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Items: 1 to 50 of 102

1.

Theoretical model, its parameters and predictions: Reply to comments on "DNA melting and energetics of the double helix".

Vologodskii A, Frank-Kamenetskii MD.

Phys Life Rev. 2018 Aug;25:42-44. doi: 10.1016/j.plrev.2018.04.003. Epub 2018 May 2. No abstract available.

PMID:
29735359
2.

DNA melting and energetics of the double helix.

Vologodskii A, Frank-Kamenetskii MD.

Phys Life Rev. 2018 Aug;25:1-21. doi: 10.1016/j.plrev.2017.11.012. Epub 2017 Nov 14. Review.

PMID:
29170011
3.

Type II topoisomerases: Experimental studies, theoretical models, and logic: Reply to comments on "Disentangling DNA molecules".

Vologodskii A.

Phys Life Rev. 2016 Sep;18:165-167. doi: 10.1016/j.plrev.2016.09.006. Epub 2016 Sep 21. No abstract available.

PMID:
27692401
4.

When Computer Simulation Excels Experiment.

Vologodskii A.

Biophys J. 2016 May 24;110(10):2136-7. doi: 10.1016/j.bpj.2016.04.016. No abstract available.

5.

Disentangling DNA molecules.

Vologodskii A.

Phys Life Rev. 2016 Sep;18:118-134. doi: 10.1016/j.plrev.2016.05.001. Epub 2016 May 4. Review.

PMID:
27173054
6.

Topological Behavior of Plasmid DNA.

Higgins NP, Vologodskii AV.

Microbiol Spectr. 2015 Apr;3(2). doi: 10.1128/microbiolspec.PLAS-0036-2014. Review.

7.

Strong bending of the DNA double helix.

Vologodskii A, Frank-Kamenetskii MD.

Nucleic Acids Res. 2013 Aug;41(14):6785-92. doi: 10.1093/nar/gkt396. Epub 2013 May 15. Review.

8.

Bending of short DNA helices.

Vologodskii A, Du Q, Frank-Kamenetskii MD.

Artif DNA PNA XNA. 2013 Jan-Mar;4(1):1-3. doi: 10.4161/adna.23892. Epub 2013 Jan 1.

9.

Unlinking of supercoiled DNA catenanes by type IIA topoisomerases.

Vologodskii A.

Biophys J. 2011 Sep 21;101(6):1403-11. doi: 10.1016/j.bpj.2011.08.011. Epub 2011 Sep 20.

10.

Temperature dependence of DNA persistence length.

Geggier S, Kotlyar A, Vologodskii A.

Nucleic Acids Res. 2011 Mar;39(4):1419-26. doi: 10.1093/nar/gkq932. Epub 2010 Oct 15.

11.

Sequence dependence of DNA bending rigidity.

Geggier S, Vologodskii A.

Proc Natl Acad Sci U S A. 2010 Aug 31;107(35):15421-6. doi: 10.1073/pnas.1004809107. Epub 2010 Aug 11.

12.

DNA-ligand binding and the force-extension experiments. Comment on "Biophysical characterization of DNA binding from single molecule force measurements" by Chaurasiya et al.

Vologodskii A.

Phys Life Rev. 2010 Sep;7(3):346-7; discussion 358-61. doi: 10.1016/j.plrev.2010.06.008. No abstract available.

PMID:
20621571
13.

Tightness of knots in a polymer chain.

Zheng X, Vologodskii A.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Apr;81(4 Pt 1):041806. Epub 2010 Apr 26.

14.

Simulation of DNA catenanes.

Vologodskii A, Rybenkov VV.

Phys Chem Chem Phys. 2009 Dec 7;11(45):10543-52. doi: 10.1039/b910812b. Epub 2009 Oct 23. Review.

15.

DNA supercoiling helps to unlink sister duplexes after replication.

Vologodskii A.

Bioessays. 2010 Jan;32(1):9-12. doi: 10.1002/bies.200900143. Review.

16.

Determining protein-induced DNA bending in force-extension experiments: theoretical analysis.

