Photophysical and calorimetric investigation on the structural reorganization of poly(A) by phenothiazinium dyes azure A and azure B

Abstract

Poly(A) has significant relevance to mRNA stability, protein synthesis and cancer biology. The ability of two phenothiazinium dyes azure A (AA) and azure B (AB) to bind single-stranded poly(A) was studied by spectroscopic and calorimetric techniques. Strong binding of the dyes and the higher affinity of AA over AB were ascertained from absorbance and fluorescence experiments. Significant perturbation of the circular dichroism spectrum of poly(A) in the presence of these molecules with formation of induced CD bands in the 300-700 nm region was observed. Strong emission polarization of the bound dyes and strong energy transfer from the adenine base pairs of poly(A) suggested intercalative binding to poly(A). Intercalative binding was confirmed from fluorescence quenching experiments and was predominantly entropy driven as evidenced from isothermal titration calorimetry data. The negative values of heat capacity indicated involvement of hydrophobic forces and enthalpy-entropy compensation suggested noncovalent interactions in the complexation for both the dyes. Poly(A) formed a self-assembled structure on the binding of both the dyes that was more favored under higher salt conditions. New insights in terms of spectroscopic and thermodynamic aspects into the self-structure formation of poly(A) by two new phenothiazinium dyes that may lead to structural and functional damage of mRNA are revealed from these studies.

Entropy driven binding of the alkaloid chelerythrine to polyadenylic acid leads to spontaneous self-assembled structure formation

“…In the present case, the TD bind S o value is positive and the binding was favored by both enthalpy and entropy changes. Similar results were reported in some cases where small molecules induced self-assembled structure in poly(A) [8,9,11]. The origin of the strong positive entropy change may also be due to cation release and change in water structure as postulated in many previous small molecule-nucleic acid interactions [39][40][41].…”

“…Binding of small molecules to poly(A) tail of mRNA could alter its conformation, prevent elongation or create alternate conformations, leading to switching off of protein synthesis. A number of alkaloids and other small molecules have recently been found to induce a unique self-assembled structure in poly(A) in vitro [4][5][6][7][8][9][10][11][12]. The effects of such transformations if mimicked in vivo may be very interesting for arresting cell division.…”

A thermodynamic investigation on the binding of phenothiazinium dyes azure A and azure B to double stranded RNA polynucleotides

“…Although the pH of the buffer solution remained more or less unchanged in this temperature range as measured, the reactants and products contain groups that can ionize and some variation Enthalpy-entropy compensation is a significant phenomenon that is associated with solvent reorganization accompanying drug-nucleic acid interactions [30,[34][35][36][37][38][39].…”

Coralyne induced self-structure in polyadenylic acid: Thermodynamics of the structural reorganization

“…The K value decreased on increasing the [K + ] from 50 to 130 mM. Earlier studies on the induction of self-structure by small molecules like methylene blue, chelerythrine, proflavine, azure A and azure B have shown that the K value increases with increase in salt concentration [30,32,34,35]. However, in the case of coralyne here the K values decreased from {(3.12 ± 0.12)Á10 6 to (2.46 ± 0.11)Á10 6 to (1.91 ± 0.09)}Á10 6 M À1 on increasing the [K + ] from {(50 ± 0.01) to (75 ± 0.01) to (100 ± 0.01)} mM.…”

“…Poly(A) has single stranded helical structure at neutral pH but some small molecules and alkaloids can induce unique self-structure (double stranded) in poly(A) at neutral pH where otherwise only single stranded structure can exist [13,15,[26][27][28][29][30][31][32][33][34][35]. Such self-structure induction can influence mRNA degradation and stop protein production in the cell.…”