J Mol Biol. 1998 Oct 2;282(4):801-18.

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

Pappalardo L, Kerwood DJ, Pelczer I, Borer PN.

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Department of Chemistry, Syracuse University, Syracuse, NY, 13244-4100, USA.

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.

PMID:: 9743628; [PubMed - indexed for MEDLINE]

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Structures reported by this article

Sl3 Hairpin From The Packaging Signal Of Hiv-1, Nmr, 11 Structures

PDB: 1BN0

Source: synthetic construct

Method: Solution Nmr

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Three-dimensional folding of an RNA hairpin required for packaging HIV-1.
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J Mol Biol. 1998 Oct 2 ;282(4):801-18.

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

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