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

Ghosh RP, Shi Q, Yang L, Reddick MP, Nikitina T, Zhurkin VB, Fordyce P, Stasevich TJ, Chang HY, Greenleaf WJ, Liphardt JT.

Nat Commun. 2019 Jul 19;10(1):3221. doi: 10.1038/s41467-019-11118-8.


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

Bass MV, Nikitina T, Norouzi D, Zhurkin VB, Grigoryev SA.

J Biol Chem. 2019 Mar 15;294(11):4233-4246. doi: 10.1074/jbc.RA118.006412. Epub 2019 Jan 10.


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

Norouzi D, Zhurkin VB.

Biophys J. 2018 Nov 6;115(9):1644-1655. doi: 10.1016/j.bpj.2018.06.032. Epub 2018 Aug 30.


DNA topology in chromatin is defined by nucleosome spacing.

Nikitina T, Norouzi D, Grigoryev SA, Zhurkin VB.

Sci Adv. 2017 Oct 27;3(10):e1700957. doi: 10.1126/sciadv.1700957. eCollection 2017 Oct.


DNA-RNA interactions are critical for chromosome condensation in Escherichia coli.

Qian Z, Zhurkin VB, Adhya S.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):12225-12230. doi: 10.1073/pnas.1711285114. Epub 2017 Oct 30.


Regulation of chromatin folding by conformational variations of nucleosome linker DNA.

Buckwalter JM, Norouzi D, Harutyunyan A, Zhurkin VB, Grigoryev SA.

Nucleic Acids Res. 2017 Sep 19;45(16):9372-9387. doi: 10.1093/nar/gkx562.


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

Bao F, LoVerso PR, Fisk JN, Zhurkin VB, Cui F.

Cell Cycle. 2017;16(21):2073-2085. doi: 10.1080/15384101.2017.1361064. Epub 2017 Sep 28.


The proto-chromatosome: A fundamental subunit of chromatin?

Ocampo J, Cui F, Zhurkin VB, Clark DJ.

Nucleus. 2016 Jul 3;7(4):382-7. doi: 10.1080/19491034.2016.1220466. Review.


Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles.

Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR.

Data Brief. 2016 May 6;7:1678-81. doi: 10.1016/j.dib.2016.04.073. eCollection 2016 Jun.


Organization of DNA in a bacterial nucleoid.

Tolstorukov MY, Virnik K, Zhurkin VB, Adhya S.

BMC Microbiol. 2016 Feb 20;16:22. doi: 10.1186/s12866-016-0637-3.


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

Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR.

J Mol Biol. 2016 Jan 16;428(1):221-237. doi: 10.1016/j.jmb.2015.12.004. Epub 2015 Dec 14.


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

Cole HA, Cui F, Ocampo J, Burke TL, Nikitina T, Nagarajavel V, Kotomura N, Zhurkin VB, Clark DJ.

Nucleic Acids Res. 2016 Jan 29;44(2):573-81. doi: 10.1093/nar/gkv943. Epub 2015 Sep 22.


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

Shchyolkina AK, Kaluzhny DN, Borisova OF, Arndt-Jovin DJ, Jovin TM, Zhurkin VB.

J Biomol Struct Dyn. 2016 Jun;34(6):1298-306. doi: 10.1080/07391102.2015.1077344. Epub 2015 Oct 15.


Topological polymorphism of the two-start chromatin fiber.

Norouzi D, Zhurkin VB.

Biophys J. 2015 May 19;108(10):2591-2600. doi: 10.1016/j.bpj.2015.04.015.


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

Norouzi D, Katebi A, Cui F, Zhurkin VB.

AIMS Biophys. 2015;2(4):613-629. doi: 10.3934/biophy.2015.4.613. Epub 2015 Nov 3.


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

Cui F, Chen L, LoVerso PR, Zhurkin VB.

BMC Bioinformatics. 2014 Sep 22;15:313. doi: 10.1186/1471-2105-15-313.


nuMap: a web platform for accurate prediction of nucleosome positioning.

Alharbi BA, Alshammari TH, Felton NL, Zhurkin VB, Cui F.

Genomics Proteomics Bioinformatics. 2014 Oct;12(5):249-53. doi: 10.1016/j.gpb.2014.08.001. Epub 2014 Sep 16.


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

Cui F, Zhurkin VB.

Nucleic Acids Res. 2014 Jan;42(2):836-47. doi: 10.1093/nar/gkt943. Epub 2013 Oct 22.


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.

Zhurkin VB, Olson WK.

Phys Life Rev. 2013 Mar;10(1):70-2; discussion 82-4. doi: 10.1016/j.plrev.2013.01.009. Epub 2013 Jan 29. No abstract available.


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

Nikitina T, Wang D, Gomberg M, Grigoryev SA, Zhurkin VB.

J Mol Biol. 2013 Jun 12;425(11):1946-1960. doi: 10.1016/j.jmb.2013.02.026. Epub 2013 Feb 28.


Transcriptional activation of yeast genes disrupts intragenic nucleosome phasing.

Cui F, Cole HA, Clark DJ, Zhurkin VB.

Nucleic Acids Res. 2012 Nov;40(21):10753-64. doi: 10.1093/nar/gks870. Epub 2012 Sep 24.


Radioprobing the conformation of DNA in a p53-DNA complex.

Karamychev VN, Wang D, Mazur SJ, Appella E, Neumann RD, Zhurkin VB, Panyutin IG.

Int J Radiat Biol. 2012 Dec;88(12):1039-45. doi: 10.3109/09553002.2012.698030. Epub 2012 Jun 21.


