Dinshaw Patel

Summary

Affiliation: Memorial Sloan-Kettering Cancer Center
Country: USA

Publications

  1. pmc Structural basis for glycosphingolipid transfer specificity
    Lucy Malinina
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nature 430:1048-53. 2004
  2. doi request reprint Readout of epigenetic modifications
    Dinshaw J Patel
    Structural Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Annu Rev Biochem 82:81-118. 2013
  3. 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
  4. pmc Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics
    Dinshaw J Patel
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Nucleic Acids Res 35:7429-55. 2007
  5. ncbi request reprint Structural analysis of nucleic acid aptamers
    D J Patel
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Curr Opin Chem Biol 1:32-46. 1997
  6. ncbi request reprint Adaptive recognition in RNA complexes with peptides and protein modules
    D J Patel
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Curr Opin Struct Biol 9:74-87. 1999
  7. ncbi request reprint Structure, recognition and discrimination in RNA aptamer complexes with cofactors, amino acids, drugs and aminoglycoside antibiotics
    D J Patel
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    J Biotechnol 74:39-60. 2000
  8. 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
  9. ncbi request reprint Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex
    Alexander J Ruthenburg
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Nat Struct Mol Biol 13:704-12. 2006
  10. 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

Collaborators

Detail Information

Publications67

  1. pmc Structural basis for glycosphingolipid transfer specificity
    Lucy Malinina
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nature 430:1048-53. 2004
    ....
  2. doi request reprint Readout of epigenetic modifications
    Dinshaw J Patel
    Structural Biology Department, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Annu Rev Biochem 82:81-118. 2013
    ..The review ends by highlighting new initiatives and advances, as well as future challenges, toward the promise of enhancing our structural and mechanistic understanding of the readout of histone PTMs at the nucleosomal level...
  3. 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
    ....
  4. pmc Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics
    Dinshaw J Patel
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Nucleic Acids Res 35:7429-55. 2007
    ....
  5. ncbi request reprint Structural analysis of nucleic acid aptamers
    D J Patel
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Curr Opin Chem Biol 1:32-46. 1997
    ..These new results provide opportunities for structure-based drug design strategies relevant to therapeutic intervention...
  6. ncbi request reprint Adaptive recognition in RNA complexes with peptides and protein modules
    D J Patel
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Curr Opin Struct Biol 9:74-87. 1999
    ..These alternative strategies of RNA recognition at the peptide and protein module level provide novel insights into the principles, patterns and diversity of the adaptive transitions associated with the recognition process...
  7. ncbi request reprint Structure, recognition and discrimination in RNA aptamer complexes with cofactors, amino acids, drugs and aminoglycoside antibiotics
    D J Patel
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    J Biotechnol 74:39-60. 2000
    ..Analysis of the structural features of these complexes allows the identification of molecular themes in RNA aptamer structure, recognition and discrimination...
  8. 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...
  9. ncbi request reprint Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex
    Alexander J Ruthenburg
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
    Nat Struct Mol Biol 13:704-12. 2006
    ..Contrary to predictions, the structures reveal that WDR5 does not read out the methylation state of K4 directly, but instead serves to present the K4 side chain for further methylation by SET1-family complexes...
  10. 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...
  11. ncbi request reprint Structure of the human telomere in K+ solution: an intramolecular (3 + 1) G-quadruplex scaffold
    Kim Ngoc Luu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    J Am Chem Soc 128:9963-70. 2006
    ..The topological characteristics of this (3 + 1) G-quadruplex scaffold should provide a unique platform for structure-based anticancer drug design targeted to human telomeric DNA...
  12. ncbi request reprint Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
    Alexander Serganov
    Nature 441:1167-71. 2006
    ..In addition, this structure provides insight into how folded RNAs can form precision binding pockets that rival those formed by protein genetic factors...
  13. ncbi request reprint Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF
    Haitao Li
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nature 442:91-5. 2006
    ..Our findings call attention to the PHD finger as a previously uncharacterized chromatin-binding module found in a large number of chromatin-associated proteins...
  14. ncbi request reprint DNA architecture: from G to Z
    Anh Tuân Phan
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Curr Opin Struct Biol 16:288-98. 2006
    ..These results will enhance our understanding of the biology of these structures and provide a platform for drug design...
