V. Zhurkin

发表

Sequence-dependent anisotropic flexibility of B-DNA. A conformational study.

N. Ulyanov, V. Zhurkin, N. B. Ulyanov, 1984, Journal of biomolecular structure & dynamics.

p53-induced DNA bending and twisting: p53 tetramer binds on the outer side of a DNA loop and increases DNA twisting.

V. Zhurkin, R. Jernigan, S. Durell, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Impact of Alu repeats on the evolution of human p53 binding sites

Feng Cui, V. Zhurkin, F. Cui, 2011, Biology Direct.

Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest

Victor B. Zhurkin, Feng Cui, V. Zhurkin, 2013, Nucleic acids research.

A role for CH...O interactions in protein-DNA recognition.

H. Margalit, V. Zhurkin, R. Jernigan, 1998, Journal of molecular biology.

The Role of Structure in Complexes Between the p53 DNA Binding Domain and DNA Response Elements

V. Zhurkin, E. Appella, A. K. Nagaich, 1997 .

Anisotropic flexibility of DNA and the nucleosomal structure.

V. Zhurkin, Y. Lysov, V. Ivanov, 1979, Nucleic acids research.

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes.

V. Zhurkin, W. Olson, A. Gorin, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Modeling DNA deformations.

V. Zhurkin, W. Olson, V B Zhurkin, 2000, Current opinion in structural biology.

Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation.

G M Clore, V. Zhurkin, G. Clore, 2001, Journal of molecular biology.

Static and statistical bending of DNA evaluated by Monte Carlo simulations.

R L Jernigan, N. Ulyanov, V. Zhurkin, 1991, Proceedings of the National Academy of Sciences of the United States of America.

DNA topology in chromatin is defined by nucleosome spacing

V. Zhurkin, Tatiana Nikitina, S. Grigoryev, 2017, Science Advances.

Nucleosome spacing periodically modulates nucleosome chain folding and DNA topology in circular nucleosome arrays

V. Zhurkin, Tatiana Nikitina, S. Grigoryev, 2019, The Journal of Biological Chemistry.

Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures.

V. Zhurkin, R. Ghirlando, Yawen Bai, 2018, Journal of molecular biology.

Noncoding RNAs Binding to the Nucleoid Protein HU in Escherichia coli

Victor Zhurkin, Feng Cui, V. Zhurkin, 2012, Journal of bacteriology.

Non-coding RNAs binding to the nucleoid protein HU in Escherichia 5 coli 6 7

V. Zhurkin, F. Cui, S. Adhya, 2012 .

B-DNA twisting correlates with base-pair morphology.

V. Zhurkin, W. Olson, A. Gorin, 1995, Journal of molecular biology.

DNA stretching and compression: large-scale simulations of double helical structures.

V. Zhurkin, W. Olson, A. Gorin, 1999, Journal of molecular biology.

[Atom--atomic potential functions for conformational calculations of nucleic acids].

V. Zhurkin, V. L. Florent’ev, V. Poltev, 1980, Molekuliarnaia biologiia.

Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions

Howard Y. Chang, V. Zhurkin, W. Greenleaf, 2019, Nature Communications.

Specific alignment of nucleosomes on DNA correlates with periodic distribution of purine—pyrimidine and pyrimidine—purine dimers

V. Zhurkin, V B Zhurkin, 1983, FEBS letters.

Formation of an intramolecular triple-stranded DNA structure monitored by fluorescence of 2-aminopurine or 6-methylisoxanthopterin.

V. Zhurkin, R. Jernigan, T. Jovin, 2004, Nucleic acids research.

A-tract clusters may facilitate DNA packaging in bacterial nucleoid

V. Zhurkin, M. Tolstorukov, S. Adhya, 2005, Nucleic acids research.

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.

V. Zhurkin, W. Olson, 2013, Physics of life reviews.

Intramolecular Recombination R-Triplex in Solution: Stabilization by bis-intercalator YOYO

V. Zhurkin, V. Florentiev, A. Shchyolkina, 2008, Journal of biomolecular structure & dynamics.

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.

