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Nucleic Acids Research, 2003, Vol. 31, No. 16 4847-4855
© 2003 Oxford University Press

Zinc finger-dependent HIV-1 nucleocapsid protein–TAR RNA interactions

Nick Lee, Robert J. Gorelick1 and Karin Musier-Forsyth*

Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, USA and 1 AIDS Vaccine Program, SAIC-Frederick, Inc., NCI at Frederick, MD 21702, USA

*To whom correspondence should be addressed. Tel: +1 612 624 0286; Fax: +1 612 626 7541; Email: musier{at}chem.umn.edu

In the minus-strand transfer step of HIV-1 reverse transcription, the nucleocapsid protein (NC) promotes annealing of the 3' ‘R’ (repeat) region of the RNA genome to its complementary sequence located in the newly synthesized minus-strand strong-stop DNA. The R region contains the highly stable transactivation response (TAR) RNA hairpin. To gain insights into the molecular details of TAR RNA–NC interactions, we carried out hydroxyl radical footprinting, as well as gel-shift and fluorescence anisotropy binding assays using wild-type and mutant forms of NC. Our results support the conclusion that NC variants with mutations in their zinc finger domains have dramatically altered TAR RNA binding interactions relative to wild-type NC. These data demonstrate that a specific zinc finger architecture is required for optimal TAR RNA binding, and help to explain the requirement for the zinc finger motifs of NC in its role as a nucleic acid chaperone in minus-strand transfer.


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