In vitro RNA folding: the principle of sequential minimization of entropy loss at work

We introduce the principle of sequential minimization of entropy loss (SMEL) in the context of biopolymer folding in vitro. This principle asserts that at each stage in the dominant folding pathway, the conformational entropy loss, denoted DeltaS loop, associated with loop closure is minimized while the number n of effective contacts is maximized to the extent that at each stage the chosen event is the one that minimizes the number Q = n-1 exp(-DeltaS loop/R). This principle is compatible with thermodynamic control exerted sequentially, that is, at every stage of the folding process. Moreover, the validity of the SMEL will be shown to be tantamount to assume kinetic control whenever folding is subject to time constraints. Because of the exponential dependence, the applicability of the SMEL principle is contingent upon a rigorous and reliable derivation of the contribution DeltaS loop. This derivation is carried out in this work for RNA by taking into account the orientational restrictions associated to the self energy of charged phosphate moieties within a loop. The predictive potential of the principle thus derived is tested by showing that the theory reproduces the consensus biologically competent secondary structures of specific ribozymes and explains how the structures emerge.