Literature DB >> 25419039

Biophysics of protein-DNA interactions and chromosome organization.

John F Marko1.   

Abstract

The function of DNA in cells depends on its interactions with protein molecules, which recognize and act on base sequence patterns along the double helix. These notes aim to introduce basic polymer physics of DNA molecules, biophysics of protein-DNA interactions and their study in single-DNA experiments, and some aspects of large-scale chromosome structure. Mechanisms for control of chromosome topology will also be discussed.

Entities:  

Keywords:  DNA; DNA-protein interactions; chromosome dynamics; chromosome structure

Year:  2015        PMID： 25419039      PMCID： PMC4235750          DOI： 10.1016/j.physa.2014.07.045

Source DB:  PubMed          Journal:  Physica A        ISSN： 0378-4371            Impact factor:   3.263


  112 in total

1.  Compaction of single DNA molecules induced by binding of integration host factor (IHF).

Authors:  B M Ali; R Amit; I Braslavsky; A B Oppenheim; O Gileadi; J Stavans
Journal:  Proc Natl Acad Sci U S A       Date:  2001-09-04       Impact factor: 11.205

2.  Single molecule statistics and the polynucleotide unzipping transition.

Authors:  David K Lubensky; David R Nelson
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2002-03-06

3.  Real-time detection of single-molecule DNA compaction by condensin I.

Authors:  Terence R Strick; Tatsuhiko Kawaguchi; Tatsuya Hirano
Journal:  Curr Biol       Date:  2004-05-25       Impact factor: 10.834

4.  Writhe formulas and antipodal points in plectonemic DNA configurations.

Authors:  Sébastien Neukirch; Eugene L Starostin
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2008-10-20

5.  Torsional directed walks, entropic elasticity, and DNA twist stiffness.

Authors:  J D Moroz; P Nelson
Journal:  Proc Natl Acad Sci U S A       Date:  1997-12-23       Impact factor: 11.205

6.  Simplification of DNA topology below equilibrium values by type II topoisomerases.

Authors:  V V Rybenkov; C Ullsperger; A V Vologodskii; N R Cozzarelli
Journal:  Science       Date:  1997-08-01       Impact factor: 47.728

7.  Topoisomerase II inhibitors affect entry into mitosis and chromosome condensation in BHK cells.

Authors:  H Anderson; M Roberge
Journal:  Cell Growth Differ       Date:  1996-01

8.  Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors:  K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal:  Nature       Date:  1997-09-18       Impact factor: 49.962

9.  Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis.

Authors:  Dunja Skoko; Daniel Yoo; Hua Bai; Bernhard Schnurr; Jie Yan; Sarah M McLeod; John F Marko; Reid C Johnson
Journal:  J Mol Biol       Date:  2006-09-22       Impact factor: 5.469

10.  DNA topoisomerase II is required for condensation and separation of mitotic chromosomes in S. pombe.

Authors:  T Uemura; H Ohkura; Y Adachi; K Morino; K Shiozaki; M Yanagida
Journal:  Cell       Date:  1987-09-11       Impact factor: 41.582
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  10 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.  Facilitated dissociation of transcription factors from single DNA binding sites.

Authors:  Ramsey I Kamar; Edward J Banigan; Aykut Erbas; Rebecca D Giuntoli; Monica Olvera de la Cruz; Reid C Johnson; John F Marko
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-31       Impact factor: 11.205

3.  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

4.  Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation.

Authors:  Brad A Krajina; Andrew J Spakowitz
Journal:  Biophys J       Date:  2016-10-04       Impact factor: 4.033

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

Authors:  Enrico Skoruppa; Stefanos K Nomidis; John F Marko; Enrico Carlon
Journal:  Phys Rev Lett       Date:  2018-08-24       Impact factor: 9.161

6.  Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion.

Authors:  Sumitabha Brahmachari; Vinícius G Contessoto; Michele Di Pierro; José N Onuchic
Journal:  Nucleic Acids Res       Date:  2022-05-06       Impact factor: 19.160

7.  Single-molecule fluorescence studies on DNA looping.

Authors:  Jiyoun Jeong; Tung T Le; Harold D Kim
Journal:  Methods       Date:  2016-04-07       Impact factor: 3.608

8.  Properties of gene expression and chromatin structure with mechanically regulated elongation.

Authors:  Stuart A Sevier; Herbert Levine
Journal:  Nucleic Acids Res       Date:  2018-07-06       Impact factor: 16.971

9.  DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases.

Authors:  Shubham Tripathi; Sumitabha Brahmachari; José N Onuchic; Herbert Levine
Journal:  Nucleic Acids Res       Date:  2022-02-22       Impact factor: 16.971

10.  Impact of linker histone in the formation of ambochlorin-calf thymus DNA complex: Multi-spectroscopic, stopped-flow, and molecular modeling approaches.

Authors:  Azam Askari; Parisa Mokaberi; Maryam Dareini; Morvarid Medalian; Mahtab Pejhan; Maryam Erfani; Maryam Asadzadeh-Lotfabad; Mohammad Reza Saberi; Jamshidkhan Chamani
Journal:  Iran J Basic Med Sci       Date:  2021-11       Impact factor: 2.699
  10 in total

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