  15. ncbi request reprint Control of stereoselectivity in an enzymatic reaction by backdoor access
    Richard Wombacher
    Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120 Heidelberg, Germany
    Angew Chem Int Ed Engl 45:2469-72. 2006
  16. ncbi request reprint Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter
    Anh Tuân Phan
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nat Chem Biol 1:167-73. 2005
    ....
  17. ncbi request reprint Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen
    Marianna Teplova
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Mol Cell 21:75-85. 2006
    ....
  18. ncbi request reprint (3 + 1) Assembly of three human telomeric repeats into an asymmetric dimeric G-quadruplex
    Na Zhang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    J Am Chem Soc 127:17277-85. 2005
    ..We discuss the possible implications of the new folding topology for understanding the structure of telomeric DNA, including t-loop formation, and for targeting G-quadruplexes in the telomeres...
  19. ncbi request reprint RNA silencing suppressor p21 of Beet yellows virus forms an RNA binding octameric ring structure
    Keqiong Ye
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Structure 13:1375-84. 2005
    ..This study reveals an RNA binding structure adopted by the p21 silencing suppressor...
  20. ncbi request reprint Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage
    Yu Ren Yuan
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Mol Cell 19:405-19. 2005
    ..We propose a four-step Ago-mediated catalytic cleavage cycle model, which provides distinct perspectives into the mechanism of guide strand-mediated mRNA cleavage within the RISC...
  21. pmc Point mutational analysis of the liganding site in human glycolipid transfer protein. Functionality of the complex
    Margarita L Malakhova
    Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA
    J Biol Chem 280:26312-20. 2005
    ..Also noteworthy was the inefficient release of glycolipid by wtGLTP into phosphatidylcholine acceptor vesicles, raising the possibility of a function other than intermembrane glycolipid transfer in vivo...
  22. pmc The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure
    Lucy Malinina
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS Biol 4:e362. 2006
    ....
  23. pmc Different loop arrangements of intramolecular human telomeric (3+1) G-quadruplexes in K+ solution
    Anh Tuân Phan
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Nucleic Acids Res 34:5715-9. 2006
    ..Furthermore, even small changes to flanking sequences can perturb the equilibrium between different coexisting G-quadruplex forms...
  24. pmc Towards deciphering the principles underlying an mRNA recognition code
    Alexander Serganov
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Curr Opin Struct Biol 18:120-9. 2008
    ..In this review, we have highlighted recent structural studies that illustrate the diversity of recognition principles used by mRNA binders for timely and specific targeting and processing of the message...
  25. 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...
  26. ncbi request reprint Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger
    Haitao Li
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Mol Cell 28:677-91. 2007
    ....
  27. ncbi request reprint How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers
    Sean D Taverna
    Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
    Nat Struct Mol Biol 14:1025-40. 2007
    ..Changes in these interactions may have far-reaching implications for human biology and disease, notably cancer...
  28. 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
    ....
  29. pmc Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution
    Anh Tuân Phan
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Nucleic Acids Res 35:6517-25. 2007
    ..This structural information might be important for our understanding of telomere G-quadruplex structures and for anticancer drug design targeted to such scaffolds...
  30. ncbi request reprint Ribozymes, riboswitches and beyond: regulation of gene expression without proteins
    Alexander Serganov
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nat Rev Genet 8:776-90. 2007
    ..These findings have implications for understanding how cellular functions might have evolved from RNA-based origins...
  31. ncbi request reprint Characterizing the relative orientation and dynamics of RNA A-form helices using NMR residual dipolar couplings
    Maximillian H Bailor
    Department of Chemistry and Biophysics Research Division, The University of Michigan, Ann Arbor, Michigan 48109, USA
    Nat Protoc 2:1536-46. 2007
    ..Following resonance assignments, the procedure is expected to take no more than 2 weeks of acquisition and data analysis time...
  32. ncbi request reprint Structure of an unprecedented G-quadruplex scaffold in the human c-kit promoter
    Anh Tuân Phan
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    J Am Chem Soc 129:4386-92. 2007
    ..This unique structural scaffold provides a highly specific platform for the future design of ligands specifically targeted to the promoter DNA of c-kit...
  33. 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...
  34. ncbi request reprint Apramycin recognition by the human ribosomal decoding site
    Thomas Hermann
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
