Targeting Double-Stranded RNA with Spermine, 1-Naphthylacetyl Spermine and Spermidine: A Comparative Biophysical Investigation

Abstract

RNA targeting is an evolving new approach to anticancer therapeutics that requires identification of small molecules to selectively target specific RNA structures. In this report, the interaction of biogenic polyamines spermine, spermidine and the synthetic analogue 1-naphthylacetyl spermine with three double-stranded RNA polynucleotides--poly(I)·poly(C), poly(C)·poly(G), and poly(A)·poly(U)--has been described to understand the structural and thermodynamic basis of the binding and the comparative efficacy of the analogue over the natural polyamines. Circular dichroism spectroscopy, thermal melting experiments, and ethidium bromide displacement assay were used to characterize the interaction. Microcalorimetry studies were performed to deduce the energetics of the interaction and atomic force microscopy experiments done to gain insight into the interaction at the molecular level. The experiments demonstrated structural perturbations in the polynucleotides on binding of the polyamines. Thermal melting studies showed enhanced stabilization of RNA-polyamine complexes with increase in the total standard molar enthalpy of transition. The binding affinity was strongest for poly(I)·poly(C) as revealed by microcalorimetry results and varied as poly(I)·poly(C) > poly(C)·poly(G) > poly(A)·poly(U). The order of affinity for the polyamines was spermine >1-naphthylacetyl spermine > spermidine. Total enthalpy-entropy compensation and high standard molar heat capacity values characterized the interactions. The results of the study on the binding of polyamines to dsRNAs presented here have been compared to those reported earlier with dsDNAs. The present findings advance our knowledge on the mechanism of interaction of polyamines with RNA and may help in the search for analogues that can interfere with biogenic polyamine metabolism and function.

DNA- and RNA-binding ability of oligoDapT, a nucleobase-decorated peptide, for biomedical applications

“…The importance of new drugs able to bind doublestranded DNA, as well as to interfere with double-stranded RNA-driven biological processes [39][40][41] or act as stabilizers and carriers of double-stranded RNA drugs, [42][43][44][45][46] prompted us to study the interaction of oligoDapT with dA 12 /dT 12 and poly(rA)/poly(rU), chosen as double-stranded DNA and RNA model systems, respectively. First, the target complexes were prepared by mixing equimolar amounts of DNA and RNA single strands, heating the resulting solutions at 90°C for 10 minutes and then slowly cooling overnight.…”

Targeting of 1-Naphthyl acetyl spermine to DNA: A calorimetric and spectroscopic investigation

“…To understand the extent of this ionic interaction a salt dependent study by ITC binding assays [23]. A study on the interaction of polyamines with double stranded RNA polynucleotides has also reported similar decrease in entropy values on increasing [Na + ] [56]. Thus, these results provide evidence for the importance of electrostatic interaction in the binding process.…”

Novel and emerging targeted-based cancer therapy agents and methods

“…RNA targeting is a developing approach to anti-tumor therapeutics that requires identification of specific inhibitors to target different RNA structures. Specific structures in RNA form several types of secondary structures like hairpin loops, internal loops, and bulged regions that are proper for the binding of inhibitors [6,41].…”

“…Polyamines are poly-cationic amines that play important roles in sustaining cellular growth and activities. In cancer cells, their concentration is high and decrease in concentration inhibits cellular growth and induces apoptosis [41]. Polyamines and analogues (e.g.…”