Literature DB >> 22297530

Single-molecule studies of viral DNA packaging.

Yann R Chemla1, Douglas E Smith.   

Abstract

Many double-stranded DNA bacteriophages and viruses use specialized ATP-driven molecular machines to package their genomes into tightly confined procapsid shells. Over the last decade, single-molecule approaches - and in particular, optical tweezers - have made key contributions to our understanding of this remarkable process. In this chapter, we review these advances and the insights they have provided on the packaging mechanisms of three bacteriophages: φ 29, λ, and T4.

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Year:  2012        PMID: 22297530      PMCID: PMC5933933          DOI: 10.1007/978-1-4614-0980-9_24

Source DB:  PubMed          Journal:  Adv Exp Med Biol        ISSN: 0065-2598            Impact factor:   2.622


  109 in total

1.  Detailed architecture of a DNA translocating machine: the high-resolution structure of the bacteriophage phi29 connector particle.

Authors:  Alicia Guasch; Joan Pous; Borja Ibarra; F Xavier Gomis-Rüth; José María Valpuesta; Natalia Sousa; José L Carrascosa; Miquel Coll
Journal:  J Mol Biol       Date:  2002-01-25       Impact factor: 5.469

2.  Optical-trap force transducer that operates by direct measurement of light momentum.

Authors:  Steven B Smith; Yujia Cui; Carlos Bustamante
Journal:  Methods Enzymol       Date:  2003       Impact factor: 1.600

3.  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

4.  Langevin dynamics simulations of genome packing in bacteriophage.

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

5.  Diffusion of isolated DNA molecules: dependence on length and topology.

Authors:  Rae M Robertson; Stephan Laib; Douglas E Smith
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-28       Impact factor: 11.205

6.  Building a virus from scratch: assembly of an infectious virus using purified components in a rigorously defined biochemical assay system.

Authors:  Hélène Gaussier; Qin Yang; Carlos Enrique Catalano
Journal:  J Mol Biol       Date:  2006-01-25       Impact factor: 5.469

Review 7.  Advances in single-molecule fluorescence methods for molecular biology.

Authors:  Chirlmin Joo; Hamza Balci; Yuji Ishitsuka; Chittanon Buranachai; Taekjip Ha
Journal:  Annu Rev Biochem       Date:  2008       Impact factor: 23.643

8.  Motif III in superfamily 2 "helicases" helps convert the binding energy of ATP into a high-affinity RNA binding site in the yeast DEAD-box protein Ded1.

Authors:  Josette Banroques; Monique Doère; Marc Dreyfus; Patrick Linder; N Kyle Tanner
Journal:  J Mol Biol       Date:  2009-12-21       Impact factor: 5.469

9.  The DNA translocating ATPase of bacteriophage T4 packaging motor.

Authors:  Kiran R Kondabagil; Zhihong Zhang; Venigalla B Rao
Journal:  J Mol Biol       Date:  2006-08-25       Impact factor: 5.469

10.  DNA packaging ATPase of bacteriophage T3.

Authors:  M Morita; M Tasaka; H Fujisawa
Journal:  Virology       Date:  1993-04       Impact factor: 3.616

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  17 in total

1.  A force sensor that converts fluorescence signal into force measurement utilizing short looped DNA.

Authors:  Golam Mustafa; Cho-Ying Chuang; William A Roy; Mohamed M Farhath; Nilisha Pokhrel; Yue Ma; Kazuo Nagasawa; Edwin Antony; Matthew J Comstock; Soumitra Basu; Hamza Balci
Journal:  Biosens Bioelectron       Date:  2018-08-31       Impact factor: 10.618

Review 2.  Assessing heterogeneity in oligomeric AAA+ machines.

Authors:  Tatyana A Sysoeva
Journal:  Cell Mol Life Sci       Date:  2016-09-26       Impact factor: 9.261

3.  DNA Conformational Changes Play a Force-Generating Role during Bacteriophage Genome Packaging.

Authors:  Kim A Sharp; Xiang-Jun Lu; Gino Cingolani; Stephen C Harvey
Journal:  Biophys J       Date:  2019-04-30       Impact factor: 4.033

Review 4.  States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM.

Authors:  Philip Serwer; Elena T Wright; Borries Demeler; Wen Jiang
Journal:  Biophys Rev       Date:  2017-12-14

Review 5.  Slow and steady wins the race: physical limits on the rate of viral DNA packaging.

Authors:  Paul J Jardine
Journal:  Curr Opin Virol       Date:  2019-04-17       Impact factor: 7.090

6.  The scrunchworm hypothesis: transitions between A-DNA and B-DNA provide the driving force for genome packaging in double-stranded DNA bacteriophages.

Authors:  Stephen C Harvey
Journal:  J Struct Biol       Date:  2014-12-05       Impact factor: 2.867

Review 7.  Mechanisms of DNA Packaging by Large Double-Stranded DNA Viruses.

Authors:  Venigalla B Rao; Michael Feiss
Journal:  Annu Rev Virol       Date:  2015-09-10       Impact factor: 10.431

8.  Repulsive DNA-DNA interactions accelerate viral DNA packaging in phage Phi29.

Authors:  Nicholas Keller; Damian delToro; Shelley Grimes; Paul J Jardine; Douglas E Smith
Journal:  Phys Rev Lett       Date:  2014-06-17       Impact factor: 9.161

9.  DNA Scrunching in the Packaging of Viral Genomes.

Authors:  James T Waters; Harold D Kim; James C Gumbart; Xiang-Jun Lu; Stephen C Harvey
Journal:  J Phys Chem B       Date:  2016-05-26       Impact factor: 2.991

10.  Dualities in the analysis of phage DNA packaging motors.

Authors:  Philip Serwer; Wen Jiang
Journal:  Bacteriophage       Date:  2012-10-01
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