Literature DB >> 17890390

Osmotic pressure and packaging structure of caged DNA.

Zhidong Li1, Jianzhong Wu, Zhen-Gang Wang.   

Abstract

We present a theoretical model for aqueous solutions of double-stranded (ds) DNA with explicit consideration of electrostatic interactions, excluded-volume effects, van der Waals attractions, and salt ions. With reasonable parameters estimated from the DNA structure and experimental data for electrolytes, we are able to reproduce the DNA osmotic pressure in the bulk in good agreement with experiment. The predicted DNA osmotic pressure in lambda-bacteriophages is found to coincide with that of the PEG8000 solution that inhibits DNA ejection as reported in recent experiments. Based on the radial distributions of DNA segments and of counterions at different degrees of packaging, we find that in the presence of Mg(2+), DNA forms a multilayer structure near the inner surface of a fully loaded bacteriophage, but at low packing density the DNA segments are depleted from the surface owing to the local condensation of DNA induced by the divalent counterions. By contrast, the multilayer DNA structure is less distinctive in the presence of Na(+) despite the increase of the DNA density at contact, and the depletion near the capsid surface is not found at low packing density.

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Year:  2007        PMID: 17890390      PMCID: PMC2186248          DOI: 10.1529/biophysj.107.112508

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


  35 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.  Do free DNA counterions control the osmotic pressure?

Authors:  E Raspaud; M da Conceiçao; F Livolant
Journal:  Phys Rev Lett       Date:  2000-03-13       Impact factor: 9.161

3.  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

4.  Mechanism of force generation of a viral DNA packaging motor.

Authors:  Yann R Chemla; K Aathavan; Jens Michaelis; Shelley Grimes; Paul J Jardine; Dwight L Anderson; Carlos Bustamante
Journal:  Cell       Date:  2005-09-09       Impact factor: 41.582

5.  Structural studies of bacteriophage lambda heads and proheads by small angle X-ray diffraction.

Authors:  W C Earnshaw; R W Hendrix; J King
Journal:  J Mol Biol       Date:  1979-11-05       Impact factor: 5.469

6.  Langevin dynamics simulations of genome packing in bacteriophage.

Authors:  Christopher Forrey; M Muthukumar
Journal:  Biophys J       Date:  2006-04-14       Impact factor: 4.033

7.  Density functional theory for polyelectrolytes near oppositely charged surfaces.

Authors:  Zhidong Li; Jianzhong Wu
Journal:  Phys Rev Lett       Date:  2006-02-02       Impact factor: 9.161

8.  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

9.  DNA arrangement in isometric phage heads.

Authors:  W C Earnshaw; S C Harrison
Journal:  Nature       Date:  1977-08-18       Impact factor: 49.962

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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  14 in total

1.  Langevin dynamics simulation of polymer-assisted virus-like assembly.

Authors:  J P Mahalik; M Muthukumar
Journal:  J Chem Phys       Date:  2012-04-07       Impact factor: 3.488

2.  Ion-dependent dynamics of DNA ejections for bacteriophage lambda.

Authors:  David Wu; David Van Valen; Qicong Hu; Rob Phillips
Journal:  Biophys J       Date:  2010-08-09       Impact factor: 4.033

3.  Polymorphism of DNA conformation inside the bacteriophage capsid.

Authors:  Amélie Leforestier
Journal:  J Biol Phys       Date:  2013-04-12       Impact factor: 1.365

Review 4.  Packaging double-helical DNA into viral capsids: structures, forces, and energetics.

Authors:  Anton S Petrov; Stephen C Harvey
Journal:  Biophys J       Date:  2008-05-16       Impact factor: 4.033

5.  A Molecular View of the Dynamics of dsDNA Packing Inside Viral Capsids in the Presence of Ions.

Authors:  Andrés Córdoba; Daniel M Hinckley; Joshua Lequieu; Juan J de Pablo
Journal:  Biophys J       Date:  2017-04-11       Impact factor: 4.033

6.  Density functional theory for encapsidated polyelectrolytes: a comparison with Monte Carlo simulation.

Authors:  Zhehui Jin; Jianzhong Wu
Journal:  J Chem Phys       Date:  2012-07-28       Impact factor: 3.488

7.  A packing for A-form DNA in an icosahedral virus.

Authors:  Fengbin Wang; Ying Liu; Zhangli Su; Tomasz Osinski; Guilherme A P de Oliveira; James F Conway; Stefan Schouten; Mart Krupovic; David Prangishvili; Edward H Egelman
Journal:  Proc Natl Acad Sci U S A       Date:  2019-10-21       Impact factor: 11.205

8.  Initial Events Associated with Virus PBCV-1 Infection of Chlorella NC64A.

Authors:  Gerhard Thiel; Anna Moroni; David Dunigan; James L Van Etten
Journal:  Prog Bot       Date:  2010-01-01

9.  Visualization of bacteriophage T3 capsids with DNA incompletely packaged in vivo.

Authors:  Ping-An Fang; Elena T Wright; Susan T Weintraub; Kevin Hakala; Weimin Wu; Philip Serwer; Wen Jiang
Journal:  J Mol Biol       Date:  2008-10-14       Impact factor: 5.469

10.  Electrostatic regulation of genome packaging in human hepatitis B virus.

Authors:  Tao Jiang; Zhen-Gang Wang; Jianzhong Wu
Journal:  Biophys J       Date:  2009-04-22       Impact factor: 4.033

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