Literature DB >> 18528632

Packing nanomechanics of viral genomes.

A Siber1, M Dragar, V A Parsegian, R Podgornik.   

Abstract

We investigate the osmotic equilibrium between a bulk polyethylene glycol (PEG) solution and DNA tightly packed in a spherical capsid. We base our analysis on the equations of thermodynamic equilibrium in terms of osmotic pressure. The equality between external osmotic pressure of PEG and osmotic pressure of tightly packed DNA gives us the DNA encapsidation curves. In this way we directly connect the wealth of existing osmotic pressure data for DNA in the bulk with the DNA encapsidation curves within small viral capsids. Specific calculations are made for a monovalent salt, Na(+) -DNA and a divalent salt, Mn(2+) -DNA that have quite different DNA encapsidation behaviors. The main conclusion of our work is that bending energy of DNA is of minor importance regarding the encapsidated DNA length, but has a non-negligible influence on the density distribution of DNA within the capsid.

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Year:  2008        PMID: 18528632      PMCID: PMC4163912          DOI: 10.1140/epje/i2008-10330-7

Source DB:  PubMed          Journal:  Eur Phys J E Soft Matter        ISSN: 1292-8941            Impact factor:   1.890


  26 in total

1.  DNA packaging and ejection forces in bacteriophage.

Authors:  J Kindt; S Tzlil; A Ben-Shaul; W M Gelbart
Journal:  Proc Natl Acad Sci U S A       Date:  2001-11-13       Impact factor: 11.205

2.  Osmotic pressure inhibition of DNA ejection from phage.

Authors:  Alex Evilevitch; Laurence Lavelle; Charles M Knobler; Eric Raspaud; William M Gelbart
Journal:  Proc Natl Acad Sci U S A       Date:  2003-07-24       Impact factor: 11.205

3.  Forces during bacteriophage DNA packaging and ejection.

Authors:  Prashant K Purohit; Mandar M Inamdar; Paul D Grayson; Todd M Squires; Jané Kondev; Rob Phillips
Journal:  Biophys J       Date:  2004-11-19       Impact factor: 4.033

Review 4.  DNA--DNA interactions.

Authors:  H H Strey; R Podgornik; D C Rau; V A Parsegian
Journal:  Curr Opin Struct Biol       Date:  1998-06       Impact factor: 6.809

5.  Theory of directed polymers.

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Journal:  Phys Rev A       Date:  1992-06-15       Impact factor: 3.140

6.  Encapsidated conformation of bacteriophage T7 DNA.

Authors:  M E Cerritelli; N Cheng; A H Rosenberg; C E McPherson; F P Booy; A C Steven
Journal:  Cell       Date:  1997-10-17       Impact factor: 41.582

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

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Authors:  V A Parsegian; R P Rand; N L Fuller; D C Rau
Journal:  Methods Enzymol       Date:  1986       Impact factor: 1.600

9.  Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: hydration forces between parallel DNA double helices.

Authors:  D C Rau; B Lee; V A Parsegian
Journal:  Proc Natl Acad Sci U S A       Date:  1984-05       Impact factor: 11.205

10.  Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus.

Authors:  Wen Jiang; Juan Chang; Joanita Jakana; Peter Weigele; Jonathan King; Wah Chiu
Journal:  Nature       Date:  2006-02-02       Impact factor: 49.962

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  6 in total

1.  Simulations of knotting in confined circular DNA.

Authors:  C Micheletti; D Marenduzzo; E Orlandini; D W Sumners
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

2.  DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting.

Authors:  Davide Marenduzzo; Enzo Orlandini; Andrzej Stasiak; De Witt Sumners; Luca Tubiana; Cristian Micheletti
Journal:  Proc Natl Acad Sci U S A       Date:  2009-12-14       Impact factor: 11.205

3.  Influence of Microscopic Interactions on the Flexible Mechanical Properties of Viral DNA.

Authors:  Cheng-Yin Zhang; Neng-Hui Zhang
Journal:  Biophys J       Date:  2018-08-04       Impact factor: 4.033

4.  Protein-DNA interactions determine the shapes of DNA toroids condensed in virus capsids.

Authors:  Amélie Leforestier; Antonio Siber; Françoise Livolant; Rudolf Podgornik
Journal:  Biophys J       Date:  2011-05-04       Impact factor: 4.033

5.  Recent Developments in Molecular Simulation Approaches to Study Spherical Virus Capsids.

Authors:  Eric R May
Journal:  Mol Simul       Date:  2014-04-01       Impact factor: 2.178

6.  pH-induced stability switching of the bacteriophage HK97 maturation pathway.

Authors:  Eric R May; Karunesh Arora; Charles L Brooks
Journal:  J Am Chem Soc       Date:  2014-02-13       Impact factor: 15.419

  6 in total

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