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

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

doi:10.1006/jmbi.1998.2046

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

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

Department of Chemistry

Research output: Contribution to journal › Article › peer-review

60 Scopus citations

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.

Original language	English (US)
Pages (from-to)	801-818
Number of pages	18
Journal	Journal of Molecular Biology
Volume	282
Issue number	4
DOIs	https://doi.org/10.1006/jmbi.1998.2046
State	Published - Oct 2 1998

Keywords

HIV-1
NMR
Packaging
RNA
Tetraloop

ASJC Scopus subject areas

Structural Biology
Molecular Biology

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10.1006/jmbi.1998.2046

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title = "Three-dimensional folding of an RNA hairpin required for packaging HIV-1",

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.",

keywords = "HIV-1, NMR, Packaging, RNA, Tetraloop",

author = "Lucia Pappalardo and Kerwood, {Deborah J.} and Istv{\'a}n Pelczer and Borer, {Philip N.}",

note = "Funding Information: This work was supported in part by NIH grant GM32691 and a Syracuse University Graduate School fellowship (to L.P.). The authors are grateful for helpful discussions with Professors M. Summers (University of Maryland, Baltimore Co.), and J. Dabrowiak and J. Goodisman (Syracuse University) and students R. DeGuzman and Z. Wu (UMBC), and B. DeCastro (SU). NMR-refined structures have been deposited with the Brookhaven Protein DataBank (accession number 1bn0).",

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doi = "10.1006/jmbi.1998.2046",

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AU - Pappalardo, Lucia

AU - Kerwood, Deborah J.

AU - Pelczer, István

AU - Borer, Philip N.

N1 - Funding Information: This work was supported in part by NIH grant GM32691 and a Syracuse University Graduate School fellowship (to L.P.). The authors are grateful for helpful discussions with Professors M. Summers (University of Maryland, Baltimore Co.), and J. Dabrowiak and J. Goodisman (Syracuse University) and students R. DeGuzman and Z. Wu (UMBC), and B. DeCastro (SU). NMR-refined structures have been deposited with the Brookhaven Protein DataBank (accession number 1bn0).

PY - 1998/10/2

Y1 - 1998/10/2

N2 - 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.

AB - 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.

KW - HIV-1

KW - NMR

KW - Packaging

KW - RNA

KW - Tetraloop

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

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Keywords

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