Structural and thermodynamic basis of interaction of the putative anticancer agent chelerythrine with single, double and triple-stranded RNAs

Abstract

A comparative study on the interaction of the natural plant alkaloid chelerythrine with triple helical poly(U)·poly(A)*poly(U), double helical poly(A)·poly(U) and single stranded poly(U) (the dot and star representing the Watson-Crick and Hoogsteen base pairing) has been performed using various biophysical and thermodynamic techniques. Chelerythrine binds to the duplex and triplexes in a cooperative manner with affinity of the order of 10⁶ M⁻¹. A weaker binding (∼10⁵ M⁻¹) in a non-cooperative mode occurred with poly(U). Chelerythrine is more selective towards RNA triplex than its parent duplex. The triplex was stabilized specifically without affecting the stability of the duplex. Fluorescence quenching, fluorescence polarization and energy transfer from the nucleotides to the alkaloid, and viscosity results gave convincing evidence for a true intercalative binding of chelerythrine to the triplex and the duplex structures, and partial base stacking with poly(U). The conformations of both double and triple helices were perturbed on binding but no effect occurred to the single strand structure. The binding of the alkaloid to all three RNA helices was found to be exothermic; to the triplex it was entropy driven with favorable enthalpy change, to the duplex enthalpy driven and to the single strand it was enthalpy driven. These results provide new knowledge on the mode, mechanism and specificity, and energetics of binding of the natural alkaloid and putative anticancer agent chelerythrine to different RNA conformations.