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Pure Appl. Chem., 2004, Vol. 76, No. 7-8, pp. 1599-1603

Conformationally restricted cationic polyamide analogs of nucleic acids: Design, synthesis, and DNA/RNA binding studies

V. A. Kumar, Moneesha D'Costa, P. S. Lonkar, Meena, P. S. Pallan and K. N. Ganesh

Division of Organic Chemistry (Synthesis), National Chemical Laboratory, Pune 411008, India

Abstract: The remarkable medicinal importance of the achiral, acyclic, and uncharged aminoethylglycyl peptide nucleic acids (aegPNAs) as DNA/RNA mimics has challenged chemists to circumvent the limitations of their in vivo efficacy. In this context, we have designed conformationally restricted five- and six-membered cyclic PNA analogs by introduction of chemical bridges in aegPNAs leading to a large variety of structures with defined configurations and conformational preferences, effecting concomitant installation of a positive charge in the backbone. The synthesis and biophysical properties of these cationic aminoethylprolyl PNAs, pyrrolidine PNAs, and piperidine PNAs endowed with increased water solubility and affinity toward target nucleic acids is presented. These nucleic acid analogs as lead structures are a part of a chemical evolution process that might give rise to a synthetic nucleic acid analog having optimum properties for medicinal applications.