Literature DB >> 30192578

Bend-Induced Twist Waves and the Structure of Nucleosomal DNA.

Enrico Skoruppa1, Stefanos K Nomidis1,2, John F Marko3, Enrico Carlon1.   

Abstract

Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we investigate its effect on bent DNA. We provide an analytical solution of the minimum-energy shape of circular DNA, showing that twist-bend coupling induces sinusoidal twist waves. This solution is in excellent agreement with both coarse-grained simulations of minicircles and nucleosomal DNA data, which is bent and wrapped around histone proteins in a superhelical conformation. Our analysis shows that the observed twist oscillation in nucleosomal DNA, so far attributed to the interaction with the histone proteins, is an intrinsic feature of free bent DNA, and should be observable in other protein-DNA complexes.

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Year:  2018        PMID： 30192578      PMCID： PMC6132066          DOI： 10.1103/PhysRevLett.121.088101

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN： 0031-9007            Impact factor:   9.161


  29 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  The structure of DNA in the nucleosome core.

Authors:  Timothy J Richmond; Curt A Davey
Journal:  Nature       Date:  2003-05-08       Impact factor: 49.962

3.  Elastic correlations in nucleosomal DNA structure.

Authors:  Farshid Mohammad-Rafiee; Ramin Golestanian
Journal:  Phys Rev Lett       Date:  2005-06-15       Impact factor: 9.161

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

Authors:  Michael Y Tolstorukov; Andrew V Colasanti; David M McCandlish; Wilma K Olson; Victor B Zhurkin
Journal:  J Mol Biol       Date:  2007-05-24       Impact factor: 5.469

5.  Experiments confirm the influence of genome long-range correlations on nucleosome positioning.

Authors:  C Vaillant; B Audit; A Arneodo
Journal:  Phys Rev Lett       Date:  2007-11-21       Impact factor: 9.161

6.  DNA elasticity from coarse-grained simulations: The effect of groove asymmetry.

Authors:  Enrico Skoruppa; Michiel Laleman; Stefanos K Nomidis; Enrico Carlon
Journal:  J Chem Phys       Date:  2017-06-07       Impact factor: 3.488

7.  Twist-Bend Coupling and the Torsional Response of Double-Stranded DNA.

Authors:  Stefanos K Nomidis; Franziska Kriegel; Willem Vanderlinden; Jan Lipfert; Enrico Carlon
Journal:  Phys Rev Lett       Date:  2017-05-26       Impact factor: 9.161

8.  Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.

Authors:  Tomáš Dršata; Nada Špačková; Petr Jurečka; Marie Zgarbová; Jiří Šponer; Filip Lankaš
Journal:  Nucleic Acids Res       Date:  2014-05-14       Impact factor: 16.971

9.  Conformational analysis of nucleic acids revisited: Curves+.

Authors:  R Lavery; M Moakher; J H Maddocks; D Petkeviciute; K Zakrzewska
Journal:  Nucleic Acids Res       Date:  2009-07-22       Impact factor: 16.971

10.  Site-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability.

Authors:  Timothy D Frouws; Philip D Barth; Timothy J Richmond
Journal:  J Mol Biol       Date:  2017-11-04       Impact factor: 5.469
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  7 in total

1.  Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond.

Authors:  Stefanos K Nomidis; Enrico Skoruppa; Enrico Carlon; John F Marko
Journal:  Phys Rev E       Date:  2019-03       Impact factor: 2.529

2.  DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles.

Authors:  Jejoong Yoo; Sangwoo Park; Christopher Maffeo; Taekjip Ha; Aleksei Aksimentiev
Journal:  Nucleic Acids Res       Date:  2021-11-18       Impact factor: 16.971

3.  Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches.

Authors:  Parth Rakesh Desai; Sumitabha Brahmachari; John F Marko; Siddhartha Das; Keir C Neuman
Journal:  Nucleic Acids Res       Date:  2020-11-04       Impact factor: 19.160

4.  The roles of HMGB1-produced DNA gaps in DNA protection and aging biomarker reversal.

Authors:  Sakawdaurn Yasom; Papitchaya Watcharanurak; Narumol Bhummaphan; Jirapan Thongsroy; Charoenchai Puttipanyalears; Sirapat Settayanon; Kanwalat Chalertpet; Wilunplus Khumsri; Aphisek Kongkaew; Maturada Patchsung; Chutha Siriwattanakankul; Monnat Pongpanich; Piyapat Pin-On; Depicha Jindatip; Rujira Wanotayan; Mingkwan Odton; Suangsuda Supasai; Thura Tun Oo; Busarin Arunsak; Wasana Pratchayasakul; Nipon Chattipakorn; Siriporn Chattipakorn; Apiwat Mutirangura
Journal:  FASEB Bioadv       Date:  2022-03-28

Review 5.  Energetics of twisted DNA topologies.

Authors:  Wenxuan Xu; David Dunlap; Laura Finzi
Journal:  Biophys J       Date:  2021-05-08       Impact factor: 3.699

6.  Twist-diameter coupling drives DNA twist changes with salt and temperature.

Authors:  Chen Zhang; Fujia Tian; Ying Lu; Bing Yuan; Zhi-Jie Tan; Xing-Hua Zhang; Liang Dai
Journal:  Sci Adv       Date:  2022-03-23       Impact factor: 14.136

7.  Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.

Authors:  Salvatore Assenza; Rubén Pérez
Journal:  J Chem Theory Comput       Date:  2022-04-08       Impact factor: 6.578
  7 in total

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