Binding of protoberberine alkaloid coralyne with double stranded poly(A): a biophysical study

Abstract

Recognition of double stranded ribonucleic acid is a critical event in many biological pathways such as trafficking, editing and maturation of mRNA, interferon antiviral response and RNA interference. In the context of probing double stranded RNA binding small molecules, the interaction of the antitumor protoberberine alkaloid coralyne with double stranded poly(A) has been studied by various biophysical techniques. Typical hypochromic and bathochromic shifts in the absorption spectrum and appreciable quenching of the intrinsic fluorescence of coralyne indicated the strong affinity of coralyne to poly(A). The corresponding intrinsic binding constant evaluated from Scatchard analysis was in the order of 10(5) M(-1). The strong binding was further characterized by significant polarization of the alkaloid fluorescence and stabilization of poly(A) helix against thermal strand separation. The binding process was manifested by remarkable perturbation of the intrinsic circular dichroic spectrum of poly(A) with concomitant generation of optical activity in the bound alkaloid molecules that are otherwise achiral. Job plot analysis showed the binding stoichiometry of the interaction process to be two base pairs per alkaloid molecule. The energetics of the strong interaction was studied by isothermal titration and differential scanning calorimetric techniques that suggested the binding to be exothermic and favoured by both negative enthalpy and positive entropy changes. All these results, together with the Stern-Volmer quenching experiment in fluorescence, revealed the molecular details of the intercalation of coralyne into poly(A) duplex leading to its potential use as an agent in gene regulation in eukaryotic cells.

Anti- Japanese-Encephalitis-Viral Effects of Kaempferol and Daidzin and Their RNA-Binding Characteristics

“…To elucidate this problem further, the binding reactions between RNA and flavonoids in an aqueous phase were studied using ITC. ITC is an important tool for measuring the thermodynamics of interactions between small molecules and biopolymers, in which all binding parameters (n, K, ΔH and ΔS) are simultaneously determined in a single ITC experiment, thus obtaining information that cannot be obtained by other methods [35]–[37]. In our research, analysis of the ITC measurements revealed two interactions to be primarily enthalpy driven.…”

Interaction of aristololactam-β-D-glucoside and daunomycin with poly(A): Spectroscopic and calorimetric studies

“…The absorption spectral titrations were performed under stirring at 20 ± 0.5°C on a Jasco V660 unit (Jasco International Co. Ltd., Tokyo, Japan) equipped with a thermoelectrically controlled cell holder and temperature controller in matched quartz cells of 1 cm path length, following generally the methods standardized in our laboratory and described earlier [25,26,41].…”

“…It is also noteworthy that polyriboadenylic acid has the unique characteristic to exist in single stranded helical structure and parallel stranded double helix [33][34][35], the later being stabilized by base paired protonated adenines. Furthermore, many small molecules, particularly alkaloids, have been shown to induce unique self-structure in poly(A), the mechanism of which is still obscure [8,9,25,26,36,37]. Apparently, molecules that could induce self-structure in poly(A) may be useful as potential lead compounds for controlling the poly(A) chain elongation and mRNA degradation.…”

“…Some RNA binding molecules like aminoglycosides have been investigated, but due to the high toxicity, their usage in RNA therapeutics is limited [22]. Our laboratory has studied the interaction of a number of natural alkaloid molecules and has provided new data on the mode, mechanism and energetics of their interaction with single and ds RNAs [23][24][25][26][27][28]. Poly(A) has been the focus of increasing attention for its importance in mRNA functioning [29,30].…”

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

“…Double stranded RNAs such as viral RNAs or siRNAs can trigger RNA interference in eukaryotes as well as interferon response in vertebrates [14][15][16]. This form of RNA is formed in cells through intra-and intermolecular RNA interactions and is involved in a range of biological processes [17]. A major event for a number of cellular pathways, such as trafficking, editing, maturation of cellular RNA, the interferon antiviral response and RNA silencing is the molecular recognition of ds RNA.…”