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

J Mol Biol. 1998 Oct 2;282(4):801-18. doi: 10.1006/jmbi.1998.2046.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Pairing
  • Base Sequence
  • Binding Sites
  • Carbon / chemistry
  • Carbon / metabolism
  • Consensus Sequence / genetics
  • Dimerization
  • Genome, Viral*
  • HIV-1 / genetics*
  • HIV-1 / physiology
  • Hydrogen / chemistry
  • Hydrogen / metabolism
  • Hydrogen Bonding
  • Hydrogen-Ion Concentration
  • Models, Molecular
  • Nitrogen / chemistry
  • Nitrogen / metabolism
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleic Acid Conformation*
  • Phosphates / chemistry
  • Phosphates / metabolism
  • RNA, Viral / chemistry*
  • RNA, Viral / genetics
  • RNA, Viral / physiology
  • Regulatory Sequences, Nucleic Acid*
  • Temperature
  • Thermodynamics
  • Virus Assembly / genetics*

Substances

  • Phosphates
  • RNA, Viral
  • Carbon
  • Hydrogen
  • Nitrogen