V. Zhurkin, R. Jernigan, R. Camerini-Otero, 1995, Journal of molecular biology.

Conformational possibilities of double-helical nucleic acids: Theory and experiment

V. Zhurkin, S. Zavriev, Y. Lysov, 1979 .

Organization of DNA in a bacterial nucleoid

V. Zhurkin, M. Tolstorukov, S. Adhya, 2016, BMC Microbiology.

A New Noncoding RNA Arranges Bacterial Chromosome Organization

V. Zhurkin, Ximiao He, E. Dimitriadis, 2015, mBio.

Polymorphic 30-nm Chromatin Fiber and Linking Number Paradox. Evidence for the Occurrence of Two Distinct Topoisomers

V. Zhurkin, D. Norouzi, 2018, bioRxiv.

DNA–RNA interactions are critical for chromosome condensation in Escherichia coli

V. Zhurkin, S. Adhya, Z. Qian, 2017, Proceedings of the National Academy of Sciences.

62 Distinct nucleosome organization around p53 response elements associated with cell cycle arrest and apoptosis

V. Zhurkin, F. Cui, 2013 .

The methyltransferases METTL 7 A and METTL 7 B confer resistance to thiol-based 1 histone deacetylase inhibitors 2 3

Pedro J. Batista, V. Zhurkin, M. Gottesman, 2022 .

Organization of DNA in a bacterial nucleoid The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters

V. Zhurkin, M. Tolstorukov, S. Adhya, 2016 .

Detecting the DNA kinks in a DNA–CRP complex in solution with iodine-125 radioprobing

V. Zhurkin, S. Garges, I. Panyutin, 1999, Nature Structural Biology.

Novel nucleosomal particles containing core histones and linker DNA but no histone H1

H. A. Cole, V. Zhurkin, Tatiana Nikitina, 2015, Nucleic acids research.

Conformational variability of recombination R-triplex formed by the mammalian telomeric sequence

V. Zhurkin, T. Jovin, D. Arndt-Jovin, 2015, Journal of biomolecular structure & dynamics.

Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching.

Robert L Jernigan, Michael Y Tolstorukov, V. Zhurkin, 2004, Journal of molecular biology.

Systematic study of nuclear Overhauser effects vis-à-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.

V. Zhurkin, A. Gorin, R. Sarma, 1992, Biochemistry.

A mutant spacer sequence between -35 and -10 elements makes the Plac promoter hyperactive and cAMP receptor protein-independent.

Victor Zhurkin, V. Zhurkin, M. Tolstorukov, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy

Ad Bax, Nico Tjandra, Frank Delaglio, 2003, Journal of biomolecular NMR.

DNA Bending and "Structural" Waters in Major and Minor Grooves of A-tracts. Monte Carlo Computer Simulations

Alexander V. Teplukhin, Valery I. Poltev, Victor B. Zhurkin, 2012, 1202.2702.

A parallel DNA triplex as a model for the intermediate in homologous recombination.

V. Zhurkin, R. Jernigan, G. Raghunathan, 1994, Journal of molecular biology.

Sequence-dependent B<-->A transition in DNA evaluated with dimeric and trimeric scales.

V. Zhurkin, R. Jernigan, V. Ivanov, 2001, Biophysical journal.

Satb1integrates DNA sequence,shape, motif densityand torsional stressto differentially bind targets in nucleosome-dense regions

Howard Y. Chang, V. Zhurkin, W. Greenleaf, 2018, bioRxiv.

p53 Binding to Nucleosomal DNA Depends on the Rotational Positioning of DNA Response Element*

V. Zhurkin, E. Appella, G. Hager, 2009, The Journal of Biological Chemistry.

Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions.

Alexander Goncearenco, David Landsman, Alexey K Shaytan, 2016, Journal of molecular biology.

A Structural Model for the P53 Complex with DNA Response Elements: Implications for P53 Function and Future Research Directions

V. Zhurkin, R. Jernigan, S. Durell, 2000 .

Prediction of nucleosome rotational positioning in yeast and human genomes based on sequence-dependent DNA anisotropy

Linlin Chen, Feng Cui, Victor Zhurkin, 2014, BMC Bioinformatics.

Jon Widom, the Scientist

V. Zhurkin, E. Trifonov, 2011 .

Mitogen-activated protein kinase phosphatase 2: a novel transcription target of p53 in apoptosis.

V. Zhurkin, Jing-jing Wu, Yuxin Yin, 2006, Cancer research.

Mitogen-Activated Protein Kinase Phosphatase 2 : A Novel Transcription Target of p 53 in Apoptosis

V. Zhurkin, Jing-jing Wu, Yuxin Yin, 2006 .

Watson–Crick Base Pairs: Character and Recognition

Andrew V. Colasanti, V. Zhurkin, W. Olson, 2008 .

A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning.

Andrew V. Colasanti, Michael Y Tolstorukov, Andrew V Colasanti, 2007, Journal of molecular biology.

DNA Simulation Benchmarks as Revealed by X-Ray Structures

Wilma K. Olson, Victor B. Zhurkin, Guohui Zheng, 2006 .

Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA.

R L Jernigan, V. Zhurkin, W. Olson, 1993, Journal of molecular biology.

