The triplex forming ability of nonnatural nucleobases: A computational approach

R. Fenyö, Z. Tímár, I. Pálinkó, B. Penke

Research output: Contribution to journalArticle

3 Citations (Scopus)


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. (C) 2000 Elsevier Science B.V.

Original languageEnglish
Pages (from-to)101-105
Number of pages5
JournalJournal of Molecular Structure: THEOCHEM
Issue number1-3
Publication statusPublished - Jan 7 2000



  • Geometric data
  • H-bond energies
  • Semiempirical methods
  • Triplet forming nucleobases

ASJC Scopus subject areas

  • Biochemistry
  • Condensed Matter Physics
  • Physical and Theoretical Chemistry

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