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Nucleic Acids Research 2006 34(9):2698-2709; doi:10.1093/nar/gkl318
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Published online 19 May 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Affinity of molecular interactions in the bacteriophage {varphi}29 DNA packaging motor

Mark A. Robinson1,3, Jonathan P.A. Wood1,3, Stephanie A. Capaldi1,3, Andrew J. Baron1,3, Christopher Gell2,3, D. Alastair Smith2,3 and Nicola J. Stonehouse1,3,*

1 Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds Leeds, LS2 9JT, UK 2 Institute of Molecular Biophysics, University of Leeds Leeds, LS2 9JT, UK 3 Astbury Centre for Structural Molecular Biology, University of Leeds Leeds, LS2 9JT, UK

*To whom correspondence should be addressed. Tel: + 44 113 343 3102; Fax: + 44 113 343 2835; Email: n.j.stonehouse{at}leeds.ac.uk

Received March 16, 2006. Revised April 4, 2006. Accepted April 12, 2006.

DNA packaging in the bacteriophage {varphi}29 involves a molecular motor with protein and RNA components, including interactions between the viral connector protein and molecules of pRNA, both of which form multimeric complexes. Data are presented to demonstrate the higher order assembly of pRNA together with the affinity of pRNA:pRNA and pRNA:connector interactions, which are used to propose a model for motor function. In solution, pRNA can form dimeric and trimeric multimers in a magnesium-dependent manner, with dissociation constants for multimerization in the micromolar range. pRNA:connector binding is also facilitated by the presence of magnesium ions, with a nanomolar apparent dissociation constant for the interaction. From studies with a mutant pRNA, it appears that multimerization of pRNA is not essential for connector binding and it is likely that connector protein is involved in the stabilization of higher order RNA multimers. It is proposed that magnesium ions may promote conformational change that facilitate pRNA:connector interactions, essential for motor function.

Present addresses: Jonathan P.A. Wood, Materials Today, Elsevier, The Boulevard, Langford Lane, Kidlington, OX5 1GB, UK

Stephanie A. Capaldi, Massachusetts Institute of Technology, Department of Biology, 31 Ames Street, 68-132 Cambridge MA 02139, USA

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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