The methyltransferases METTL7A and METTL7B confer resistance to thiol-based histone deacetylase inhibitors

Pedro J. Batista, V. Zhurkin, M. Gottesman, 2023, bioRxiv.

CRP-DNA complexes: inducing the A-like form in the binding sites with an extended central spacer.

V. Zhurkin, V. Ivanov, B. Chernov, 1995, Journal of molecular biology.

CRP-binding sites: evidence for two structural classes with 6-bp and 8-bp spacers.

V. Zhurkin, S. Adhya, A. Barber, 1993, Gene.

CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

Christopher T. Clarkson, V. Zhurkin, V. B. Teif, 2019, bioRxiv.

DNA and RNA Folds in Transcription Complex as Evidenced by Iodine-125 Radioprobing

V. Zhurkin, I. Panyutin, R. Neumann, 2000, Journal of biomolecular structure & dynamics.

The p53 tumor suppressor network is a key responder to microenvironmental components of chronic inflammatory stress.

John N Weinstein, Frank Staib, X. Wang, 2005, Cancer research.

CTCF binding strength modulates chromatin architecture through the changes of the local nucleosome repeat length

Christopher T. Clarkson, V. Zhurkin, V. B. Teif, 2019 .

DNA trajectory in the Gal repressosome.

V. Zhurkin, S. Semsey, S. Adhya, 2004, Genes & development.

"Antiparallel" DNA loop in gal repressosome visualized by atomic force microscopy.

V. Zhurkin, M. Tolstorukov, Y. Lyubchenko, 2003, Journal of molecular biology.

Gal repressosome contains an antiparallel DNA loop

Victor B. Zhurkin, George Vasmatzis, Mark Geanacopoulos, 2001, Nature Structural Biology.

Architectural Accommodation in the Complex of Four p53 DNA Binding Domain Peptides with the p21/waf1/cip1 DNA Response Element*

V. Zhurkin, A. Gronenborn, G. Clore, 1997, The Journal of Biological Chemistry.

p53 binding sites in normal and cancer cells are characterized by distinct chromatin context

V. Zhurkin, F. Cui, P. LoVerso, 2017, bioRxiv.

Sequence-dependent Kink-and-Slide Deformations of Nucleosomal DNA Facilitated by Histone Arginines Bound in the Minor Groove

V. Zhurkin, Difei Wang, N. B. Ulyanov, 2010, Journal of biomolecular structure & dynamics.

Recombination R-triplex: H-bonds contribution to stability as revealed with minor base substitutions for adenine

V. Zhurkin, T. Jovin, D. Arndt-Jovin, 2006, Nucleic acids research.

Radioprobing of a RecA-three-stranded DNA complex with iodine 125: evidence for recognition of homology in the major groove of the target duplex.

V. Zhurkin, R. Camerini-Otero, I. Panyutin, 2000, Journal of molecular biology.

Torsional flexibility of B-DNA as revealed by conformational analysis.

V. Zhurkin, V. Florentiev, Y. Lysov, 1982, Nucleic acids research.

Structure-based Analysis of DNA Sequence Patterns Guiding Nucleosome Positioning in vitro

Feng Cui, V. Zhurkin, F. Cui, 2010, Journal of biomolecular structure & dynamics.

Dynamics of Chromatin Fibers: Comparison of Monte Carlo Simulations with Force Spectroscopy

V. Zhurkin, D. Norouzi, 2018, Biophysical journal.

Regulation of chromatin folding by conformational variations of nucleosome linker DNA

A. Harutyunyan, V. Zhurkin, S. Grigoryev, 2017, Nucleic acids research.

Topological polymorphism of nucleosome fibers and folding of chromatin

V. Zhurkin, D. Norouzi, 2021, Biophysical journal.

Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing

H. A. Cole, V. Zhurkin, F. Cui, 2012, Nucleic acids research.

Nucleotide sequence analysis of the spacer regions flanking the rat rRNA transcription unit and identification of repetitive elements.

V. Zhurkin, V. Nosikov, A. Hadjiolov, 1986, Nucleic acids research.

Analysis of the interaction between the p53 binding domain and the p21/CiP1 DNA response element: a novel architectural organization.

V. Zhurkin, E. Appella, A. K. Nagaich, 1998, Journal of protein chemistry.

Structural organization of rat ribosomal RNA genes: interspersed sequences and their putative role in the alignment of nucleosomes.

V. Zhurkin, V. Nosikov, E. Braga, 1985, Gene.

Sequence-dependent bending of DNA and phasing of nucleosomes.

