Abstract

Synthesis of cationic, chiral PNA analogues with an extra atom in the backbone ( bepPNA) is reported. The (2 S,4 S) geometry of the pyrrolidine ring, and an additional carbon atom in the backbone of homopyrimidine- bepPNAs resulted in the optimization of the inter-nucleobase distance, such that selective binding to complementary RNA over DNA was observed in the triplex mode. It was evident from circular dichroism studies that oligomers with mixed aminoethylglycyl–bep ( aeg– bep) repeating units, and also bepPNA with homogeneous backbone attained structures quite different from those of aegPNA 2:RNA/DNA complexes. The bepPNA, when incorporated in a duplex forming mixed purine–pyrimidine sequence, also showed a preference for binding complementary RNA over DNA.

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