RNA targeting through binding of small molecules: Studies on t-RNA binding by the cytotoxic protoberberine alkaloidcoralyne

Abstract

Interaction of the protoberberine alkaloid coralyne with t-RNA(phe) was investigated using various biophysical techniques. Results of absorption and fluorescence studies revealed that the alkaloid binds to t-RNA exhibiting positive cooperativity. Isothermal titration calorimetry results suggested that the binding of the alkaloid was predominantly enthalpy driven with a smaller favourable entropy term. A surprisingly large favourable component for non-electrostatic contribution to the binding of coralyne to t-RNA was revealed from salt dependence data and the dissection of the free energy. The alkaloid enhanced the thermal stability of t-RNA and the binding affinity values obtained from optical thermal melting data was in agreement with that from calorimetry. The heat capacity change of -125 cal mol(-1) K(-1) and the observed significant enthalpy-entropy compensation phenomenon confirmed the involvement of multiple weak noncovalent interactions. Circular dichroism studies provided evidence for significant perturbation of the t-RNA structure with concomitant induction of optical activity in the bound achiral alkaloid molecules. Binding isotherms generated from circular dichroic data confirmed the cooperative binding mode of the alkaloid as deduced from spectroscopic data. Docking studies provided further insights into the partially intercalated state of coralyne inside the t-RNA structure. This study presents a complete binding and thermodynamic profile of coralyne interaction to t-RNA.

DNA minor groove binding of small molecules: Experimental and computational evidence

“…27 Similar trend was also observed in case of drug-tRNA binding. 28,29 It can be concluded that intermolecular interactions in all the 32 drug-DNA complexes were also supported by intermolecular H-bonds, besides other factors like van der Waal's forces, etc. as revealed by the higher values of energy terms for van der Waal's interactions and electrostatic (table 2).…”

Biophysical studies on the base specificity and energetics of the DNA interaction of photoactive dye thionine: Spectroscopic and calorimetric approach

“…The free energy contribution from the hydrophobic transfer step of binding of these molecules may be calculated from the relationship [50], ΔG hyd =80(±10) × ΔCp. The ΔG hyd values for thionine binding to CP, HT and ML DNAs were deduced to be −8.1, −10.7 and −16.7 kcal/mol, that are well within the range that was observed for typical intercalating DNA and RNA intercalating molecules [21,24,36,42,44,48,51].…”

“…A MicroCal VP-ITC unit (MicroCal, Inc., Northampton, MA, USA) using protocols developed in our laboratory and described in details previously [25,30,35,36] was used for all ITC experiments. A reverse titration protocol of injecting aliquots of DNA solution from a rotating syringe (290 rpm) into the calorimetric cell containing the thionine solution (1.4235 mL) under identical buffer conditions was adopted.…”

Protoberberine Alkaloids Berberine, Palmatine, and Coralyne Binding to Poly(dT)⋅(Poly(dA)⋅Poly(dT)) Triplex: Comparative Structural Aspects and Energetics Profiles of the Interaction

“…ITC was performed on a MicroCal VP-ITC microcalorimeter (MicroCal, Inc.). Data acquisition and instrument control were carried out using the dedicated Origin software package using standard protocols reported in [34] [49]. All experiments were conducted at 208.…”