Structural studies on nucleic acids are essential to understand the genetics of living organisms. This proposal will continue the crystal structural work on A-form oligonucleotides and drug complexes of B-DNA and RNA. The work will provide the limits of nucleic acid conformation, details of the tertiary structures of the duplexes, novel base-pairing schemes, base triples and quartets and multiple modes of drug interactions. Since A-DNA packs with the termini abutting into the body of neighboring duplexes, different from the packing of other nucleic acids, other packing modes will be sought. Alternating sequences with a 5'-purine start generally form A-DNA, but the all-GC decamer d(GCGCGCGCGC) sequence forms a left-handed Z-DNA. While the decamer d(GCACGCGTCG) with all four bases, AT interposing the GC's, is A-DNA. This case will be investigated with a single A*T base pair substituting for a G*C base pair at different positions in a 10-mer and a 12-mer. Drug complexes of different B-DNA sequences will be studied to see whether they form side-by-side or end-to-end complexes or other binding modes. Hybrid DNA-RNA structures will be investigated to determine if the sugar puckering modes are like B-DNA (C2'-endo) or RNA (C3'-endo) or a mixture. The O2'-hydroxyl group, which makes RNA different from DNA, will be studied for its role in intra and inter-duplex hydrogen bonding and formation of tertiary structures. Long (16-mers and longer) RNA oligonucleotides, both with and without mispairs and bulges, will be investigated. The crystal structures will be compared with the solution structures to gain further insight into the differences between the solid state and the solution state. The oligonucleotides will be synthesized and crystallized and the intensity data collected on an in-house R-Axis IIc Imaging plate/Siemens area detector systems. The structures will be solved by molecular replacement or by the heavy atom method and refined by XPLOR. The structural work will be invaluable to better understand health, gene regulation and rational drug design.