    Blood Cells Mol Dis 38:193-8. 2007
    ..The binding mode of apramycin at the human decoding-site RNA is distinct from aminoglycoside recognition of the bacterial target, suggesting a molecular basis for the actions of apramycin in eukaryotes and bacteria...
  35. ncbi request reprint Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs
    Sean D Taverna
    Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
    Mol Cell 24:785-96. 2006
    ..Our data support a general mechanism of transcriptional control through which histone acetylation upstream of gene activation is promoted partially through availability of H3K4me3, "read" by binding modules in select subunits...
  36. ncbi request reprint Evidence that electrostatic interactions dictate the ligand-induced arrest of RNA global flexibility
    Stephen W Pitt
    Department of Pharmacology, Weil Medical College of Cornell University, New York, NY 10021, USA
    Angew Chem Int Ed Engl 44:3412-5. 2005
  37. ncbi request reprint Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein
    Jin Biao Ma
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nature 434:666-70. 2005
    ....
  38. ncbi request reprint Mg2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings
    Hashim M Al-Hashimi
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    J Mol Biol 329:867-73. 2003
    ..Results demonstrate that RDC-NMR methodology can provide new insight into the effects of Mg(2+) on both the conformation and dynamics of RNA...
  39. ncbi request reprint RNA-structural mimicry in Escherichia coli ribosomal protein L4-dependent regulation of the S10 operon
    Ulrich Stelzl
    Memorial Sloan Kettering Cancer Center, Cellular Biochemistry and Biophysics Program, New York, New York 10021, USA
    J Biol Chem 278:28237-45. 2003
    ..In vitro binding of L4 induces structural changes of the S10 leader RNA, providing a first clue for how protein L4 may provoke transcription termination...
  40. pmc Ribosomal protein S15 represses its own translation via adaptation of an rRNA-like fold within its mRNA
    Alexander Serganov
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    EMBO J 22:1898-908. 2003
    ..Our results highlight an astonishing plasticity of mRNA in its ability to adapt to evolutionary constraints, that contrasts with the extreme conservation of the rRNA-binding site...
  41. 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...
  42. ncbi request reprint Encapsulating streptomycin within a small 40-mer RNA
    Valentina Tereshko
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Chem Biol 10:175-87. 2003
    ..By contrast, the majority of intermolecular interactions involve contacts to backbone phosphates in the published structure of streptomycin bound to the 16S rRNA...
  43. ncbi request reprint Differentiation between unlabeled and very-low-level fully 15N,13C-labeled nucleotides for resonance assignments in nucleic acids
    Anh Tuân Phan
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    J Biomol NMR 23:257-62. 2002
    ..We expect this approach to be useful for selective monitoring of important functional domains and of their interactions in large nucleic acids...
  44. ncbi request reprint Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold
    Keqiong Ye
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, USA
    Eur J Biochem 269:5182-91. 2002
    ..It appears probable that functional properties of pY are not identical to those of dsRBDs, as the postulated RNA-binding site in pY does not coincide with the RNA-binding surface of the dsRBDs...
  45. 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...
  46. ncbi request reprint Structural biology: a molecular propeller
    Dinshaw J Patel
    Nature 417:807-8. 2002
  47. ncbi request reprint Towards structural genomics of RNA: rapid NMR resonance assignment and simultaneous RNA tertiary structure determination using residual dipolar couplings
    Hashim M Al-Hashimi
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    J Mol Biol 318:637-49. 2002
    ....
  48. ncbi request reprint Residual dipolar couplings: synergy between NMR and structural genomics
    Hashim M Al-Hashimi
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    J Biomol NMR 22:1-8. 2002
    ..Both an expansion in the domain of NMR application, and important contributions to future structural genomics efforts can be anticipated...
  49. ncbi request reprint A site-specific low-enrichment (15)N,(13)C isotope-labeling approach to unambiguous NMR spectral assignments in nucleic acids
    Anh Tuân Phan
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center New York, New York 10021, USA
    J Am Chem Soc 124:1160-1. 2002
    ..This simple and cost-effective methodology is demonstrated on the d(GGGTTCAGG) DNA sequence, which forms a dimeric G-quadruplex containing G.G.G.G tetrads sandwiched between G.(C-A) triads...
  50. ncbi request reprint Identifying hydrogen bond alignments in multistranded DNA architectures by NMR
    Ananya Majumdar
    Cellular Biochemistry and Biophysics Department, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
    Acc Chem Res 35:1-11. 2002
    ..We demonstrate the utility of these methods for identifying hydrogen bonds in two quadruplex DNA structures, containing triad, tetrad, and hexad motifs involving Watson-Crick, G.G and sheared G.A mismatch base pairing...