Working the kinks out of nucleosomal DNA.

Olson WK, Zhurkin VB.

Curr Opin Struct Biol. 2011 Jun;21(3):348-57. doi: 10.1016/ Epub 2011 Apr 7. Review.


The first thirty years of nucleosome positioning: comment on "Cracking the chromatin code: precise rule of nucleosome positioning" by Trifonov.

Zhurkin VB.

Phys Life Rev. 2011 Mar;8(1):64-6; discussion 69-72. doi: 10.1016/j.plrev.2011.02.001. Epub 2011 Feb 16. No abstract available.


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

Cui F, Sirotin MV, Zhurkin VB.

Biol Direct. 2011 Jan 6;6:2. doi: 10.1186/1745-6150-6-2.


p53 binding to nucleosomal DNA depends on the rotational positioning of DNA response element.

Sahu G, Wang D, Chen CB, Zhurkin VB, Harrington RE, Appella E, Hager GL, Nagaich AK.

J Biol Chem. 2010 Jan 8;285(2):1321-32. doi: 10.1074/jbc.M109.081182. Epub 2009 Nov 3.


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

Cui F, Zhurkin VB.

Nucleic Acids Res. 2009 May;37(9):2818-29. doi: 10.1093/nar/gkp113. Epub 2009 Mar 12.


Intramolecular recombination R-triplex in solution: stabilization by bis-intercalator YOYO.

Kaluzhny DN, Timoshin VV, Borisova OF, Zhurkin VB, Florentiev VL, Shchyolkina AK.

J Biomol Struct Dyn. 2008 Dec;26(3):301-6.


nuScore: a web-interface for nucleosome positioning predictions.

Tolstorukov MY, Choudhary V, Olson WK, Zhurkin VB, Park PJ.

Bioinformatics. 2008 Jun 15;24(12):1456-8. doi: 10.1093/bioinformatics/btn212. Epub 2008 Apr 29.


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

Tolstorukov MY, Colasanti AV, McCandlish DM, Olson WK, Zhurkin VB.

J Mol Biol. 2007 Aug 17;371(3):725-38. Epub 2007 May 24.


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

Shchyolkina AK, Kaluzhny DN, Arndt-Jovin DJ, Jovin TM, Zhurkin VB.

Nucleic Acids Res. 2006 Jun 23;34(11):3239-45. Print 2006.


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

Shen WH, Wang J, Wu J, Zhurkin VB, Yin Y.

Cancer Res. 2006 Jun 15;66(12):6033-9.


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

Staib F, Robles AI, Varticovski L, Wang XW, Zeeberg BR, Sirotin M, Zhurkin VB, Hofseth LJ, Hussain SP, Weinstein JN, Galle PR, Harris CC.

Cancer Res. 2005 Nov 15;65(22):10255-64.


A-tract clusters may facilitate DNA packaging in bacterial nucleoid.

Tolstorukov MY, Virnik KM, Adhya S, Zhurkin VB.

Nucleic Acids Res. 2005 Jul 15;33(12):3907-18. Print 2005.


DNA trajectory in the Gal repressosome.

Semsey S, Tolstorukov MY, Virnik K, Zhurkin VB, Adhya S.

Genes Dev. 2004 Aug 1;18(15):1898-907.


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

Tolstorukov MY, Jernigan RL, Zhurkin VB.

J Mol Biol. 2004 Mar 12;337(1):65-76.


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

Shchyolkina AK, Kaluzhny DN, Borisova OF, Hawkins ME, Jernigan RL, Jovin TM, Arndt-Jovin DJ, Zhurkin VB.

Nucleic Acids Res. 2004 Jan 22;32(2):432-40. Print 2004.


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

Karamychev VN, Tatusov A, Komissarova N, Kashlev M, Neumann RD, Zhurkin VB, Panyutin IG.

Methods Enzymol. 2003;371:106-20. No abstract available.


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

Virnik K, Lyubchenko YL, Karymov MA, Dahlgren P, Tolstorukov MY, Semsey S, Zhurkin VB, Adhya S.

J Mol Biol. 2003 Nov 14;334(1):53-63.


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

Tolstorukov MY, Ivanov VI, Malenkov GG, Jernigan RL, Zhurkin VB.

Biophys J. 2001 Dec;81(6):3409-21.


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

Murphy EC, Zhurkin VB, Louis JM, Cornilescu G, Clore GM.

J Mol Biol. 2001 Sep 21;312(3):481-99.


Gal repressosome contains an antiparallel DNA loop.

Geanacopoulos M, Vasmatzis G, Zhurkin VB, Adhya S.

Nat Struct Biol. 2001 May;8(5):432-6.


Modeling DNA deformations.

Olson WK, Zhurkin VB.

Curr Opin Struct Biol. 2000 Jun;10(3):286-97.


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

Malkov VA, Panyutin IG, Neumann RD, Zhurkin VB, Camerini-Otero RD.

J Mol Biol. 2000 Jun 9;299(3):629-40.


DNA bending and sugar switching.

Kamath S, Sarma MH, Zhurkin VB, Turner CJ, Sarma RH.

J Biomol Struct Dyn. 2000;17 Suppl 1:317-25.


DNA and RNA folds in transcription complex as evidenced by iodine-125 radioprobing.

Karamychev VN, Panyutin IG, Neumann RD, Zhurkin VB.

J Biomol Struct Dyn. 2000;17 Suppl 1:155-67.


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

Karamychev VN, Zhurkin VB, Garges S, Neumann RD, Panyutin IG.

Nat Struct Biol. 1999 Aug;6(8):747-50.


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