(2)-epsilon G from actively transcribed DNA...
  53. doi request reprint Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4
    Olga Rechkoblit
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    Nat Struct Mol Biol 17:379-88. 2010
    ..Further extension leads to semitargeted mutations via this proposed polymerase-guided mechanism...
  54. pmc 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
    Shuang Ding
    Department of Biology, New York University, New York, 10003, USA
    Chem Res Toxicol 21:1739-48. 2008
    ..The absolute configurations of the 4-OHEN-dA adducts were thus deduced by comparing the experimental ORD with computed ORD values of 4-OHEN-A adducts...
  55. pmc Transcription of DNA containing the 5-guanidino-4-nitroimidazole lesion by human RNA polymerase II and bacteriophage T7 RNA polymerase
    Alexandra Dimitri
    Department of Biology, New York University, New York, NY 10003 6688, USA
    DNA Repair (Amst) 7:1276-88. 2008
    ..These influence the kinetics of lesion bypass and may well play a role in TM and TCR in cells...
  56. pmc Conformational properties of equilenin-DNA adducts: stereoisomer and base effects
    Shuang Ding
    Departments of Biology and Chemistry, New York University, 100 Washington Square East, New York City, New York 10003, USA
    Chem Res Toxicol 21:1064-73. 2008
    ..These differences may underlie observed differential stereoisomer and base-dependent mutagenicities and repair susceptibilities of these adducts...
  57. pmc Human RNA polymerase II is partially blocked by DNA adducts derived from tumorigenic benzo[c]phenanthrene diol epoxides: relating biological consequences to conformational preferences
    Thomas M Schinecker
    Department of Biology, New York University, 100 Washington Square East, MC 5181, New York, NY 10003, USA
    Nucleic Acids Res 31:6004-15. 2003
    ....
  58. ncbi request reprint 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
    Lihua Wang
    Biology Department and Chemistry Department, New York University, New York, New York 10003, USA
    Chem Res Toxicol 17:311-24. 2004
    ..Stereochemistry-dependent differences in adduct orientation could be expected to produce different biochemical effects, as has been observed in adducts derived from polycyclic aromatic hydrocarbons...
  59. pmc Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses
    Linjing Yang
    Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and the Howard Hughes Medical Institute, New York, New York, USA
    Biophys J 86:3392-408. 2004
    ....
  60. ncbi request reprint Altering DNA polymerase incorporation fidelity by distorting the dNTP binding pocket with a bulky carcinogen-damaged template
    S Frank Yan
    Department of Chemistry, New York University, New York, New York 10003, USA
    Biochemistry 43:7750-65. 2004
    ..Furthermore, plausible structural explanations for the observed effects of [BP]-N(6)-dA adduct stereochemistry on the observed stalling patterns are proposed...
  61. ncbi request reprint Conformational analysis of a 4-hydroxyequilenin Guanine adduct using density functional theory
    Shixiang Yan
    Department of Chemistry, New York University, 1001 Main Building, 31 Washington Place, New York 10003, USA
    Chem Res Toxicol 15:648-53. 2002
    ..Since the Watson-Crick hydrogen bonding edge of the modified guanine is obstructed by the formation of this bulky nonplanar adduct, it likely would reside in a groove of the DNA double helix...

Research Grants46

  1. Carcinogen-DNA Adducts: Topology, Conformation and Repair (Renewal)
    Suse Broyde; Fiscal Year: 2010
    ..In addition, design of more efficacious cancer chemotherapeutic agents will be facilitated. ..
  2. CARCINOGEN-DNA ADDUCTS--LINKAGE SITE AND CONFORMATION
    Suse Broyde; Fiscal Year: 1990
    ..In addition, it is planned to automate and document DUPLEX, and release it to the scientific community...
  3. Aromatic Amine DNA Structures--Mutagenic Relevance
    Suse Broyde; Fiscal Year: 2002
    ..Molecular dynamics trajectories yield ensembles of structures that will be used to compute free energy differences between conformers in solution, and binding free energies of polymerase-primer-template complexes. ..