Vologodskii A.

Biophys J. 2009 May 6;96(9):3591-9. doi: 10.1016/j.bpj.2009.02.022.

17.

Theoretical models of DNA topology simplification by type IIA DNA topoisomerases.

Vologodskii A.

Nucleic Acids Res. 2009 Jun;37(10):3125-33. doi: 10.1093/nar/gkp250. Epub 2009 Apr 21. Review.

18.

Theoretical analysis of disruptions in DNA minicircles.

Zheng X, Vologodskii A.

Biophys J. 2009 Feb 18;96(4):1341-9. doi: 10.1016/j.bpj.2008.11.013.

19.

Kinking the double helix by bending deformation.

Du Q, Kotlyar A, Vologodskii A.

Nucleic Acids Res. 2008 Mar;36(4):1120-8. Epub 2007 Dec 20.

20.

Probability of the site juxtaposition determines the rate of protein-mediated DNA looping.

Polikanov YS, Bondarenko VA, Tchernaenko V, Jiang YI, Lutter LC, Vologodskii A, Studitsky VM.

Biophys J. 2007 Oct 15;93(8):2726-31. Epub 2007 Jun 15.

21.

Protein-induced local DNA bends regulate global topology of recombination products.

Du Q, Livshits A, Kwiatek A, Jayaram M, Vologodskii A.

J Mol Biol. 2007 Apr 20;368(1):170-82. Epub 2007 Feb 11.

22.

Brownian dynamics simulation of knot diffusion along a stretched DNA molecule.

Vologodskii A.

Biophys J. 2006 Mar 1;90(5):1594-7. Epub 2005 Dec 16.

23.

Cyclization of short DNA fragments and bending fluctuations of the double helix.

Du Q, Smith C, Shiffeldrim N, Vologodskaia M, Vologodskii A.

Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5397-402. Epub 2005 Apr 4.

24.

Gapped DNA and cyclization of short DNA fragments.

Du Q, Vologodskaia M, Kuhn H, Frank-Kamenetskii M, Vologodskii A.

Biophys J. 2005 Jun;88(6):4137-45. Epub 2005 Mar 18.

25.

Braiding DNA: experiments, simulations, and models.

Charvin G, Vologodskii A, Bensimon D, Croquette V.

Biophys J. 2005 Jun;88(6):4124-36. Epub 2005 Mar 18.

26.

Computational analysis of DNA gyrase action.

Vologodskii A.

Biophys J. 2004 Nov;87(5):3066-73. Epub 2004 Aug 31.

27.

Dynamics of DNA loop capture by the SfiI restriction endonuclease on supercoiled and relaxed DNA.

Embleton ML, Vologodskii AV, Halford SE.

J Mol Biol. 2004 May 21;339(1):53-66.

PMID:
15123420
28.

Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases.

Stone MD, Bryant Z, Crisona NJ, Smith SB, Vologodskii A, Bustamante C, Cozzarelli NR.

Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):8654-9. Epub 2003 Jul 11.

29.

The flexibility of DNA double crossover molecules.

Sa-Ardyen P, Vologodskii AV, Seeman NC.

Biophys J. 2003 Jun;84(6):3829-37.

30.

Symmetric DNA sites are functionally asymmetric within Flp and Cre site-specific DNA recombination synapses.

Grainge I, Pathania S, Vologodskii A, Harshey RM, Jayaram M.

J Mol Biol. 2002 Jul 12;320(3):515-27.

PMID:
12096907
31.

Computational analysis of the chiral action of type II DNA topoisomerases.

Klenin K, Langowski J, Vologodskii A.

J Mol Biol. 2002 Jul 5;320(2):359-67.

PMID:
12079392
32.

Contribution of the intrinsic curvature to measured DNA persistence length.

Vologodskaia M, Vologodskii A.

J Mol Biol. 2002 Mar 22;317(2):205-13.

PMID:
11902837
33.

Cooperative helix stabilization by complex Arg-Glu salt bridges.

Olson CA, Spek EJ, Shi Z, Vologodskii A, Kallenbach NR.

