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Nucleic Acids Research 2004 32(15):4585-4595; doi:10.1093/nar/gkh800
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Published online 27 August 2004

Nucleic Acids Research, Vol. 32 No. 15 © Oxford University Press 2004; all rights reserved

Splicing affects presentation of RNA dimerization signals in HIV-2 in vitro

Jean-Marc Lanchy, Quenna N. Szafran and J. Stephen Lodmell*

Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA

* To whom correspondence should be addressed. Tel: +1 406 243 6393; Fax: +1 406 243 4304; Email: stephen.lodmell{at}umontana.edu

Received May 25, 2004; Revised and Accepted August 11, 2004

During retroviral replication, full-length viral RNAs are encapsidated into new virus particles, while spliced RNAs are excluded. The Retroviridae are unique among viruses in that infectious viral particles contain a dimer of two identical genomic RNA strands. A variety of experimental data has suggested that dimerization and encapsidation of full-length viral RNAs are linked processes, although whether dimerization is a prerequisite for encapsidation, or conversely, dimerization follows encapsidation, has not been firmly established. If dimerization was the sole determinant for encapsidation, then spliced viral RNAs might be expected to display a reduced capacity for dimerization, resulting in their exclusion from the dimerization pool. Here, we studied the in vitro dimerization properties of unspliced and spliced HIV-2 RNA. We find that the rate and yield of dimerization of Nef, Rev and Tat spliced RNAs exceeded those of unspliced RNA. Although these data do not support a simple correlation between dimerization efficiency and the presence of introns, they establish that splicing affects the presentation of dimerization signal(s), which we corroborate with structure probing. This change in RNA conformation likely affects the RNA's suitability for packaging. Furthermore, the presence of upstream and downstream elements that affect the conformation of the packaging signal represents a potentially efficient viral strategy for correctly sorting spliced versus unspliced RNAs.


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