Theory of oligonucleotide stabilization. I. The effect of single-strand stacking

Certain theoretical difficulties present in the analysis of thermal transition properties of short complementary double-stranded RNA oligomers can be resolved in part by introducing the stability of the component single-stranded systems explicitly into the model. The stability constant S of the usual theories is redefined so as to contain double-stranded pairing (τt) and single-stranded stacking (ρ) contributions, and we analyze the statistics of two experimental systems—acid oligo(A) and oligo (A_n·U_n) dimers—to exhibit the underlying stability parameters. We present a fitting procedure to extract values of the heats and entropies of the separated components when the required single-strand data is unreliable or not available. The theory leads to length dependent heats and entropies for short single strands in a natural way, and permits a more accurate assessment of the contribution of partially bonded states in thermal transitions than has previously been possible.