Sequence-dependent structural variations in nucleic acids are important for protein-nucleic acid and RNA-DNA interactions essential for life as well as for nucleic acid packaging. It is proposed that methodological developments be continued which have the aim of determining the dynamic nature of the structure of nucleic acids. The principal tool to be utilized is NMR. Computational methods of analyzing the NMR data are proposed. Primary emphasis, however, is on applying the methodology to determine structure and dynamics in several systems of nucleic acids. Systems include DNA promoter sequences, RNA-DNA bybrids including a hybrid with a mismatch, slipped loop and pseudosquare knot DNA and slipped loop RNA, nicked DNA, and duplexes formed between the target RNA and antisense DNA oligonucleotides. With the increasing numbers of high-definition structures becoming available, statistical analyses of solution structures of DNA duplexes and RNA-DNA hybrids will be carried out to discern sequence-dependent structural features which may have useful predictive value. Molecular motions, or conformational fluctuations, will be investigated by measuring imino proton exchange kinetics and heteronuclear relaxation parameters, using DNA labeled either selectively or uniformly with 13C, 15N, or 2H. Structural and stability studies of sequences composed of RNA complexed by complementary antisense DNA strands containing chirally pure methylophonates at alternating backbone positions, as well as chirally pure phosphorothioates or phosphorodithioates at each position, and 2'-O-alkoxy derivatives, will be compared with the RNA bound by the normal complementary DNA. To date, there has been little structural information available on these antisense nucleotides, in spite of their growing use as therapeutic and diagnostic agents. Slipped loop and the related pseudosquare knot DNA structures are potentially formed with short direct repeats; while some trinucleotide repeats have been associated with genomic instability leading to diseases such as myotonic dystrophy, somewhat longer direct repeats often occur in gene regulatory regions and have been postulated as significant for regulation.
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