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Items: 1 to 20 of 87

1.

Cooperative kinking at distant sites in mechanically stressed DNA.

Lionberger TA, Demurtas D, Witz G, Dorier J, Lillian T, Meyhöfer E, Stasiak A.

Nucleic Acids Res. 2011 Dec;39(22):9820-32. doi: 10.1093/nar/gkr666. Epub 2011 Sep 14.

2.

Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles.

Demurtas D, Amzallag A, Rawdon EJ, Maddocks JH, Dubochet J, Stasiak A.

Nucleic Acids Res. 2009 May;37(9):2882-93. doi: 10.1093/nar/gkp137. Epub 2009 Mar 12.

3.

Influence of DNA sequence on the structure of minicircles under torsional stress.

Wang Q, Irobalieva RN, Chiu W, Schmid MF, Fogg JM, Zechiedrich L, Pettitt BM.

Nucleic Acids Res. 2017 Jul 27;45(13):7633-7642. doi: 10.1093/nar/gkx516.

4.

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.

5.

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.

6.

Bending the rules of transcriptional repression: tightly looped DNA directly represses T7 RNA polymerase.

Lionberger TA, Meyhöfer E.

Biophys J. 2010 Aug 9;99(4):1139-48. doi: 10.1016/j.bpj.2010.04.074.

7.

The absence of supercoiling in kinetoplast DNA minicircles.

Rauch CA, Perez-Morga D, Cozzarelli NR, Englund PT.

EMBO J. 1993 Feb;12(2):403-11.

8.

Kinking occurs during molecular dynamics simulations of small DNA minicircles.

Lankas F, Lavery R, Maddocks JH.

Structure. 2006 Oct;14(10):1527-34.

9.

Modelling DNA loops using continuum and statistical mechanics.

Balaeff A, Koudella CR, Mahadevan L, Schulten K.

Philos Trans A Math Phys Eng Sci. 2004 Jul 15;362(1820):1355-71.

10.

Twisting and bending stress in DNA minicircles.

Zoli M.

Soft Matter. 2014 Jun 28;10(24):4304-11. doi: 10.1039/c3sm52953c.

PMID:
24791278
11.

Modeling protein-induced configurational changes in DNA minicircles.

Martino JA, Olson WK.

Biopolymers. 1997 Apr 5;41(4):419-30.

PMID:
9080777
12.

Finite-element analysis of the displacement of closed DNA loops under torsional stress.

White JH, Bauer WR.

Philos Trans A Math Phys Eng Sci. 2004 Jul 15;362(1820):1335-53.

13.

3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy.

Amzallag A, Vaillant C, Jacob M, Unser M, Bednar J, Kahn JD, Dubochet J, Stasiak A, Maddocks JH.

Nucleic Acids Res. 2006;34(18):e125. Epub 2006 Sep 29.

14.

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.

15.

Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA.

Mitchell JS, Laughton CA, Harris SA.

Nucleic Acids Res. 2011 May;39(9):3928-38. doi: 10.1093/nar/gkq1312. Epub 2011 Jan 18.

16.
17.

Radiosensitivity of DNA minicircles.

Culard F, Spotheim-Maurizot M, Sabattier R, Charlier M.

Int J Radiat Biol. 1994 Jun;65(6):651-6.

PMID:
7912714
18.

Computer simulation of protein-induced structural changes in closed circular DNA.

Zhang P, Tobias I, Olson WK.

J Mol Biol. 1994 Sep 23;242(3):271-90. Erratum in: J Mol Biol 1995 Sep 1;251(5):721.

PMID:
8089847
19.

Transcription-driven twin supercoiling of a DNA loop: a Brownian dynamics study.

Mielke SP, Fink WH, Krishnan VV, Grønbech-Jensen N, Benham CJ.

J Chem Phys. 2004 Oct 22;121(16):8104-12.

20.

Implications of the dependence of the elastic properties of DNA on nucleotide sequence.

Olson WK, Swigon D, Coleman BD.

Philos Trans A Math Phys Eng Sci. 2004 Jul 15;362(1820):1403-22.

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