Dimer initiation sequence of HIV-1(Lai) genomic RNA: NMR solution structure of the extended duplex

The genome of all retrovirus consists of two copies of genomic RNA which ar e noncovalently linked near their 5' end. A sequence localized immediately upstream from the splice donor site inside the HIV-1 Psi-RNA region was ide ntified as the domain responsible for the dimerization initiation. It was s hown that a kissing complex and a stable dimer are both involved in the HIV -1(Lai) RNA dimerization process in vitro. The NCp7 protein activates the d imerization by converting a transient loop-loop complex into a more stable dimer. The structure of this transitory loop-loop complex was recently eluc idated by Mujeeb et al. In work presented here, we use NMR spectroscopy to determine the stable extended dimer structure formed from a 23 nucleotides RNA fragment, part of the 35 nucleotides SL1 sequence. By heating to 90 deg rees C, then slowly cooling this sequence, we were able to show that an ext ended dimer is formed. We present evidence for the three dimensional struct ure of this dimer. NMR data yields evidence for a zipper like motif A8A9.A1 6 existence. This motif enables the surrounding bases to be positioned more closely and permit the G7 and C17 bases to be paired. This is different to other related sequences where only the kissing complex is observed, we sug gest that the zipper like motif AA.A could be an important stabilization fa ctor of the extended duplex.