3′ Terminal Nucleotides Determine Thermodynamic Stabilities of Mismatches at the Ends of RNA Helices

The thermodynamic stabilities of consecutive mismatches at the ends of RNA helices are determined by the 3' terminal nucleotides. More than 40 RNA duplexes containing terminal motifs of 3 or more nucleotides were studied by optical melting experiments. Up to three noncanonical pairs of nucleotides at the end of RNA helices provide additional thermodynamic stability. 3' nucleotides contribute more stability than 5' nucleotides, and purines contribute more stability than pyrimidines. The additional stability of a second or third 3' nucleotide stacking on a purine is the same for both dangling ends and consecutive terminal mismatches. Current predictions underestimate RNA duplex stabilities with terminal motifs by 1.4 kcal/mol on average, which is an order of magnitude in a binding constant at 37 degrees C. Accurate thermodynamic parameters for these terminal motifs will contribute to improvements in RNA secondary structure predictions, identification of microRNA targets, and design of siRNA therapeutics with fewer off-target effects.