  4. Carcinogen - DNA Adducts: Linkage Site and Conformation
    Suse Broyde; Fiscal Year: 2006
    ..The long term goals are to define conformational details governing NER and translesion DNA synthesis to gain predictive power relating lesion structure with carcinogenic hazard. ..
  5. Aromatic Amine DNA Structures--Mutagenic Relevance
    Suse Broyde; Fiscal Year: 2004
    ..Molecular dynamics trajectories yield ensembles of structures that will be used to compute free energy differences between conformers in solution, and binding free energies of polymerase-primer-template complexes. ..
  6. Aromatic Amine DNA Structures--Mutagenic Relevance
    Suse Broyde; Fiscal Year: 2001
    ..Molecular dynamics trajectories yield ensembles of structures that will be used to compute free energy differences between conformers in solution, and binding free energies of polymerase-primer-template complexes. ..
  7. Aromatic Amine DNA Structures--Mutagenic Relevance
    Suse Broyde; Fiscal Year: 2005
    ..Molecular dynamics trajectories yield ensembles of structures that will be used to compute free energy differences between conformers in solution, and binding free energies of polymerase-primer-template complexes. ..
  8. CARCINOGEN/DNA ADDUCTS--LINKAGE SITE AND CONFORMATION
    Suse Broyde; Fiscal Year: 1999
    ....
  9. DNA Lesion Structures: Mutagenicity and Repair
    Suse Broyde; Fiscal Year: 2010
    ....
  10. DNA Lesion Structures: Mutagenicity and Repair
    Suse Broyde; Fiscal Year: 2006
    ....
  11. AF AND AAF MODIFIED DNA STRUCTURES--MUTAGENIC RELEVANCE
    Suse Broyde; Fiscal Year: 2000
    ....
  12. Carcinogen - DNA Adducts: Linkage Site and Conformation
    Suse Broyde; Fiscal Year: 2007
    ..The long term goals are to define conformational details governing NER and translesion DNA synthesis to gain predictive power relating lesion structure with carcinogenic hazard. ..
  13. DNA Lesion Structures: Mutagenicity and Repair
    Suse Broyde; Fiscal Year: 2007
    ....
  14. DNA Lesion Structures: Mutagenicity and Repair
    Suse Broyde; Fiscal Year: 2009
    ....
  15. Carcinogen - DNA Adducts: Linkage Site and Conformation
    Suse Broyde; Fiscal Year: 2009
    ..The long term goals are to define conformational details governing NER and translesion DNA synthesis to gain predictive power relating lesion structure with carcinogenic hazard. ..
  16. CARCINOGEN-DNA ADDUCTS LINKAGE SITE AND CONFORMATION
    Suse Broyde; Fiscal Year: 1993
    ..In addition, it is planned to automate and document DUPLEX, and release it to the scientific community...
  17. CARCINOGEN-DNA ADDUCTS LINKAGE SITE AND CONFORMATION
    Suse Broyde; Fiscal Year: 1992
    ..In addition, it is planned to automate and document DUPLEX, and release it to the scientific community...
  18. Carcinogen - DNA Adducts: Linkage Site and Conformation
    Suse Broyde; Fiscal Year: 2005
    ..The long term goals are to define conformational details governing NER and translesion DNA synthesis to gain predictive power relating lesion structure with carcinogenic hazard. ..
  19. AF AND AAF MODIFIED DNA STRUCTURES--MUTAGENIC RELEVANCE
    Suse Broyde; Fiscal Year: 1999
    ....
  20. CARCINOGEN-DNA ADDUCTS LINKAGE SITE AND CONFORMATION
    Suse Broyde; Fiscal Year: 1991
    ..In addition, it is planned to automate and document DUPLEX, and release it to the scientific community...
  21. Aromatic Amine DNA Structures--Mutagenic Relevance
    Suse Broyde; Fiscal Year: 2003
    ..Molecular dynamics trajectories yield ensembles of structures that will be used to compute free energy differences between conformers in solution, and binding free energies of polymerase-primer-template complexes. ..