Thermodynamics of RNA Secondary Strucutre Formation
Sequences with identical composition but different permutations of base pairs may have different free energy changes for duplex formation. For example, the duplexes (5'GUUCGAAC3')2 and (5'UUGGCCAA3')2 both have four AU and four GC base pairs, but have free energy changes of duplex formation at 37 C of -8.8 and -11.0 kcal mol-1, respectively. This difference of 2.2 kcal mol-1 translates into a 35-fold difference in equilibrium constants for duplex formation at 37 C. Thus, stability depends on more than the number of hydrogen bonds formed. Presumably, vertical stacking interactions between neighboring base pairs are the sequence-dependent variable.