Victor B Zhurkin

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Distinctive sequence patterns in metazoan and yeast nucleosomes: implications for linker histone binding to AT-rich and methylated DNA
    Feng Cui
    Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    Nucleic Acids Res 37:2818-29. 2009
  2. pmc Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing
    Feng Cui
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Building 37, Room 3035A, Convent Dr, Bethesda, MD 20892, USA
    Nucleic Acids Res 40:10753-64. 2012
  3. pmc Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest
    Feng Cui
    Thomas H Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive Rochester, NY 14623, USA and Laboratory of Cell Biology, National Cancer Institute, NIH Bg 37, Room 3035A, Convent Dr, Bethesda, MD 20892, USA
    Nucleic Acids Res 42:836-47. 2014
  4. pmc Recombination R-triplex: H-bonds contribution to stability as revealed with minor base substitutions for adenine
    Anna K Shchyolkina
    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
    Nucleic Acids Res 34:3239-45. 2006
  5. pmc Radioprobing the conformation of DNA in a p53-DNA complex
    Valeri N Karamychev
    Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD, USA
    Int J Radiat Biol 88:1039-45. 2012
  6. pmc Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin
    Anna K Shchyolkina
    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
    Nucleic Acids Res 32:432-40. 2004
  7. ncbi request reprint Intramolecular recombination R-triplex in solution: stabilization by bis-intercalator YOYO
    Dmitry N Kaluzhny
    Engelhardt Institute of Molecular Biology RASc, Vavilova 32, 119991 Moscow, Russia
    J Biomol Struct Dyn 26:301-6. 2008
  8. pmc DNA trajectory in the Gal repressosome
    Szabolcs Semsey
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genes Dev 18:1898-907. 2004
  9. pmc Impact of Alu repeats on the evolution of human p53 binding sites
    Feng Cui
    Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    Biol Direct 6:2. 2011
  10. pmc p53 binding to nucleosomal DNA depends on the rotational positioning of DNA response element
    Geetaram Sahu
    Laboratory of Chemistry, Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA
    J Biol Chem 285:1321-32. 2010