  51. ncbi request reprint Two-repeat human telomeric d(TAGGGTTAGGGT) sequence forms interconverting parallel and antiparallel G-quadruplexes in solution: distinct topologies, thermodynamic properties, and folding/unfolding kinetics
    Anh Tuân Phan
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    J Am Chem Soc 125:15021-7. 2003
    ....
  52. ncbi request reprint Recognition of small interfering RNA by a viral suppressor of RNA silencing
    Keqiong Ye
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nature 426:874-8. 2003
    ..Our structure provides an illustration of siRNA sequestering by a viral protein...
  53. ncbi request reprint Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+-induced conformational stabilization
    Stephen W Pitt
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    J Mol Biol 338:7-16. 2004
    ..The combined conformational analysis of TAR under three states reveals that ligands and divalent ions can stabilize similar RNA global conformations through distinct interactions involving different hydrogen bond alignments in the RNA...
  54. ncbi request reprint Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation
    Alexander Serganov
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nat Struct Mol Biol 12:218-24. 2005
    ..We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions...
  55. 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...
  56. pmc An interlocked dimeric parallel-stranded DNA quadruplex: a potent inhibitor of HIV-1 integrase
    Anh Tuân Phan
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 102:634-9. 2005
    ..Finally, we propose a model, based on molecular docking approaches, for positioning the 93del dimeric DNA quadruplex within a basic channel/canyon formed between subunits of a dimer of dimers of HIV-1 integrase...
  57. ncbi request reprint Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs
    Alexander Serganov
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Chem Biol 11:1729-41. 2004
    ..Recognition specificity is associated with Watson-Crick pairing of the encapsulated adenine and guanine ligands with uridine and cytosine, respectively...
  58. ncbi request reprint Crystallographic structure of the nuclease domain of 3'hExo, a DEDDh family member, bound to rAMP
    Yuan Cheng
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    J Mol Biol 343:305-12. 2004
    ....
  59. 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
    ....
  60. pmc Crystallographic identification of Ca2+ and Sr2+ coordination sites in synaptotagmin I C2B domain
    Yuan Cheng
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Protein Sci 13:2665-72. 2004
    ..In the presence of Sr(2+), which is also capable of triggering exocytosis, but with lower efficiency, only one cation binding site (site 1) was occupied in the crystallographic structure...
  61. ncbi request reprint Propeller-type parallel-stranded G-quadruplexes in the human c-myc promoter
    Anh Tuân Phan
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    J Am Chem Soc 126:8710-6. 2004
    ..The central loop contains two or six residues, while the two other loops contain only one residue...
  62. ncbi request reprint Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain
    Jin Biao Ma
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York 10021, USA
    Nature 429:318-22. 2004
    ....
  63. ncbi request reprint Specific recognition of rpsO mRNA and 16S rRNA by Escherichia coli ribosomal protein S15 relies on both mimicry and site differentiation
    Nathalie Mathy
    UPR9073 du CNRS, Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
    Mol Microbiol 52:661-75. 2004
    ..However, specific S15-rpsO mRNA interactions can also be found, probably with A(-46) in loop L1 of the pseudoknot, demonstrating that mimicry between the two targets is limited...
  64. ncbi request reprint An efficient system for small protein expression and refolding
    Yuan Cheng
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Biochem Biophys Res Commun 317:401-5. 2004
    ..The final product yielded well-resolved NMR spectra, with a topology corresponding to the natural product. We conclude that GB1 not only increases the expression level but also enhances the refolding of small proteins...
  65. ncbi request reprint Two-repeat Tetrahymena telomeric d(TGGGGTTGGGGT) Sequence interconverts between asymmetric dimeric G-quadruplexes in solution
    Anh Tuân Phan
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    J Mol Biol 338:93-102. 2004
    ..In contrast to the human telomere counterpart, the proportions of the two forms here are similar for a wide range of temperatures; their unfolding rates are also similar, with an activation enthalpy of 153 kJ/mol...
  66. ncbi request reprint Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings
    Hashim M Al-Hashimi
    Cellular Biochemistry and Biophysics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    J Mol Biol 315:95-102. 2002
    ..These results demonstrate the utility of RDC-NMR for simultaneously characterizing RNA tertiary dynamics and average conformation, and indicate an avenue for TAR complex formation involving tertiary structure capture...
  67. ncbi request reprint Kurt Wüthrich and NMR of biological macromolecules
    Arthur G Palmer
    Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10025, USA
    Structure 10:1603-4. 2002
    ..Wüthrich shared the prize with John B. Fenn and Koichi Tanaka, who were recognized for the development of ionization methods for the analysis of proteins using mass spectrometry...

