Biopolym. Cell. 2006; 22(5):339-349.
http://dx.doi.org/10.7124/bc.000741
Structure and Function of Biopolymers
Structural characteristics of intercalation complex of deoxyheptanucleotide hairpin d(GCGAAGC) with anthracycline antibiotic daunomycin
1Kostjukov V. V., 1Pahomov V. I., 1Dimant L. N.
  1. Sevastopol National Technical University
    33, Universytetska Str., Sevastopol, Ukraine, 99053

Abstract

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