Biopolymers and cell. 2006; 22 (5): 339 - 349

Structural Characteristics of Intercalation Complex of Deoxyheptanucleotide Hairpin d(GCGAAGC) with Anthracycline Antibiotic Daunomycin

V. V. Kostjukov, V. I. Pahomov, L. N. Dimant

The investigation of intercalation complex of deoxyheptanucleotide d(GCGAAGC) hairpin and anthracycline antibiotic daunomycin (DAU) in aqueous-saline solution has been performed by one- and two-dimensional ¹H NMR spectroscopy and molecular mechanics methods. The equilibrium thermodynamic parameters of complexation have been obtained. The spatial structure of the complex has been calculated and the comparative analysis of conformational and energetic parameters of associated and free heptamer hairpin has been carried out. The molecular dynamics of the complex in nanosecond time scale has been studied and mobility of structure elements has been evaluated. The interaction of the complex of heptamer-DAU with nearest hydration shell has been analyzed.

Key words: hairpin d(GCGAAGC), daunomycin, intercalation, ¹H NMR spectroscopy, molecular dynamics.