Proteins. 2001 Aug 1;44(2):123-32.

PMID:
11391775
34.

[Distributions of circular DNA according its topological states].

Vologodskiń≠ AV.

Mol Biol (Mosk). 2001 Mar-Apr;35(2):285-97. Review. Russian.

PMID:
11357411
35.

Mechanism of topology simplification by type II DNA topoisomerases.

Vologodskii AV, Zhang W, Rybenkov VV, Podtelezhnikov AA, Subramanian D, Griffith JD, Cozzarelli NR.

Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3045-9.

36.

Dynamics of site juxtaposition in supercoiled DNA.

Huang J, Schlick T, Vologodskii A.

Proc Natl Acad Sci U S A. 2001 Jan 30;98(3):968-73.

37.

Positive torsional strain causes the formation of a four-way junction at replication forks.

Postow L, Ullsperger C, Keller RW, Bustamante C, Vologodskii AV, Cozzarelli NR.

J Biol Chem. 2001 Jan 26;276(4):2790-6. Epub 2000 Oct 30.

38.

Multimerization-cyclization of DNA fragments as a method of conformational analysis.

Podtelezhnikov AA, Mao C, Seeman NC, Vologodskii A.

Biophys J. 2000 Nov;79(5):2692-704.

39.

Tightness of random knotting.

Katritch V, Olson WK, Vologodskii A, Dubochet J, Stasiak A.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 May;61(5 Pt B):5545-9.

PMID:
11031608
40.

Experimental and theoretical analysis of the invasive signal amplification reaction.

Lyamichev VI, Kaiser MW, Lyamicheva NE, Vologodskii AV, Hall JG, Ma WP, Allawi HT, Neri BP.

Biochemistry. 2000 Aug 8;39(31):9523-32.

PMID:
10924149
41.

The kinetics of oligonucleotide replacements.

Reynaldo LP, Vologodskii AV, Neri BP, Lyamichev VI.

J Mol Biol. 2000 Mar 24;297(2):511-20.

PMID:
10715217
42.

Mechanisms of separation of the complementary strands of DNA during replication.

Alexandrov AI, Cozzarelli NR, Holmes VF, Khodursky AB, Peter BJ, Postow L, Rybenkov V, Vologodskii AV.

Genetica. 1999;106(1-2):131-40. Review.

PMID:
10710719
43.

Equilibrium distributions of topological states in circular DNA: interplay of supercoiling and knotting.

Podtelezhnikov AA, Cozzarelli NR, Vologodskii AV.

Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):12974-9.

44.

Large-scale effects of transcriptional DNA supercoiling in vivo.

Krasilnikov AS, Podtelezhnikov A, Vologodskii A, Mirkin SM.

J Mol Biol. 1999 Oct 8;292(5):1149-60.

PMID:
10512709
45.

Effect of magnesium on cruciform extrusion in supercoiled DNA.

Vologodskaia MY, Vologodskii AV.

J Mol Biol. 1999 Jun 18;289(4):851-9.

PMID:
10369766
46.

Internal motion of supercoiled DNA: brownian dynamics simulations of site juxtaposition.

Jian H, Schlick T, Vologodskii A.

J Mol Biol. 1998 Nov 27;284(2):287-96.

PMID:
9813118
47.

Sedimentation and electrophoretic migration of DNA knots and catenanes.

Vologodskii AV, Crisona NJ, Laurie B, Pieranski P, Katritch V, Dubochet J, Stasiak A.

J Mol Biol. 1998 Apr 24;278(1):1-3.

PMID:
9571029
48.

Exploiting circular DNA.

Vologodskii A.

Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4092-3. Review. No abstract available.

49.

Non-complementary DNA helical structure induced by positive torsional stress.

Vologodskii AV, Yang X, Seeman NC.

Nucleic Acids Res. 1998 Mar 15;26(6):1503-8.

50.

Torsional control of double-stranded DNA branch migration.

Yang X, Vologodskii AV, Liu B, Kemper B, Seeman NC.

Biopolymers. 1998;45(1):69-83.

PMID:
9433186

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