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.