Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

RNA Binding Aspects of Isoquinoline Alkaloids: Affinity, Specificity, and Energetics

Alkaloids of plant origin have the potential of use in therapeutic applications. Berberine, palmatine, and coralyne represent alkaloids of the isoquinoline group that were shown previously to have excellent DNA binding activities. Since the current focus of therapeutic targeting is RNA we studied their interaction with double and single stranded ribonucleic acids, poly(A)·poly(U), poly(I)·poly(C) and poly(C)·poly(G), poly(G), poly(I), poly(U) and poly(C) using various biophysical techniques. Absorbance and fluorescence studies showed that the alkaloids bound cooperatively to the ds RNAs with binding affinities of the order 104 M-1 while with single stranded RNAs non-cooperative binding was seen with affinity in the order 105 M-1 to poly(G) and poly(I) and in the order 103 M-1 with poly(C) and poly(U). 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. Similarly with the single stranded RNAs, the perturbation was more in poly(I) and poly(U) compared to poly(G) and none with poly(C). Fluorescence quenching studies gave evidence for partial intercalation of berberine and palmatine and complete intercalation of coralyne to the RNA duplexes. Partial intercalation was observed with ploy(G) and poly(I). Isothermal titration calorimetric studies revealed that the binding with these RNAs 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 was in agreement with that obtained from other techniques. The overall binding affinity of the alkaloids to the double and single 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 berberine, palmatine, and coralyne to poly(A)·poly(U), poly(I)·poly(C), poly(G), poly(I), and of palmatine and coralyne to poly(I)·poly(C) suggesting substantial hydrophobic contribution in the binding process. Further, enthalpy-entropy compensation to different extents 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 RNA sequences.

Md. Maidul Islam
Gopinatha Suresh Kumar

Biophysical Chemistry Laboratory
Indian Institute of Chemical Biology
Council of Scientific and Industrial Research
Kolkata 700 032, India

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