Design and synthesis of RNA-specific groove-binding cations: implications for antiviral drug design

As as initial step in the design of structure-specific RNA-interactive molecules as potential antiviral agents, we have focused on the synthesis of molecules that exhibit strong and preferential binding to duplex RNA. A series of polycationic ligands have been synthesized, and the degree of preferential binding to RNA has initially been determined by thermal denaturation (delta Tm) with both RNA [poly(A).poly(U)] and DNA [poly(dA).poly(dT)] polymers at a variety of pH values. Seven compounds from the series exhibit a substantial degree of RNA-selective binding. The relatively high delta Tm values obtained suggest a specific mode of interaction between these ligands and the RNA helix. By contrast, the much lower delta Tm values with poly(dA).poly(dT) DNA reflect a more nonspecific interaction mode. A viscometric titration study with poly(A).poly(U) confirms that they do not bind by intercalation. The results, combined with the known structure and electronegative potential of duplex RNA, suggest that these molecules bind in the major groove via specific electrostatic and/or hydrogen-bonded interactions.