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Our Science – Zhurkin Website

Victor B. Zhurkin, Ph.D.

Selected Publications

1)  Cui F, Zhurkin VB.
Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest.
Nucleic Acids Res. 42: 836-47, 2014.
2)  Zhurkin VB, Olson WK.
Can nucleosomal DNA be described by an elastic model?: Comment on "Sequence-dependent collective properties of DNAs and their role in biological systems" by Pasquale De Santis and Anita Scipioni.
Phys Life Rev. 10: 70-2, 2013.
3)  Nikitina T, Wang D, Gomberg M, Grigoryev SA, Zhurkin VB.
Combined micrococcal nuclease and exonuclease III digestion reveals precise positions of the nucleosome core/linker junctions: implications for high-resolution nucleosome mapping.
J. Mol. Biol. 425: 1946-60, 2013.
4)  Macvanin M, Edgar R, Cui F, Trostel A, Zhurkin V, Adhya S.
Noncoding RNAs binding to the nucleoid protein HU in Escherichia coli.
J. Bacteriol. 194: 6046-55, 2012.
5)  Karamychev VN, Wang D, Mazur SJ, Appella E, Neumann RD, Zhurkin VB, Panyutin IG.
Radioprobing the conformation of DNA in a p53-DNA complex.
Int. J. Radiat. Biol. 88: 1039-45, 2012.
6)  Cui F, Cole HA, Clark DJ, Zhurkin VB.
Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing.
Nucleic Acids Res. 40: 10753-64, 2012.
7)  Cui F, Sirotin MV, Zhurkin VB.
Impact of Alu repeats on the evolution of human p53 binding sites.
Biol. Direct. 6: 2, 2011.
8)  Zhurkin VB.
The first thirty years of nucleosome positioning: comment on.
Phys Life Rev. 8: 64-6; discussion 69-72, 2011.
9)  Olson WK, Zhurkin VB.
Working the kinks out of nucleosomal DNA.
Curr. Opin. Struct. Biol. 21: 348-57, 2011.
10)  Sahu G, Wang D, Chen CB, Zhurkin VB, Harrington RE, Appella E, Hager GL, Nagaich AK.
p53 binding to nucleosomal DNA depends on the rotational positioning of DNA response element.
J. Biol. Chem. 285: 1321-32, 2010.
11)  Wang D, Ulyanov NB, Zhurkin VB.
Sequence-dependent Kink-and-Slide deformations of nucleosomal DNA facilitated by histone arginines bound in the minor groove.
J. Biomol. Struct. Dyn. 27: 843-59, 2010.
12)  Cui F, Zhurkin VB.
Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro.
J. Biomol. Struct. Dyn. 27: 821-41, 2010.
13)  Cui F, Zhurkin VB.
Distinctive sequence patterns in metazoan and yeast nucleosomes: Implications for linker histone binding to AT-rich and methylated DNA.
Nucleic Acids Res. 37: 2818-29, 2009.
14)  Kaluzhny DN, Timoshin VV, Borisova OF, Zhurkin VB, Florentiev VL, Shchyolkina AK.
Intramolecular recombination R-triplex in solution: stabilization by bis-intercalator YOYO.
J. Biomol. Struct. Dyn. 26: 301-6, 2008.
15)  Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ.
nuScore: a web-interface for nucleosome positioning predictions.
Bioinformatics. 24: 1456-8, 2008.
16)  Tolstorukov MY, Colasanti AV, McCandlish DM, Olson WK, Zhurkin VB.
A Novel Roll-and-Slide Mechanism of DNA Folding in Chromatin: Implications for Nucleosome Positioning.
J. Mol. Biol. 371: 725-38, 2007.
17)  Cui F, Sirotin M, Zhurkin V.
The p53-DNA Binding in the Chromatin Context: p53-induced Activation of the Apoptotic and Cell Cycle Arrest Genes (Albany 2007, The 15-th Conversation).
Volume JBSD, 24 (6). p. 644-645. [Meeting Proceeding]
18)  Cui F, Sirotin M, Zhurkin V.
Comparative Sequence Analysis of the p53 Response Elements Associated with Apoptosis and Cell Cycle Arrest (2006 International Conference on Bioinformatics & Computational Biology (BIOCOMP’06).
Arabnia H, Valafar H, eds.
. p. 48-55. [Meeting Proceeding]
19)  Shen WH, Wang J, Wu J, Zhurkin VB, Yin Y.
