Molecular mechanisms of caffeine interaction with different structural forms of polyriboadenylic acid: experiment and computer simulation

Abstract

The investigation of interaction of caffeine (Cf) with neutral single-stranded (polyrA) and protonated double-helical forms of polyriboadenylic acid (рolyr(AH-AH) has been carried out by IR-spectroscopy, piezogravimetry and Monte Carlo methods. The hydration isotherms and IR-spectra for wet films of complexes at various relative humidity have been obtained. It was shown that Cf does not influence on formation of the ordered forms of polyrA. In complex with single-helical polyrA Cf decreases the hydration of polynucleotide matrix, but in the complex double-helical polyrA-Cf the hydration of polynucleotide matrix is increased in the comparison with their hydration in isolated state. The data obtained by computer modeling (energetic and structural characteristics and instantaneous configurations) allows us to suggest the molecular models of investigated complexes. In Cf-single-helical polyrA complex two types of Cf binding are possible. The first type is the external binding of Cf molecules and the second type is the partial intercalation of Cf molecule between planes of adjacent adenines. In the complex of Cf with double-stranded helical polyrA only one type of Cf binding near sugar-phosphate backbone of polynucleotide matrix is realized. The results of Monte Carlo simulations are in agree with experimental data for all investigated systems.