Collaborators

Detail Information

Publications17

  1. pmc Distinctive sequence patterns in metazoan and yeast nucleosomes: implications for linker histone binding to AT-rich and methylated DNA
    Feng Cui
    Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    Nucleic Acids Res 37:2818-29. 2009
    ..The same mechanism accounts for the high affinity of LH to methylated DNA-a feature critical for stabilization of the higher-order structure of chromatin and for repression of transcription...
  2. pmc Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing
    Feng Cui
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Building 37, Room 3035A, Convent Dr, Bethesda, MD 20892, USA
    Nucleic Acids Res 40:10753-64. 2012
    ..This unusual pattern suggests that the +1 nucleosomes might be prone to sliding, thereby facilitating transcription...
  3. pmc Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest
    Feng Cui
    Thomas H Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive Rochester, NY 14623, USA and Laboratory of Cell Biology, National Cancer Institute, NIH Bg 37, Room 3035A, Convent Dr, Bethesda, MD 20892, USA
    Nucleic Acids Res 42:836-47. 2014
    ..The distinct chromatin organization of the CCA response elements appears to be one of the key factors facilitating p53-DNA binding and subsequent activation of genes associated with cell cycle arrest. ..
  4. pmc Recombination R-triplex: H-bonds contribution to stability as revealed with minor base substitutions for adenine
    Anna K Shchyolkina
    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
    Nucleic Acids Res 34:3239-45. 2006
    ..The observed energy advantage of a 'correct' base in the third strand opposite the Watson-Crick base pair may be a powerful mechanism for securing selectivity of recognition between the single strand and the duplex...
  5. pmc Radioprobing the conformation of DNA in a p53-DNA complex
    Valeri N Karamychev
    Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD, USA
    Int J Radiat Biol 88:1039-45. 2012
    ..In contrast, gel electrophoresis and electron microscopy data showed strong DNA bending and overtwisting upon binding to the native p53 tetramer...
  6. pmc Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin
    Anna K Shchyolkina
    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
    Nucleic Acids Res 32:432-40. 2004
    ..We consider the data in the light of alternative 'branch migration' and 'strand exchange' structures and discuss why these are less likely than the R-type triplex...
  7. ncbi request reprint Intramolecular recombination R-triplex in solution: stabilization by bis-intercalator YOYO
    Dmitry N Kaluzhny
    Engelhardt Institute of Molecular Biology RASc, Vavilova 32, 119991 Moscow, Russia
    J Biomol Struct Dyn 26:301-6. 2008
    ..Further increase in the YOYO concentration resulted in binding of up to five YOYO molecules to R(2AP)CW triplex and up to six YOYO molecules to CW hairpin...
  8. pmc DNA trajectory in the Gal repressosome
    Szabolcs Semsey
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genes Dev 18:1898-907. 2004
    ..In this structure the center of the HU-binding site is located at the apex of the DNA loop. The approach reported here can be used to distinguish between otherwise indistinguishable DNA trajectories in complex nucleoprotein machines...
  9. pmc Impact of Alu repeats on the evolution of human p53 binding sites
    Feng Cui
    Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    Biol Direct 6:2. 2011
    ..The relationship between these BSs and functional p53 response elements (REs) remains unknown, however. We sought to understand whether the p53 REs also reside in transposable elements and particularly in the most-abundant Alu repeats...
  10. pmc p53 binding to nucleosomal DNA depends on the rotational positioning of DNA response element
    Geetaram Sahu
    Laboratory of Chemistry, Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA
    J Biol Chem 285:1321-32. 2010
    ..Our observations indicate that the orientation of the binding sites on a nucleosome may play a significant role in the initial p53-DNA recognition and subsequent cofactor recruitment...
  11. pmc A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning
    Michael Y Tolstorukov
    National Cancer Institute, Bethesda, MD 20892, USA
    J Mol Biol 371:725-38. 2007
    ..The close correspondence between the predicted and observed nucleosome locations demonstrates the potential advantage of our "structural" approach in the computer mapping of nucleosome positioning...
  12. pmc A-tract clusters may facilitate DNA packaging in bacterial nucleoid
    Michael Y Tolstorukov
    Laboratory of Experimental and Computational Biology, National Cancer Institute Bethesda, MD 20892, USA
    Nucleic Acids Res 33:3907-18. 2005
    ....
  13. pmc Sequence-dependent Kink-and-Slide deformations of nucleosomal DNA facilitated by histone arginines bound in the minor groove
    Difei Wang
    Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    J Biomol Struct Dyn 27:843-59. 2010
    ....
  14. ncbi request reprint Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching
    Michael Y Tolstorukov
    Laboratory of Experimental and Computational Biology, National Cancer Institute, National Institutes of Health, Bg 12B, Rm B116, Bethesda, MD 20892 5677, USA
    J Mol Biol 337:65-76. 2004
    ..The sequence preference for the B-to-A sugar repuckering, observed for pyrimidines, suggests that the described DNA deformations contribute to specificity of the protein-DNA recognition in the minor groove...
  15. doi request reprint Combined micrococcal nuclease and exonuclease III digestion reveals precise positions of the nucleosome core/linker junctions: implications for high-resolution nucleosome mapping
    Tatiana Nikitina
    Laboratory of Cell Biology, CCR, National Cancer Institute, NIH, Bethesda, MD, USA
    J Mol Biol 425:1946-60. 2013
    ..The same approach can be also used for the precise mapping of the extent of linker DNA protection by H1 and other protein factors associated with nucleosome linkers...
  16. pmc Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro
    Feng Cui
    Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    J Biomol Struct Dyn 27:821-41. 2010
    ..The results presented here may be useful for genome-wide classification of nucleosomes, linking together structural and thermodynamic characteristics of nucleosomes with the underlying DNA sequence patterns guiding their positions...
  17. ncbi request reprint Iodine-125 radioprobing of E. coli RNA polymerase transcription elongation complexes
    Valeri N Karamychev
    Department of Nuclear Medicine, Warren G Magnuson Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, USA
    Methods Enzymol 371:106-20. 2003