Mitogen-activated protein kinase phosphatase 2: a novel transcription target of p53 in apoptosis.
Cancer Res. 66: 6033-9, 2006.
20)  Shchyolkina AK, Kaluzhny DN, Arndt-Jovin DJ, Jovin TM, Zhurkin VB.
Recombination R-triplex: H-bonds contribution to stability as revealed with minor base substitutions for adenine.
Nucleic Acids Res. 34: 3239-45, 2006.
21)  Zhurkin V, Tolstorukov M, Xu F, Colasanti A, Olson W.
Ohyama T, eds.
Sequence dependent variability of B-DNA: An update on bending and curvature. In: DNA Conformation and Transcription.
Austin, TX: LANDES Bioscience; 2005. p. 1-17 [Book Chapter]
22)  Tolstorukov MY, Virnik KM, Adhya S, Zhurkin VB.
A-tract clusters may facilitate DNA packaging in bacterial nucleoid.
Nucleic Acids Res. 33: 3907-18, 2005.
23)  Staib F, Robles AI, Varticovski L, Wang XW, Zeeberg BR, Sirotin M, Zhurkin VB, Hofseth LJ, Hussain SP, Weinstein JN, Galle PR, Harris CC.
The p53 tumor suppressor network is a key responder to microenvironmental components of chronic inflammatory stress.
Cancer Res. 65: 10255-64, 2005.
24)  Liu M, Tolstorukov M, Zhurkin V, Garges S, Adhya S.
A mutant spacer sequence between -35 and -10 elements makes the Plac promoter hyperactive and cAMP receptor protein-independent.
Proc Natl Acad Sci U S A. 101: 6911-6, 2004.
25)  Semsey S, Tolstorukov MY, Virnik K, Zhurkin VB, Adhya S.
DNA trajectory in the Gal repressosome.
Genes Dev. 18: 1898-907, 2004.
26)  Shchyolkina AK, Kaluzhny DN, Borisova OF, Hawkins ME, Jernigan RL, Jovin TM, Arndt-Jovin DJ, Zhurkin VB.
Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin.
Nucleic Acids Res. 32: 432-40, 2004.
27)  Tolstorukov MY, Jernigan RL, Zhurkin VB.
Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching.
J Mol Biol. 337: 65-76, 2004.
28)  Virnik K, Lyubchenko YL, Karymov MA, Dahlgren P, Tolstorukov MY, Semsey S, Zhurkin VB, Adhya S.
"Antiparallel" DNA loop in gal repressosome visualized by atomic force microscopy.
J Mol Biol. 334: 53-63, 2003.
29)  Zhurkin VB, Sirotin M, Robles A, Rauf K, Jernigan RL, Zhurkin M.
Distribution of p53 Sites in the Human Genome Reflects the Versatility of p53 Binding and Its Tumor Suppressor Functions.
J. Biomol. Struct. Dynam. 20: 858-859, 2003.
30)  Karamychev VN, Tatusov A, Komissarova N, Kashlev M, Neumann RD, Zhurkin VB, Panyutin IG.
Iodine-125 radioprobing of E. coli RNA polymerase transcription elongation complexes.
Methods Enzymol. 371: 106-20, 2003.
31)  Wu Z, Delaglio F, Tjandra N, Zhurkin VB, Bax A.
Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy.
J Biomol NMR. 26: 297-315, 2003.
32)  Geanacopoulos M, Vasmatzis G, Zhurkin VB, Adhya S.
Gal repressosome contains an antiparallel DNA loop.
Nat Struct Biol. 8: 432-6, 2001.
33)  Tolstorukov MY, Ivanov VI, Malenkov GG, Jernigan RL, Zhurkin VB.
Sequence-dependent B<-->A transition in DNA evaluated with dimeric and trimeric scales.
Biophys J. 81: 3409-21, 2001.
34)  Murphy EC, Zhurkin VB, Louis JM, Cornilescu G, Clore GM.
Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation.
J Mol Biol. 312: 481-99, 2001.
35)  Karamychev VN, Panyutin IG, Neumann RD, Zhurkin VB.
DNA and RNA folds in transcription complex as evidenced by iodine-125 radioprobing.
J. Biomol. Struct. Dyn, Conversation 11. 1: 155-67, 2000.
36)  Wu Z, Delaglio F, Tjandra N, Zhurkin VB, Bax A.
DNA bending and sugar switching.
