Crystallization of the dimerization-initiation site of genomic HIV-1 RNA: Preliminary crystallographic results

The genomic RNA of all retroviruses is encapsidated in virions as a dimer o f single-stranded chains held together near their 5'-end. For HIV-1, the in itial site of dimerization has been shown to be a hairpin with a nine-resid ue loop containing a self-complementary sequence of six residues. This stru cture is proposed to promote dimerization by loop-loop interaction and form ation of a so-called 'kissing complex'. A 23-nucleotide RNA strand containi ng the loop enclosed by a seven base-pair stem has been synthesized;ed. Thi s oligomer was crystallized by the vapour-diffusion method at 310 K, pH 6.5 , with methyl diol as the precipitant agent in the presence of MgCl2, KCl a nd spermine. Quasi-complete diffraction data were obtained at 2.7 Angstrom resolution with a conventional X-ray source and at 2.3 Angstrom resolution on a synchrotron beamline. The space group is P3(1)21 or its P3(2)21, with cell parameters a = b = 60.1, c = 65.9 Angstrom at ambient temperature, or a = b = 59.0, c = 64.3 Angstrom in a nitrogen-gas stream. There are two oli gomers per asymmetric unit as determined from absorbance measurements of a dissolved crystal whose volume was carefully determined. In some cases, eit her perfectly or partially twinned crystals were obtained. Perfect twinning is detected by an apparent hexagonal symmetry and yields unusable crystall ographic data, whilst partial twinning yields usable data after adequate pr ocessing. Structure solution is under way by searching for heavy atom deriv atives and systematically substituting bromo- or iodouridines for uridines.