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Nucleic Acids Research 2005 33(22):7151-7163; doi:10.1093/nar/gki1015
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Published online 20 December 2005

© The Author 2005. 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{at}oxfordjournals.org

Article

Structural polymorphism of the HIV-1 leader region explored by computational methods

Wojciech Kasprzak, Eckart Bindewald and Bruce A. Shapiro1,*

Basic Research Program, SAIC Frederick, NCI-Frederick Building 469, Room 150, Frederick, MD 21702, USA 1Center for Cancer Research Nanobiology Program, National Cancer Institute Building 469, Room 150, NCI-Frederick, Frederick, MD 21702, USA

*To whom correspondence should be addressed. Tel: +1 301 846 5536; Fax: +1 301 846 5598; Email: bshapiro{at}ncifcrf.gov

Received September 1, 2005. Revised October 24, 2005. Accepted November 28, 2005.

Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5'-untranslated leader region (5'-UTR) can fold in vitro into two alternative conformations, branched (BMH) and ‘linearized’ (LDI) and switch between them to achieve different functionality. In this study we computationally explored in detail, with our massively parallel genetic algorithm (MPGAfold), the propensity of 13 HIV-1 5'-UTRs to fold into the BMH and the LDI conformation types. Besides the BMH conformations these results predict the existence of two functionally equivalent types of LDI conformations. One is similar to what has been shown in vitro to exist in HIV-1 LAI, the other is a novel conformation exemplified by HIV-1 MAL long-distance interactions. These novel MPGAfold results are further corroborated by a consensus probability matrix algorithm applied to a set of 155 HIV-1 sequences. We also have determined in detail the impact of various strain mutations, domain sizes and folds of elongating sequences simulating folding during transcription on HIV-1 RNA secondary structure folding dynamics.


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