The triplex forming ability of nonnatural nucleobases: a computational approach

Fenyő, R. and Timár, Zoltán and Pálinkó, István and Penke, Botond (2000) The triplex forming ability of nonnatural nucleobases: a computational approach. JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 496. pp. 101-105. ISSN 0166-1280

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Abstract

Nucleotide bases with the capability of specific H-bonding interactions with base pairs in the major groove of DNA have been designed. During the procedure several factors were taken into account: the molecule (i) should contain substructure capable of Hoogsteen H-bonding with the purine base of the Watson-Crick doublet; (ii) should be cyclic and planar; (iii) for practical purposes it should be chemically stable; and (iv) the triplet should also be stable. Calculations by semiempirical methods lead to four compounds as possible triplet forming nucleobases: quinolin-2-ylamine, indol-2-ylamine, pyridin-2-ylamine and 2-aminopyrrol. They all meet the above criteria. Geometry optimization of the triplets resulted in H-bond distances as well as H-bond energies.

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