The interaction of substituted 2‐phenylquinoline intercalates with poly(A) · poly(U): Classical and threading intercalation modes with RNA

The interaction of a series of 2‐phenylquinoline derivatives with RNA was investigated by means of viscometric, pKa, spectroscopic, binding, T m , and kinetic methods. Compounds 1 , 2 , and 3 have a piperazyl substituent at the para , meta , or ortho position, respectively, while 4 has an unsubstituted phenyl ring. The pKa results suggest that 1 has three charges, 2 and 3 have more than two charges, and 4 has two charges at pH 6.2. Spectroscopic and T m results indicate that 1 binds more strongly to RNA than 2–4 . Kinetic and modeling results indicate that 1 is a threading intercalator while 2 and 4 are classical intercalators. All experimental results indicate that 3 , which has a large twist between the phenyl and quinoline rings, binds weakly with RNA. © 1994 John Wiley & Sons, Inc.