This proposal is designed to study the molecular basis of the conformational variabilities of nucleic acids, including DNA, RNA and DNA- RNA hybrid molecules by using single crystal x-ray diffraction technique as the major tool. It will be complemented by other spectroscopic studies, in particular high resolution nuclear magnetic resonance spectroscopy. Large amounts of pure DNA and RNA oligonucleotides with carefully chosen sequences will be synthesized on solid support resins either manually in solution, or by automated DNA synthesizer. Long RNA molecules will be prepared by T7 RNA polymerase system on DNA templates and they will be suitably purified for crystallization experiments. The following DNA and RNA molecular systems will be the major focus of this proposal. 1. Higher-ordered structures: triple-stranded, hairpins, cruciforms, pseudoknots, circular molecules, branched RNAs. 2. Sequence-dependent conformational analysis of double helical nucleic acids, including DNA, RNA, DNA-RNA hybrids. 3. Stable alternative nucleic acid conformations: Z-DNA, P-DNA, Hoogsteen Helix. 4. Nucleic acids with defects: Mismatch, bulge, missing base(apurine/apyrimidine), modified base (O6-mG/O4-mT), phosphotriester. The results from these structural studies both in solution and in solid states will be compared and they will be the basis for further theoretical analysis in order to fully understand the structure, dynamics and energetics of nucleic acids at the molecular level.
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