POLYPURINE TRACT DNA SEQUENCE, CAAAGAAAAG CONTAINING 2 MOLECULES IN ASYMMETRIC UNIT. IS THE 2ND HELIX DISORDERED? Gye Won Han, Mary L. Kopka, David S. Goodsell and Richard E. Dickerson, Molecular Biology Institute, Department of Chemistry and Biochemistry, University of California at Los Angeles, CA 90095, USA

The DNA duplex decamer CAAAGAAAAG : CTTTTCTTTG was synthesized and crystallized to explore the structure of the polypurine tract of HIV-1. Although the polypurine tract consists of 16 purines, initially a 10-mer was used because of stacking considerations. A 15-mer also was synthesized for crystallization. This sequence is highly conserved in HIV, thus making an attractive target for drug design.

The native crystal is monoclinic in space group C2 with 2 helices (A and B) in asymmetric unit. Cell dimensions are a=59.82 Å, b=28.28 Å, c=72.49 Å and (=103.9deg.. X-ray data were collected using RAXIS-II at -180deg.C up to 1.85 Å resolution.

Using single isomorphous replacement methods with CAAAGAAAAG : CTU_BrTTCTTTG gives only one Br site in difference Patterson map, and this is consistent with the molecular replacement result where a clear hydration spine appeared in helix A, but not in the 2nd helix.

Diffusion of cisplatin (cis-dichlorodiamino platinum (II)) into the native crystal once again gives only one Pt site in helix A in the Difference Fourier map using SIR_Br phases. We believe the 2nd helix may be disordered and in order to improve the phases, a second derivative CAAAGAAAAG : CTTTTC_BrTTTG for MIR method will be used.