Three-dimensional folding of an RNA hairpin required for packaging HIV-1

Lucia Pappalardo, Deborah J. Kerwood, István Pelczer, Philip N. Borer

Research output: Contribution to journalArticlepeer-review

60 Scopus citations


An NMR-based structure is presented for a 20 mer hairpin model of the SL3 stem-loop from the HIV-1 packaging signal. The stem has an A-family structure. However, the GGAG tetraloop appears to be flexible with the second (G10) and fourth (G12) bases extruded from the normal stacking arrangement. The A-base (A11) occupies a cavity large enough for it to jump rapidly between stacking upon G9 (in the loop) and G13 (from the base-pair adjacent to the loop). The H-bonding loci of G10, A11, and G12 are unoccupied in the free RNA structure. The loop should be easily adaptable to binding by the HIV-1 nucleocapsid protein or loop receptors.

Original languageEnglish (US)
Pages (from-to)801-818
Number of pages18
JournalJournal of Molecular Biology
Issue number4
StatePublished - Oct 2 1998


  • HIV-1
  • NMR
  • Packaging
  • RNA
  • Tetraloop

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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