The primary focus of this competing renewal application is on the structure and recognition of multi-stranded DNA architectures adopted by guanine plus adenine rich sequences. Such sequences are frequently located within gene regulatory regions and recombination hot spot sites, at the replication origin of signal-stranded bacteriophages, and as tandem repeats in telomeric, centromeric and triplet repeat disease sequences. Such guanine plus adenine rich sequences can align through mismatch, triple orientation of strands and pairing alignments. Our research program applies NMR techniques to architectures, their cation dependent structural transitions and identify unique topologies associated with discriminative recognition. The three areas of focus are: (1) Identification and characterization of base triads involving alignments of two adjacent in-plane bases from one strand (a platform) and a third from a complimentary strand. We propose to elucidate the potential of triad DNA involving stacked triads as a structural motif for the higher order folds of triplet repeat d(GGC)n, d(CAG)n and d(GAA)n disease quadruplex folds in the Tetrahymena telomere d (T2G4)n and mouse Ms6-hm hypervariable microsatellite d(CAG3)n repeats to define the range of strand directionalities, loop connectivities and tetrad alignments. (3) The demonstration and structural characterization of A.(G.G.G.G).A hexads, formed by adenines through in-plane sheared G.A mismatch alignment, with G-tetrads. Such hexad and related octad alignments represent a novel approach towards G-quadruplex recognition and stabilization. G- quadruplexes represent an attractive anti-tumor drug design target since the reverse transcriptase replicative activity of telomerase has an absolute requirement for competing single-stranded telomeric ends.
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