The crystal structure of the dimerization initiation site of genomic HIV-1RNA reveals an extended duplex with two adenine bulges

Background: An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the fo rmation of a transient 'kissing-loop complex' that is thought to be subsequ ently matured into an extended duplex by the nucleocapsid protein (NCp). Al though chemical probing and nuclear magnetic resonance spectroscopy have pr ovided insight into the structure of the kissing-loop structure, no structu ral information concerning the extended-duplex state is available so far. Results: The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 Angstrom resolution in two different space groups. I t reveals a 22 base pair extended duplex with two noncanonical Watson-Crick -like G-A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G-A base-pair conforma tions. A network of eight magnesium cations was clearly identified, one bei ng unusually chelated by the 3' phosphate of each bulge across an extremely narrowed deep major groove. Conclusions: These crystal structures represent the putative matured form o f the initial kissing-loop complex. They show the ability of this self-comp lementary RNA hairpin loop to acquire a more stable extended duplex structu re. Both bulged adenines form a striking 'base grip' that could be a recogn ition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promo te and stabilize the observed extrahelical conformation of these bulges.