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Nucleic Acids Research 2004 32(11):3493-3502; doi:10.1093/nar/gkh668
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Published online 1 July 2004

Nucleic Acids Research, Vol. 32 No. 11 © Oxford University Press 2004; all rights reserved

Binding of phage {Phi}29 architectural protein p6 to the viral genome: evidence for topological restriction of the phage linear DNA

Víctor González-Huici, Martín Alcorlo, Margarita Salas* and José M. Hermoso

Instituto de Biología Molecular ‘Eladio Viñuela’ (CSIC), Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain

* To whom correspondence should be addressed. Tel: +34 91 4978435; Fax: +34 91 4978490; Email: msalas{at}cbm.uam.es

Received April 8, 2004; Revised May 18, 2004; Accepted June 6, 2004

Bacillus subtilis phage {Phi}29 protein p6 is required for DNA replication and promotes the switch from early to late transcription. In vivo it binds all along the viral linear DNA, which suggests a global role as an architectural protein; in contrast, binding to bacterial DNA is negligible. This specificity could be due to the p6 binding preference for less negatively supercoiled DNA, as is presumably the case with viral (with respect to bacterial) DNA. Here we demonstrate that p6 binding to {Phi}29 DNA is greatly increased when negative supercoiling is decreased by novobiocin; in addition, gyrase is required for DNA replication. This indicates that, although non-covalently closed, the viral genome is topologically constrained in vivo. We also show that the p6 binding to different {Phi}29 DNA regions is modulated by the structural properties of their nucleotide sequences. The higher affinity for DNA ends is possibly related to the presence of sequences in which their bendability properties favor the formation of the p6–DNA complex, whereas the lower affinity for the transcription control region is most probably due to the presence of a rigid intrinsic DNA curvature.


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