J. Biomol. Struct. Dyn. Conversation 11. 2: 317-25, 2000.
37)  Olson WK, Zhurkin VB.
Modeling DNA deformations.
Curr Opin Struct Biol. 10: 286-97, 2000.
38)  Malkov VA, Panyutin IG, Neumann RD, Zhurkin VB, Camerini-Otero RD.
Radioprobing of a RecA-three-stranded DNA complex with iodine 125: evidence for recognition of homology in the major groove of the target duplex.
J Mol Biol. 299: 629-40, 2000.
39)  Karamychev VN, Zhurkin VB, Garges S, Neumann RD, Panyutin IG.
Detecting the DNA kinks in a DNA-CRP complex in solution with iodine-125 radioprobing.
Nat Struct Biol. 6: 747-50, 1999.
40)  Kosikov KM, Gorin AA, Zhurkin VB, Olson WK.
DNA stretching and compression: large-scale simulations of double helical structures.
J Mol Biol. 289: 1301-26, 1999.
41)  Nagaich AK, Zhurkin VB, Durell SR, Jernigan RL, Appella E, Harrington RE.
p53-induced DNA bending and twisting: p53 tetramer binds on the outer side of a DNA loop and increases DNA twisting.
Proc Natl Acad Sci U S A. 96: 1875-80, 1999.
42)  Mandel-Gutfreund Y, Margalit H, Jernigan RL, Zhurkin VB.
A role for CH...O interactions in protein-DNA recognition.
J Mol Biol. 277: 1129-40, 1998.
43)  Appella E, Nagaich AK, Zhurkin VB, Harrington RE.
Analysis of the interaction between the p53 binding domain and the p21/CiP1 DNA response element: a novel architectural organization.
J Protein Chem. 17: 527-8, 1998.
44)  Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB.
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes.
Proc Natl Acad Sci U S A. 95: 11163-8, 1998.
45)  Nagaich AK, Zhurkin VB, Sakamoto H, Gorin AA, Clore GM, Gronenborn AM, Appella E, Harrington RE.
Architectural accommodation in the complex of four p53 DNA binding domain peptides with the p21/waf1/cip1 DNA response element.
J Biol Chem. 272: 14830-41, 1997.
46)  Teplukhin AV, Zhurkin VB, Dzhernigan R, Poltev VI.
[Modeling DNA hydration using the Monte Carlo method. Interaction of adenines with water in a nonglycoside A-tract grove stabilizes the B'- conformation].
Mol Biol (Mosk). 30: 121-35, 1996.
47)  Gorin AA, Zhurkin VB, Olson WK.
B-DNA twisting correlates with base-pair morphology.
J Mol Biol. 247: 34-48, 1995.
48)  Ivanov VI, Minchenkova LE, Chernov BK, McPhie P, Ryu S, Garges S, Barber AM, Zhurkin VB, Adhya S.
CRP-DNA complexes: inducing the A-like form in the binding sites with an extended central spacer.
J Mol Biol. 245: 228-40, 1995.
49)  Kim MG, Zhurkin VB, Jernigan RL, Camerini-Otero RD.
Probing the structure of a putative intermediate in homologous recombination: the third strand in the parallel DNA triplex is in contact with the major groove of the duplex.
J Mol Biol. 247: 874-89, 1995.
50)  Zhurkin VB, Raghunathan G, Ulyanov NB, Camerini-Otero RD, Jernigan RL.
A parallel DNA triplex as a model for the intermediate in homologous recombination.
J Mol Biol. 239: 181-200, 1994.
51)  Barber AM, Zhurkin VB, Adhya S.
CRP-binding sites: evidence for two structural classes with 6-bp and 8-bp spacers.
Gene. 130: 1-8, 1993.
52)  Ulyanov NB, Sarma MH, Zhurkin VB, Sarma RH.
Decreased interstrand H2-H1' distance in the GC-rich part of the duplex d(CCTCAAACTCC).d(GGAGTTTGAGG) in solution at low temperature: proton nuclear magnetic resonance investigation.
Biochemistry. 32: 6875-83, 1993.
53)  Olson WK, Marky NL, Jernigan RL, Zhurkin VB.
Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA.
J Mol Biol. 232: 530-54, 1993.
54)  Ulyanov NB, Gorin AA, Zhurkin VB, Chen BC, Sarma MH, Sarma RH.
Systematic study of nuclear Overhauser effects vis-a-vis local helical parameters, sugar puckers, and glycosidic torsions in B DNA: insensitivity of NOE to local transitions in B DNA oligonucleotides due to internal structural compensations.