Research Grants65

  1. DNA/RNA G-Quadruplexes: Structures, Transitions and Recognition
    Dinshaw J Patel; Fiscal Year: 2010
    ....
  2. MOLECULAR BASIS OF GLYCOSPHINGOLIPID BINDING SPECIFICITY
    Dinshaw J Patel; Fiscal Year: 2010
    ..using structural, dynamical, and mutational approaches by taking advantage of the structural expertise of the Dinshaw Patel (Sloan-Kettering Institute, NY) and the molecular biological and glycosphingolipid expertise of the Rhoderick ..
  3. MOLECULAR EVENTS IN MAMMARY/TESTES TUMOR CARCINOGENESIS
    Dinshaw Patel; Fiscal Year: 2003
    ..dG-dC) steps and linked platinum intercalator complexes. Overall, our research should contribute to the development of structure-mutagenesis relationships in chemical carcinogenesis. ..
  4. MULTI-STRANDED DNA STRUCTURES: TRIADS TETRADS & HEXADS
    Dinshaw Patel; Fiscal Year: 2003
    ..G- quadruplexes represent an attractive anti-tumor drug design target since the reverse transcriptase replicative activity of telomerase has an absolute requirement for competing single-stranded telomeric ends. ..
  5. TUMORIGENIC DNA DAMAGE AND PEPTIDE-RNA RECOGNITION
    Dinshaw Patel; Fiscal Year: 2002
    ..Such studies should provide insights into the recognition and discrimination of damaged substrates by the repair machinery. ..
  6. ANTITUMOR DRUG DNA AND DNA APTAMER COMPLEXES IN SOLUTION
    Dinshaw Patel; Fiscal Year: 2002
    ....
  7. siRNA-Mediated Silencing of Viral Infection & Viral Suppressors of RNA Silencing
    Dinshaw J Patel; Fiscal Year: 2010
    ..abstract_text> ..
  8. REPLICATION OF OXIDATIVE LESIONS BY BYPASS POLYMERASES
    Dinshaw Patel; Fiscal Year: 2009
    ..abstract_text> ..
  9. MOLECULAR BASIS OF GLYCOSPHINGOLIPID BINDING SPECIFICITY
    Dinshaw Patel; Fiscal Year: 2009
    ..using structural, dynamical, and mutational approaches by taking advantage of the structural expertise of the Dinshaw Patel (Sloan-Kettering Institute, NY) and the molecular biological and glycosphingolipid expertise of the Rhoderick ..
  10. PROTEIN-RNA RECOGNITION IN NEURODEGENERATIVE SYNDROMES
    Dinshaw Patel; Fiscal Year: 2007
    ..abstract_text> ..
  11. REPLICATION OF OXIDATIVE LESIONS BY BYPASS POLYMERASES
    Dinshaw Patel; Fiscal Year: 2007
    ..abstract_text> ..
  12. MOLECULAR BASIS OF GLYCOSPHINGOLIPID BINDING SPECIFICITY
    Dinshaw Patel; Fiscal Year: 2007
    ..using structural, dynamical, and mutational approaches by taking advantage of the structural expertise of the Dinshaw Patel (Sloan-Kettering Institute, NY) and the molecular biological and glycosphingolipid expertise of the Rhoderick ..
  13. RNA REGULATORY DOMAINS: FOLDING, RECOGNITION & CATALYSIS
    Dinshaw Patel; Fiscal Year: 2007
    ....
  14. Multistranded DNAs: Structures, Transitions, Recognition
    Dinshaw Patel; Fiscal Year: 2007
    ..Parallel structure-energetics studies will be undertaken on two repeat centromeric sequences. ..
  15. DNA ARCHITECTURE AND CHEMOTHERAPEUTIC RECOGNITION
    Dinshaw Patel; Fiscal Year: 1993
    ..The role of neocarzinostatin cofactor in ligand-protein and ligand-DNA interactions will be pursued in the present application...
  16. ANTITUMOR DRUG-DNA COMPLEXES IN SOLUTION
    Dinshaw Patel; Fiscal Year: 1993
    ..In the longer run, these studies will be extended to antitumor drug recognition by other higher order DNA structures...
  17. siRNA-Mediated Silencing of Viral Infection & Viral Suppressors of RNA Silencing
    Dinshaw Patel; Fiscal Year: 2007
    ....