Methylxanthines binding with yeast total RNA in the presence of Mg2+: a speed vac-centrifugation-facilitated solid-state Fourier transform infrared analysis

• DOI: 10.1016/j.ab.2004.09.032
• Publication Date: 2005-02-11T09:15:45Z
• Authors: I. Maria Johnson; R. Malathi
• Keywords: Theobromine

Interaction of naturally occurring methylxanthines (theophylline, theobromine, and caffeine) with yeast total RNA has been studied in presence of Mg to understand the modulation of its binding efficacy using Fourier transform infrared (FTIR) spectroscopy, wherein the samples were prepared by transforming the mixture from solution to solid-state employing speed vac centrifugation. The method was found to be a simple and short alternative for solution IR in studying RNA:drug/ligand interaction. The RNA and methylxanthines were complexed in 2:1 ratio in RNase-free water (made up to 1 ml in diethyl phosphoryl-pyrocarbonate-treated sterile microfuge tube) with different MgCl2 concentrations (1, 5, 10, and 35 mM); after a thorough mixing and overnight incubation at 37 C, the samples were concentrated by speed vac centrifugation (SC 110; Savant, USA) under normal physiological temperature and pressure. RNA– Mg and RNA–Mg–drug complexes were prepared and studied in solid-state using KBr pellet. It has been found that concentrating the samples by speed vac centrifugation does not affect the recovery; especially there has not been appreciable structural variation of samples (it is presumed that the transformation of the reaction state of molecules from solution to solid might cause drastic variation in RNA structure) observed as compared to that in the published papers [1,2]. Furthermore the IR spectrum obtained presently using the speed vac procedure leads to the elimination of water but does not lead to removal of ionic strength from the solution nor