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J. Biol. Chem., Vol. 277, Issue 49, 46900-46911, December 6, 2002
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From the Recombination promotes retrovirus evolution. It
involves transferring a growing DNA primer from one genomic RNA
template in the virus to the other. Strand transfer results in
vitro suggested that pausing of the reverse transcriptase during
synthesis allows enhanced RNase H cleavage of the initial, or donor,
RNA template that facilitates primer interaction with the acceptor
template. Hairpins are common structures in retrovirus RNAs that induce pausing. Analyzing primer transfers in hairpins by base substitution markers showed transfer sites well beyond the site of pausing. We
developed methods to distinguish the initial site of primer-acceptor template interaction from the site of primer terminus transfer. The
strand transfer mechanism was confirmed to involve two steps. In the
first, the acceptor template invades the primer-donor complex. However,
the primer terminus continues elongation on the donor RNA. The
interacting primer and acceptor strands then propagate by branch
migration to catch the advancing primer terminus. Some distance
downstream of the invasion site the primer terminus transfers, marking
the genetic shift from donor to acceptor. Nucleocapsid protein (NC) is
known to influence primer elongation and strand exchange. The presence
of NC increased the efficiency of transfers but did not appear to alter
the fundamental transfer mechanism.
Strand Transfer Occurs in Retroviruses by a Pause-initiated
Two-step Mechanism*
§,,¶,
,, and**
Department of Biochemistry and Biophysics,
University of Rochester Medical Center, Rochester, New York 14642 and
the Departement de Pharmacochimie Moleculaire et Structurale,
INSERM U266, CNRS UMR 8600, Unite d'Enseignement de la Recherche
(UER) des Sciences Pharmaceutiques et Biologiques,
Paris 75270, France
*
This work was supported in part by National Institutes of
Health (NIH) Grant GM49573 (to R. A. B. and P. J. F.).The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
"advertisement" in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
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