Literature DB >> 25028868

DNA, flexibly flexible.

Jason D Kahn1.   

Abstract

Investigators have constructed dsDNA molecules with several different base modifications and have characterized their bending and twisting flexibilities using atomic force microscopy, DNA ring closure, and single-molecule force spectroscopy with optical tweezers. The three methods provide persistence length measurements that agree semiquantitatively, and they show that the persistence length is surprisingly similar for all of the modified DNAs. The circular dichroism spectra of modified DNAs differ substantially. Simple explanations based on base stacking strength, polymer charge, or groove occupancy by functional groups cannot explain the results, which will guide further high-resolution theory and experiments.
Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2014        PMID: 25028868      PMCID: PMC4104031          DOI: 10.1016/j.bpj.2014.06.007

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  13 in total

Review 1.  Ten years of tension: single-molecule DNA mechanics.

Authors:  Carlos Bustamante; Zev Bryant; Steven B Smith
Journal:  Nature       Date:  2003-01-23       Impact factor: 49.962

2.  High flexibility of DNA on short length scales probed by atomic force microscopy.

Authors:  Paul A Wiggins; Thijn van der Heijden; Fernando Moreno-Herrero; Andrew Spakowitz; Rob Phillips; Jonathan Widom; Cees Dekker; Philip C Nelson
Journal:  Nat Nanotechnol       Date:  2006-11-03       Impact factor: 39.213

3.  Dynamic DNA underpins chromosome dynamics.

Authors:  Andrew Travers
Journal:  Biophys J       Date:  2013-11-19       Impact factor: 4.033

4.  Flexibility of native DNA from the sedimentation behavior as a function of molecular weight and temperature.

Authors:  H B Gray; J E Hearst
Journal:  J Mol Biol       Date:  1968-07-14       Impact factor: 5.469

5.  DNA flexibility studied by covalent closure of short fragments into circles.

Authors:  D Shore; J Langowski; R L Baldwin
Journal:  Proc Natl Acad Sci U S A       Date:  1981-08       Impact factor: 11.205

6.  Probing the elasticity of DNA on short length scales by modeling supercoiling under tension.

Authors:  Robert Schöpflin; Hergen Brutzer; Oliver Müller; Ralf Seidel; Gero Wedemann
Journal:  Biophys J       Date:  2012-07-17       Impact factor: 4.033

7.  Sequence dependence of transcription factor-mediated DNA looping.

Authors:  Stephanie Johnson; Martin Lindén; Rob Phillips
Journal:  Nucleic Acids Res       Date:  2012-06-19       Impact factor: 16.971

8.  Rationally designed coiled-coil DNA looping peptides control DNA topology.

Authors:  Daniel B Gowetski; Erin J Kodis; Jason D Kahn
Journal:  Nucleic Acids Res       Date:  2013-07-03       Impact factor: 16.971

9.  Mechanical properties of DNA-like polymers.

Authors:  Justin P Peters; Shweta P Yelgaonkar; Seergazhi G Srivatsan; Yitzhak Tor; L James Maher
Journal:  Nucleic Acids Res       Date:  2013-09-05       Impact factor: 16.971

10.  A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

Authors:  Richard Lavery; Krystyna Zakrzewska; David Beveridge; Thomas C Bishop; David A Case; Thomas Cheatham; Surjit Dixit; B Jayaram; Filip Lankas; Charles Laughton; John H Maddocks; Alexis Michon; Roman Osman; Modesto Orozco; Alberto Perez; Tanya Singh; Nada Spackova; Jiri Sponer
Journal:  Nucleic Acids Res       Date:  2009-10-22       Impact factor: 16.971

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  3 in total

1.  Flexibility of short ds-DNA intercalated by a dipyridophenazine ligand.

Authors:  Fuchao Jia; Stéphane Despax; Jean-Pierre Münch; Pascal Hébraud
Journal:  Front Chem       Date:  2015-04-16       Impact factor: 5.221

2.  Information Thermodynamics of Cytosine DNA Methylation.

Authors:  Robersy Sanchez; Sally A Mackenzie
Journal:  PLoS One       Date:  2016-03-10       Impact factor: 3.240

Review 3.  Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.

Authors:  Runjhun Saran; Yong Wang; Isaac T S Li
Journal:  Sensors (Basel)       Date:  2020-12-08       Impact factor: 3.576

  3 in total

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