Thermodynamic study of the discrimination between uridine and thymidine derivatives by hydrophobic, stacking, and intercalating interactions

M. V. Rekharsky, Asao Nakamura, G. A. Hembury, Y. Inoue

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Thermodynamic parameters for the complexation reactions of uridine/thymidine nucleobases and related compounds, with hosts of differing binding modes and properties (natural cyclodextrins, 5,10,15,20-tetrakis (1-methlpyridinium-4-yl) porphyrin tetrachloride and bis-intercaland macrocycle) have been determined by titration microcalorimetry and/or fluorometry, in an aqueous buffer. For each of these hosts the effect of the 5-methyl group on the binding affinities was investigated. Although the affinities of uridine and thymidine towards cyclodextrins and 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin tetrachloride are very similar, the intercalation of these compounds into the bis-intercaland macrocycle has been shown to result in a high degree of discrimination of approximately 10 times. On the basis of thermodynamic data, the obtained contribution made by the 5-methyl group of thymidine to the structural characteristics of DNA and RNA is discussed.

Original languageEnglish
Pages (from-to)449-457
Number of pages9
JournalBulletin of the Chemical Society of Japan
Issue number3
Publication statusPublished - 2001 Mar
Externally publishedYes


ASJC Scopus subject areas

  • Chemistry(all)

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