V. Zhurkin, V B Zhurkin, 1985, Journal of biomolecular structure & dynamics.

64 Hoogsteen or not Hoogsteen? Iodine-125 radioprobing of the p53-induced DNA deformations

V. Zhurkin, E. Appella, S. Mazur, 2013 .

Different families of double‐stranded conformations of DNA as revealed by computer calculations

V. Zhurkin, Y. Lysov, V. Ivanov, 1978 .

Correlations between deoxyribonucleic acid structural parameters and calculated circular dichroism spectra.

V. Zhurkin, I. Tinoco, V. Ivanov, 1981, Biochemistry.

The DNA Phosphate orientation. Infrared data and energetically favorable structures

V. Zhurkin, W. Pohle, H. Fritzsche, 1984, Biopolymers.

Interaction of spermine with different forms of DNA. A conformational study

V. Zhurkin, Y. Lysov, V. Ivanov, 1980, Biopolymers.

Computer analysis of conformational possibilities of double‐helical DNA

V. Zhurkin, Y. Lysov, V B Zhurkin, 1975, FEBS letters.

Nucleosome reorganisation in breast cancer tissues

Christopher T. Clarkson, V. Zhurkin, V. B. Teif, 2023, bioRxiv.

Combined micrococcal nuclease and exonuclease III digestion reveals precise positions of the nucleosome core/linker junctions: implications for high-resolution nucleosome mapping.

V. Zhurkin, Tatiana Nikitina, S. Grigoryev, 2013, Journal of molecular biology.

Magnetic circular dichroism studies of myoglobin, hemoglobin and peroxidase at room and low temperatures. Ferrous high spin derivatives

V. Zhurkin, Y. Sharonov, M. Livshitz, 1978, Biophysics of structure and mechanism.

Nucleosome reorganisation in breast cancer tissues

Christopher T. Clarkson, V. Zhurkin, V. B. Teif, 2023, bioRxiv.

Distinctive sequence patterns in metazoan and yeast nucleosomes: Implications for linker histone binding to AT-rich and methylated DNA

Victor B. Zhurkin, Feng Cui, V. Zhurkin, 2009, Nucleic acids research.

Periodicity in DNA primary structure is defined by secondary structure of the coded protein.

V. Zhurkin, V B Zhurkin, 1981, Nucleic acids research.

CAP binding sites reveal pyrimidine-purine pattern characteristic of DNA bending.

V. Zhurkin, V B Zhurkin, A M Barber, 1990, Journal of biomolecular structure & dynamics.

Sequence-Dependent Variability of B-DNA

Andrew V. Colasanti, V. Zhurkin, M. Tolstorukov, 2005 .

Topological polymorphism of the two-start chromatin fiber.

V. Zhurkin, D. Norouzi, 2015, Biophysical journal.

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.

V. Zhurkin, R. Sarma, M. Sarma, 1993, Biochemistry.

Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription

Ataur R. Katebi, V. Zhurkin, F. Cui, 2015, AIMS biophysics.

Iodine-125 radioprobing of E. coli RNA polymerase transcription elongation complexes.

V. Zhurkin, M. Kashlev, I. Panyutin, 2003, Methods in enzymology.

Working the kinks out of nucleosomal DNA.

Wilma K Olson, V. Zhurkin, W. Olson, 2011, Current opinion in structural biology.

nuScore: a web-interface for nucleosome positioning predictions

Peter J. Park, Wilma K. Olson, Victor Zhurkin, 2008, Bioinform..

Relation Between Obesity and Blunted Striatal Response to Food Is Moderated by TaqIA A1 Allele

J. Michael Schurr, V. Zhurkin, E. Siggia, 2008, Science.

The proto-chromatosome: A fundamental subunit of chromatin?

V. Zhurkin, F. Cui, D. Clark, 2016, Nucleus.

Radioprobing the conformation of DNA in a p53-DNA complex

V. Zhurkin, E. Appella, S. Mazur, 2012, International journal of radiation biology.

Relation Between Obesity and Blunted Striatal Response to Food Is Moderated by TaqIA A1 Allele

J. Michael Schurr, V. Zhurkin, E. Siggia, 2008, Science.

Histone N-tails modulate sequence-specific positioning of nucleosomes

V. Zhurkin, F. Cui, Tatiana Nikitina, 2023, bioRxiv.

Organization of DNA in a bacterial nucleoid

V. Zhurkin, M. Tolstorukov, S. Adhya, 2016, BMC Microbiology.

Nucleosome reorganisation in breast cancer tissues

Christopher T. Clarkson, V. Zhurkin, V. B. Teif, 2023, bioRxiv.

Topological polymorphism of the two-start chromatin fiber.

V. Zhurkin, D. Norouzi, 2015, Biophysical Journal.