Biochemistry. 31: 3918-30, 1992.
55)  Zhurkin VB, Ulyanov NB, Gorin AA, Jernigan RL.
Static and statistical bending of DNA evaluated by Monte Carlo simulations.
Proc Natl Acad Sci U S A. 88: 7046-50, 1991.
56)  Gorin AA, Ul'ianov NB, Zhurkin VB.
[S-N transition of the saccharide ring in B-form DNA].
Mol Biol (Mosk). 24: 1300-13, 1990.
57)  Shliakhtenko LS, Liubchenko IuL, Chernov BK, Zhurkin VB.
[The effect of temperature and ionic strength on the electrophoretic motility of synthetic DNA fragments].
Mol Biol (Mosk). 24: 79-95, 1990.
58)  Barber AM, Zhurkin VB.
CAP binding sites reveal pyrimidine-purine pattern characteristic of DNA bending.
J Biomol Struct Dyn. 8: 213-32, 1990.
59)  Dickerson RE, Bansal M, Calladine CR, Diekmann S, Hunter WN, Kennard O, Lavery R, Nelson HCM, Olson WK, Saenger W, Shakked Z, Sklenar H, Soumpasis DM, Tung CS, Kitzing EV, Wang AH, Zhurkin VB.
Definitions and nomenclature of nucleic acid structure parameters.
EMBO J. 8: 1-4, 1989.
60)  Dickerson RE, Bansal M, Calladine CR, Diekmann S, Hunter WN, Kennard O, Lavery R, Nelson HCM, Olson WK, Saenger W, Shakked Z, Sklenar H, Soumpasis DM, Tung CS, Kitzing EV, Wang AH, Zhurkin VB.
Definitions of nucleic acid structure parameters.
J. Mol. Biol. 205: 787-91, 1989.
61)  Yavachev LP, Georgiev OI, Braga EA, Avdonina TA, Bogomolova AE, Zhurkin VB, Nosikov VV, Hadjiolov AA.
Nucleotide sequence analysis of the spacer regions flanking the rat rRNA transcription unit and identification of repetitive elements.
Nucleic Acids Res. 14: 2799-810, 1986.
62)  Pohle W, Fritzsche H, Zhurkin VB.
The phosphate geometry in ordered nucleic acid structures: are the results of infrared linear dichroism and x-ray fiber diffraction really incompatible?.
Comments Mol. Cell. Biophys. 3: 179-94, 1986.
63)  Zhurkin VB.
Sequence-dependent bending of DNA and phasing of nucleosomes.
J Biomol Struct Dyn. 2: 785-804, 1985.
64)  Braga EA, Avdonina TA, Zhurkin VB, Nosikov VV.
Structural organization of rat ribosomal RNA genes: interspersed sequences and their putative role in the alignment of nucleosomes.
Gene. 36: 249-62, 1985.
65)  Ul'ianov NB, Zhurkin VB.
[Anisotropic flexibility of DNA depends on the base sequence. Conformation calculations of double-stranded tetranucleotides AAAA:TTTT, (AATT)2, (TTAA)2, GGGG:CCCC, (GGCC)2, (CCGG)2].
Mol Biol (Mosk). 18: 1664-85, 1984.
66)  Ulyanov NB, Zhurkin VB.
Sequence-dependent anisotropic flexibility of B-DNA. A conformational study.
J Biomol Struct Dyn. 2: 361-85, 1984.
67)  Pohle W, Zhurkin VB, Fritzsche H.
The DNA phosphate orientation. Infrared data and energetically favorable structures.
Biopolymers. 23: 2603-22, 1984.
68)  Zhurkin VB.
[Local mobility of the DNA double helix. Comparison of conformational analysis with experiments].
Mol Biol (Mosk). 17: 622-38, 1983.
69)  Zhurkin VB.
Specific alignment of nucleosomes on DNA correlates with periodic distribution of purine-pyrimidine and pyrimidine-purine dimers.
FEBS Lett. 158: 293-7, 1983.
70)  Lysov IuP, Zhurkin VB, Ivanov VI, Florent'ev VL.
[Conformational possibilities of the regular single-stranded polyribonucleotides].
Mol Biol (Mosk). 16: 1063-74, 1982.
71)  Ul'ianov NB, Zhurkin VB.
[Study of the flexibility of complementary dinucleoside phosphates by the Monte-Carlo method].
