HIV-1 Nucleocapsid Protein Switches the Pathway of Transactivation Response Element RNA/DNA Annealing from Loop-Loop "Kissing" to "Zipper"

My Nuong Vo, George Barany, Ioulia Rouzina, Karin Musier-Forsyth

Research output: Contribution to journalArticlepeer-review

46 Scopus citations

Abstract

The chaperone activity of HIV-1 (human immunodeficiency virus type 1) nucleocapsid protein (NC) facilitates multiple nucleic acid rearrangements that are critical for reverse transcription of the single-stranded RNA genome into double-stranded DNA. Annealing of the transactivation response element (TAR) RNA hairpin to a complementary TAR DNA hairpin is an essential step in the minus-strand transfer step of reverse transcription. Previously, we used truncated 27-nt mini-TAR RNA and DNA constructs to investigate this annealing reaction pathway in the presence and in the absence of HIV-1 NC. In this work, full-length 59-nt TAR RNA and TAR DNA constructs were used to systematically study TAR hairpin annealing kinetics. In the absence of NC, full-length TAR hairpin annealing is ∼ 10-fold slower than mini-TAR annealing. Similar to mini-TAR annealing, the reaction pathway for TAR in the absence of NC involves the fast formation of an unstable "kissing" loop intermediate, followed by a slower conversion to an extended duplex. NC facilitates the annealing of TAR by ∼ 105-fold by stabilizing the bimolecular intermediate (∼ 104-fold) and promoting the subsequent exchange reaction (∼ 10-fold). In contrast to the mini-TAR annealing pathway, wherein NC-mediated annealing can initiate through both loop-loop kissing and a distinct "zipper" pathway involving nucleation at the 3′-/5′-terminal ends, full-length TAR hairpin annealing switches predominantly to the zipper pathway in the presence of saturated NC.

Original languageEnglish (US)
Pages (from-to)789-801
Number of pages13
JournalJournal of Molecular Biology
Volume386
Issue number3
DOIs
StatePublished - Feb 27 2009

Keywords

  • HIV-1 nucleocapsid protein
  • TAR RNA/DNA annealing
  • minus-strand transfer
  • nucleic acid aggregation
  • nucleic acid chaperone activity

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