Structural basis for the binding affinity of xanthines with the DNA intercalator acridine orange

M. B. Lyles, I. L. Cameron, H. R. Rawls

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16 Scopus citations


Caffeine (CAF), a methyl-substituted xanthine, interacts with polyaromatic DNA intercalators and has been hypothesized to interfere with their intercalation into DNA. Optical absorption spectroscopy was used to determine the binding affinities (Kassoc) and structural effects of a series of methyl-substituted xanthines and a series of methyl-substituted uric acids (8-oxoxanthine) with the known DNA intercalator acridine orange (AO). There is evidence that complexation occurred (Kassoc ≥150 M-1.; binding curve saturation ∼ ≥50%) between AO and 1,7-dimethylxanthine (155 M-1), 1,3-dimethylxanthine (theophylline, 157 M-1), 1,3,7-trimethylxanthine (CAF, 256 M-1), 1,3-dimethyl-8-chloroxanthine (413 M-1), 1,3,7,9-tetramethyl-8-oxyxanthine (tetramethyl uric acid or TMU, 552 M-1), and theophylline ethylenediamine (aminophylline, 596 M-1). No definitive evidence of complexation occurred between AO and 16 other substituted xanthines or purines, although there was some evidence of weak complexation (Kassoc < 150 M-1) between AO and eight of the sixteen. Three common structural similarities were identified among those compounds found to form significant bonding with AO: (i) the N1 or N3 on the xanthine structure must be substituted with a methyl group; (ii) oxygen or chlorine substitution at C8 increases binding affinity to AO when resonate states remain unchanged; and (iii) Kassoc increases with an increase in number of methyl group substitutions on the 1-or 3-methylxanthine core structure. These results are explained on the basis of complex stabilization due predominately to hydrophobic attraction, with a contribution from charge transfer between donor and acceptor components. This information can be used in the manipulation of the physical or chemical characteristics of biologically active polyaromatic molecules.

Original languageEnglish (US)
Pages (from-to)4650-4660
Number of pages11
JournalJournal of Medicinal Chemistry
Issue number26
StatePublished - Dec 20 2001

ASJC Scopus subject areas

  • Molecular Medicine
  • Drug Discovery


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