Effects of terminal mismatches on RNA stability: thermodynamics of duplex formation for ACCGGGp, ACCGGAp, and ACCGGCp

Abstract

The thermodynamics of ACCGGCp, ACCGGAp, and ACCGGGp helix formation have been measured in 1 M NaCl. The terminal mispairs stabilize the CCGG core duplex at 10(-4) M in the order AC approximately equal to AA less than AG approximately equal to AU. The data reported provide thermodynamic parameters for RNA structure prediction and suggest useful approximations for including other mismatches in current algorithms.