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We have determined solution structure of r (GGAGGUUUUGGAGG) (R14) by NMR; the RNA 14-mer forms an intra-strand parallel quadruplex with a G-tetrad and a hexad, in which a G-tetrad core is augmented by association of two A residues. The quadruplex further forms a dimer through stacking interaction between the hexads. We also synthesized the corresponding DNA 14-mer, d (GGAGGTTTTGGAGG) (D14), and examined its properties and structure by CD, gel electrophoresis, and NMR. The CD and gel electrophoretic studies suggest that D14 forms a quadruplex entirely different from that of R14 in the presence of K+ ions; two molecules of D14 form a quadruplex containing antiparalle strands and diagonal loops. The NMR study also gave the results that are consistent with such structure: alternate glycosidic conformation, 5'G(syn)-G(anti)3', and characteristic chemical shift data.

Quadruplex structures of RNA 14-mer, r(GGAGGUUUUGGAGG) and DNA 14-mer, d(GGAGGTTTTGGAGG)