RNA HAIRPIN LOOP STABILITY DEPENDS ON CLOSING BASE-PAIR

Thermodynamic parameters are reported for hairpin formation in 1 M NaC l by RNA sequences of the type GGXAUAAUAYCC, where X and Y are CG, GC, AU, UA, GU, or UG. A nearest neighbor analysis of the data indicates the free energy change for loop formation at 37-degrees-C, DELTA-degre es-G/,37, averages 3.4 kcal/mol for hairpin loops closed with C.G, G.C , and G.U pairs. In contrast, DELTAG/,37-degrees averages 4.6 kcal/mol for loops closed with A.U, U.A, or U.G pairs. Thus the stability of a n RNA hairpin depends on the closing base pair. The hairpin with a GA mismatch that is formed by GGCGUAAUAGCC is more stable than the corres ponding hairpin with an AA mismatch. Thus hairpin stability also depen ds on loop sequence. These effects are not included in current algorit hms for prediction of RNA structure from sequence.