Spectroscopic and Calorimetric Studies on the Binding of Alkaloids Berberine, Palmatine and Coralyne to Double Stranded RNA Polynucleotides

Abstract

The interaction of two natural protoberberine plant alkaloids berberine and palmatine and a synthetic derivative coralyne to three double stranded ribonucleic acids, poly(A). poly(U), poly(I).poly(C) and poly(C).poly(G) was studied using various biophysical techniques. Absorbance and fluorescence studies showed that the alkaloids bound cooperatively to these RNAs with the binding affinities of the order 10(4) M(-1). Circular dichroic results suggested that the conformation of poly(A). poly(U) was perturbed by all the three alkaloids, that of poly(I).poly(C) by coralyne only and that of poly(C).poly(G) by none. Fluorescence quenching studies gave evidence for partial intercalation of berberine and palmatine and complete intercalation of coralyne to these RNA duplexes. Isothermal titration calorimetric studies revealed that the binding was characterized by negative enthalpy and positive entropy changes and the affinity constants derived were in agreement with the overall binding affinity from spectral data. The binding of all the three alkaloids considerably stabilized the melting of poly(A). poly(U) and poly(I).poly(C) and the binding data evaluated from the melting data were in agreement with that obtained from other techniques. The overall binding affinity of the alkaloids to these double stranded RNAs varied in the order, berberine = palmatine < coralyne. The temperature dependence of the enthalpy changes afforded large negative values of heat capacity changes for the binding of palmatine and coralyne to poly(A).poly(U) and of coralyne to poly(I).poly(C), suggesting substantial hydrophobic contribution in the binding process. Further, enthalpy-entropy compensation was also seen in almost all the systems that showed binding. These results further advance our understanding on the binding of small molecules that are specific binders to double stranded RNA sequences.

Therapeutic potential of harmaline, a novel alkaloid, against cervical cancer cells in vitro: Apoptotic induction and DNA interaction study

“…(4). Generally, cooperative binding is mediated by allosteric effects [21,24,25,[29][30][31]. Scatchard plot from the interaction of harmaline with CT DNA indicates [inset of Figure 4a] intrinsic binding affinity, K i ω (product of cooperative binding affinity and the cooperative factor) in the order of 5.60 × 10 5 /M with a stoichiometry of 4 nucleotide phosphates.…”

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

“…Thermal-melting profiles of the triplex and triplexÀalkaloid complexes were recorded on a Shimadzu Pharmaspec 1700 unit equipped with a Peltier-controlled TMSPC-model accessory monitoring the absorbance change at 260 nm as described in [33] [49].…”

“…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.…”

“…data were fitted using a non-linear least-squares minimization algorithm to a theoretical titration curve using equations included in the software package of Origin 7.0, and fit with a model of one site binding site to estimate the binding affinity (K a ), the binding stoichiometry (N), and the enthalpy of binding (DH). The binding free energy and the entropic contribution to the binding were subsequently calculated from standard relationships described in [33] [49].…”

Palmatine Attenuates Osteoclast Differentiation and Function through Inhibition of Receptor Activator of Nuclear Factor-.KAPPA.B Ligand Expression in Osteoblast Cells

“…[14][15][16][17][18][19][20][21][22] In addition to its medicinal uses, palmatine is also used as a fluorescent probe of DNA, RNA, and enzymes in biochemical research. [23][24][25][26] In spite of these broad uses, the effects of palmatine on osteoclastogenesis remain uncertain.…”