Literature DB >> 16935960

The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force.

Gerald S Manning1.   

Abstract

To understand better the effect of electrostatics on the rigidity of the DNA double helix, we define DNA*, the null isomer of DNA, as the hypothetical structure that would result from DNA if its phosphate groups were not ionized. For the purposes of theoretical analysis, we model DNA* as identical to ordinary DNA but supplemented by a longitudinal compression force equal in magnitude but oppositely directed to the stretching (tension) force on DNA caused by phosphate-phosphate repulsions. The null isomer DNA* then becomes an elastically buckled form of fully ionized DNA. On this basis, we derive a nonadditive relationship between the persistence length P of DNA and the persistence length P* of its null isomer. From the formula obtained we can predict the value of P* if P is known, and we can predict the ionic strength dependence of P under the assumption that P* does not depend on ionic strength. We predict a value of P* for null DNA drastically lower than the value of P for DNA in its ordinary state of fully ionized phosphates. The predicted dependence of P on salt concentration is log-c over most of the concentration range, with no tendency toward a salt-independent value in the range of validity of the theory. The predictions are consistent with much of the persistence-length data available for DNA. Alternate theories of the Odijk-Skolnik-Fixman type, including one by the author, are considered skeptically on the grounds that the underlying model may not be realistic. Specifically, we doubt the accuracy for real polyelectrolytes of the Odijk-Skolnik-Fixman assumption that the polymer structure is invariant to changes in electrostatic forces.

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Year:  2006        PMID: 16935960      PMCID: PMC1630458          DOI: 10.1529/biophysj.106.089029

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


  22 in total

Review 1.  Electrostatic mechanisms of DNA deformation.

Authors:  L D Williams; L J Maher
Journal:  Annu Rev Biophys Biomol Struct       Date:  2000

Review 2.  Role of DNA sequence in nucleosome stability and dynamics.

Authors:  J Widom
Journal:  Q Rev Biophys       Date:  2001-08       Impact factor: 5.318

3.  Comments on selected aspects of nucleic acid electrostatics.

Authors:  Gerald S Manning
Journal:  Biopolymers       Date:  2003-05       Impact factor: 2.505

4.  Electrostatic free energy of the DNA double helix in counterion condensation theory.

Authors:  Gerald S Manning
Journal:  Biophys Chem       Date:  2002-12-10       Impact factor: 2.352

Review 5.  Flexibility of DNA.

Authors:  P J Hagerman
Journal:  Annu Rev Biophys Biophys Chem       Date:  1988

6.  Three persistence lengths for a stiff polymer with an application to DNA B-Z junctions.

Authors:  G S Manning
Journal:  Biopolymers       Date:  1988-10       Impact factor: 2.505

7.  An absolute method for the determination of the persistence length of native DNA from electron micrographs.

Authors:  C Frontali; E Dore; A Ferrauto; E Gratton; A Bettini; M R Pozzan; E Valdevit
Journal:  Biopolymers       Date:  1979-06       Impact factor: 2.505

8.  Flow birefringence of T7 phage DNA: dependence on salt concentration.

Authors:  K L Cairney; R E Harrington
Journal:  Biopolymers       Date:  1982-05       Impact factor: 2.505

9.  Flow dichroism of T7 DNA as a function of salt concentration.

Authors:  V Rizzo; J Schellman
Journal:  Biopolymers       Date:  1981-10       Impact factor: 2.505

10.  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

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  35 in total

1.  Self-assembly of DNA nanotubes with controllable diameters.

Authors:  Ofer I Wilner; Ron Orbach; Anja Henning; Carsten Teller; Omer Yehezkeli; Michael Mertig; Daniel Harries; Itamar Willner
Journal:  Nat Commun       Date:  2011-11-15       Impact factor: 14.919

2.  A computational framework for mechanical response of macromolecules: application to the salt concentration dependence of DNA bendability.

Authors:  Liang Ma; Arun Yethiraj; Xi Chen; Qiang Cui
Journal:  Biophys J       Date:  2009-05-06       Impact factor: 4.033

Review 3.  DNA curvature and flexibility in vitro and in vivo.

Authors:  Justin P Peters; L James Maher
Journal:  Q Rev Biophys       Date:  2010-05-18       Impact factor: 5.318

4.  DNA deformations near charged surfaces: electron and atomic force microscopy views.

Authors:  F G A Faas; B Rieger; L J van Vliet; D I Cherny
Journal:  Biophys J       Date:  2009-08-19       Impact factor: 4.033

5.  Transverse polarizability of an aligned assembly of charged rods.

Authors:  G S Manning
Journal:  Eur Phys J E Soft Matter       Date:  2009-12-03       Impact factor: 1.890

6.  A counterion condensation theory for the relaxation, rise, and frequency dependence of the parallel polarization of rodlike polyelectrolytes.

Authors:  G S Manning
Journal:  Eur Phys J E Soft Matter       Date:  2011-04-19       Impact factor: 1.890

7.  Microscopic basis for the mesoscopic extensibility of dendrimer-compacted DNA.

Authors:  Maria Mills; Brad Orr; Mark M Banaszak Holl; Ioan Andricioaei
Journal:  Biophys J       Date:  2010-03-03       Impact factor: 4.033

8.  Structural Flexibility of DNA-RNA Hybrid Duplex: Stretching and Twist-Stretch Coupling.

Authors:  Ju-Hui Liu; Kun Xi; Xi Zhang; Lei Bao; Xinghua Zhang; Zhi-Jie Tan
Journal:  Biophys J       Date:  2019-05-23       Impact factor: 4.033

9.  Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling.

Authors:  Lei Bao; Xi Zhang; Ya-Zhou Shi; Yuan-Yan Wu; Zhi-Jie Tan
Journal:  Biophys J       Date:  2017-03-28       Impact factor: 4.033

Review 10.  Supercoiling biases the formation of loops involved in gene regulation.

Authors:  Laura Finzi; David Dunlap
Journal:  Biophys Rev       Date:  2016-07-05
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