Literature DB >> 20478077

DNA curvature and flexibility in vitro and in vivo.

Justin P Peters1, L James Maher.   

Abstract

It has been more than 50 years since the elucidation of the structure of double-helical DNA. Despite active research and progress in DNA biology and biochemistry, much remains to be learned in the field of DNA biophysics. Predicting the sequence-dependent curvature and flexibility of DNA is difficult. Applicability of the conventional worm-like chain polymer model of DNA has been challenged. The fundamental forces responsible for the remarkable resistance of DNA to bending and twisting remain controversial. The apparent 'softening' of DNA measured in vivo in the presence of kinking proteins and superhelical strain is incompletely understood. New methods and insights are being applied to these problems. This review places current work on DNA biophysics in historical context and illustrates the ongoing interplay between theory and experiment in this exciting field.

Entities:  

Mesh:

Substances:

Year:  2010        PMID: 20478077      PMCID: PMC4190679          DOI: 10.1017/S0033583510000077

Source DB:  PubMed          Journal:  Q Rev Biophys        ISSN: 0033-5835            Impact factor:   5.318


  214 in total

Review 1.  DNA-cation interactions: The major and minor grooves are flexible ionophores.

Authors:  N V Hud; M Polak
Journal:  Curr Opin Struct Biol       Date:  2001-06       Impact factor: 6.809

2.  Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping.

Authors:  Giuseppe Lia; David Bensimon; Vincent Croquette; Jean-Francois Allemand; David Dunlap; Dale E A Lewis; Sankar Adhya; Laura Finzi
Journal:  Proc Natl Acad Sci U S A       Date:  2003-09-18       Impact factor: 11.205

3.  Protein-mediated DNA loops: effects of protein bridge size and kinks.

Authors:  Nicolas Douarche; Simona Cocco
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-12-02

4.  The B-DNA dodecamer at high resolution reveals a spine of water on sodium.

Authors:  X Shui; L McFail-Isom; G G Hu; L D Williams
Journal:  Biochemistry       Date:  1998-06-09       Impact factor: 3.162

5.  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

6.  Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release.

Authors:  P L deHaseth; T M Lohman; M T Record
Journal:  Biochemistry       Date:  1977-11-01       Impact factor: 3.162

7.  Bending of DNA by asymmetric charge neutralization: all-atom energy simulations.

Authors:  Konstantin M Kosikov; Andrey A Gorin; Xiang-Jun Lu; Wilma K Olson; Gerald S Manning
Journal:  J Am Chem Soc       Date:  2002-05-01       Impact factor: 15.419

8.  Enhancement of DNA flexibility in vitro and in vivo by HMGB box A proteins carrying box B residues.

Authors:  Nadia T Sebastian; Emily M Bystry; Nicole A Becker; L James Maher
Journal:  Biochemistry       Date:  2009-03-17       Impact factor: 3.162

9.  Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures.

Authors:  Guohui Zheng; Xiang-Jun Lu; Wilma K Olson
Journal:  Nucleic Acids Res       Date:  2009-05-27       Impact factor: 16.971

10.  The role of DNA shape in protein-DNA recognition.

Authors:  Remo Rohs; Sean M West; Alona Sosinsky; Peng Liu; Richard S Mann; Barry Honig
Journal:  Nature       Date:  2009-10-29       Impact factor: 49.962

View more
  77 in total

1.  Identification of novel DNA-binding proteins using DNA-affinity chromatography/pull down.

Authors:  Brandon L Jutras; Ashutosh Verma; Brian Stevenson
Journal:  Curr Protoc Microbiol       Date:  2012-02

2.  Nanomanufacturing: A Perspective.

Authors:  J Alexander Liddle; Gregg M Gallatin
Journal:  ACS Nano       Date:  2016-02-22       Impact factor: 15.881

3.  E. coli Gyrase Fails to Negatively Supercoil Diaminopurine-Substituted DNA.

Authors:  Mónica Fernández-Sierra; Qing Shao; Chandler Fountain; Laura Finzi; David Dunlap
Journal:  J Mol Biol       Date:  2015-04-19       Impact factor: 5.469

4.  CTCF-Induced Circular DNA Complexes Observed by Atomic Force Microscopy.

Authors:  Matthew T Mawhinney; Runcong Liu; Fang Lu; Jasna Maksimoska; Kevin Damico; Ronen Marmorstein; Paul M Lieberman; Brigita Urbanc
Journal:  J Mol Biol       Date:  2018-01-31       Impact factor: 5.469

Review 5.  On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease.

Authors:  David N Cooper; Albino Bacolla; Claude Férec; Karen M Vasquez; Hildegard Kehrer-Sawatzki; Jian-Min Chen
Journal:  Hum Mutat       Date:  2011-09-02       Impact factor: 4.878

Review 6.  Evolution of multisubunit RNA polymerases in the three domains of life.

Authors:  Finn Werner; Dina Grohmann
Journal:  Nat Rev Microbiol       Date:  2011-02       Impact factor: 60.633

7.  Modulation of DNA loop lifetimes by the free energy of loop formation.

Authors:  Yi-Ju Chen; Stephanie Johnson; Peter Mulligan; Andrew J Spakowitz; Rob Phillips
Journal:  Proc Natl Acad Sci U S A       Date:  2014-11-19       Impact factor: 11.205

8.  Determinants of cyclization-decyclization kinetics of short DNA with sticky ends.

Authors:  Jiyoun Jeong; Harold D Kim
Journal:  Nucleic Acids Res       Date:  2020-05-21       Impact factor: 16.971

9.  Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding.

Authors:  Alexey Savelyev; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2015-08-26       Impact factor: 6.006

10.  Temperature dependence of DNA persistence length.

Authors:  Stephanie Geggier; Alexander Kotlyar; Alexander Vologodskii
Journal:  Nucleic Acids Res       Date:  2010-10-15       Impact factor: 16.971

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.