Mol Biol (Mosk). 16: 1075-85, 1982.
72)  Ul'yanov NB, Zhurkin VB, Ivanov VI.
Analysis of the DNA conformational flexibility for the different nucleotide sequences.
Stud Biophys. 87: 99-100, 1982.
73)  Lysov YP, Zavgorodnii SG, Zhurkin VB, Florent'ev VL.
Conformational properties of anhydronucleosides.
Bioorg. Khim. 8: 1535-53, 1982.
74)  Zhurkin VB.
Periodicity in DNA primary structure and specific alignment of nucleosomes.
Stud. Biophys. 87: 151-2, 1982.
75)  Zhurkin VB, Lysov YP, Florentiev VL, Ivanov VI.
Torsional flexibility of B-DNA as revealed by conformational analysis.
Nucleic Acids Res. 10: 1811-30, 1982.
76)  Johnson BB, Dahl KS, Tinoco I, Ivanov VI, Zhurkin VB.
Correlations between deoxyribonucleic acid structural parameters and calculated circular dichroism spectra.
Biochemistry. 20: 73-8, 1981.
77)  Zhurkin VB.
Periodicity in DNA primary structure is defined by secondary structure of the coded protein.
Nucleic Acids Res. 9: 1963-71, 1981.
78)  Zhurkin VB, Poltev VI, Florent'ev VL.
[Atom--atomic potential functions for conformational calculations of nucleic acids].
Mol Biol (Mosk). 14: 1116-30, 1980.
79)  Zhurkin VB, Lysov YP, Florentiev VO, Ivanov VI.
Flexibility of B-DNA Conformational Study.
Stud. Biophys. 79: 27-28, 1980.
80)  Zhurkin VB, Lysov YP, Ivanov VI.
Interaction of spermine with different forms of DNA. A conformational study.
Biopolymers. 19: 1415-34, 1980.
81)  Pohle W, Fritzsche H, Zhurkin VB, Ivanov VI.
The DNA backbone geometry as obtained by infrared linear dichroism and conforamtional analysis.
Stud. Biophys. 79: 73-74, 1980.
82)  Lysov IuP, Zhurkin VB, Tychinskaia LIu, Florent'ev VL.
[Eight types of stacking interaction in dinucleotides. Conformational analysis of ApA, ApC, CpA, CpC, GpG].
Mol Biol (Mosk). 13: 1161-88, 1979.
83)  Zhurkin VB, Lysov YP, Ivanov VI.
Anisotropic flexibility of DNA and the nucleosomal structure.
Nucleic Acids Res. 6: 1081-96, 1979.
84)  Ivanov VI, Zhurkin VB, Zavriev SK, Lysov YP, Minchenkova LE, Minyat EE, Frank-Kamenetskii MD, Schyolkina AK.
Conformational possibilities of double-helical nucleic acids: theory and experiment.
Int. J. Quant. Chem. 16: 189-201, 1979.
85)  Zhurkin VB, Lysov YP, Ivanov VI.
Conformational study of spermine-DNA interaction with different forms of DNA.
Stud. Biophys. 67: 91-2, 1978.
86)  Zhurkin VB, Lysov YP, Ivanov VI.
Different families of double-stranded conformations of DNA as revealed by computer calculations.
Biopolymers. 17: 377-412, 1978.
87)  Sharonov YA, Mineyev AP, Livshitz MA, Sharonova NA, Zhurkin VB, Lysov YP.
Magnetic circular dichroism studies of myoglobin, hemoglobin and peroxidase at room and low temperatures. Ferrous high spin derivatives.
Biophys Struct Mech. 4: 139-58, 1978.
88)  Zhurkin VB, Lysov YP, Ivanov VI.
Conformational possibilities of double-helical DNA.
Studia Biophys. 55: 5-13, 1976.
89)  Zhurkin VB, Lysov IuP, Ivanov VI, Malenkov GG.
[A stereochemical model for DNA-Na+ (H20) complex].
Mol Biol (Mosk). 9: 95-104, 1975.
90)  Zhurkin VB, Lysov YP, Ivanov VI, Malenkov GG.
A three-dimensional model of the DNA-hydrated Na+ complex.
Mol. Biol. 9: 75-82, 1975.
91)  Zhurkin VB, Lysov YP, Ivanov VI.
Computer analysis of conformational possibilities of double-helical DNA.
FEBS Lett. 59: 44-7, 1975.
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This page was last updated on 5/21/2014.