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Nucleic Acids Research, Vol 26, Issue 15 3567-3571, Copyright © 1998 by Oxford University Press

ARTICLES

Solution studies of the dimerization initiation site of HIV-1 genomic RNA

F Dardel, R Marquet, C Ehresmann, B Ehresmann and S Blanquet
Laboratoire de Biochimie, UMR 7654 du CNRS, Ecole Polytechnique, 91128 Palaiseau Cedex, France. fred@botrytis.polytechnique.fr

Dimerization of HIV-1 genomic RNA is an essential step of the viral cycle, initiated at a conserved stem-loop structure which forms a 'kissing complex' involving loop-loop interactions (dimerization initiation site, DIS). A 19mer RNA oligonucleotide (DIS-19) has been synthesized which forms a stable symmetrical dimer in solution at millimolar concentrations. Dimerization does not depend on addition of Mg2+. RNA ligation experiments unambiguously indicate that the formed dimer is a stable kissing complex under the NMR experimental conditions.1H NMR resonance assignments were obtained for DIS-19 at 290 K and pH 6.5. Analysis of the pattern of NOE connectivities reveals that the helix formed by loop-loop base pairing is stacked onto the two terminal stems. Non-canonical base pairs between two essential and conserved adenines are found at the junctions between the two intramolecular and the single intramolecular helices.
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