Hairpin secondary structural elements play important roles in the folding and function of RNA and DNA molecules. Previous work from our lab on small DNA hairpin loop motifs, d(cGNAg) and d(cGNABg) (where B is C, G, or T), showed that folding is highly cooperative and obeys indirect coupling, consistent with a concerted transition. Herein, we investigate folding of the related, exceptionally stable RNA hairpin motif, r(cGNRAg) (where R is A or G). Previous NMR characterization identified a complex network of seven hydrogen bonds in this loop. We inserted three carbon (C3) spacers throughout the loop and found coupling between G1 of the loop and the CG closing base pair, similar to that found in DNA. These data support a GNRA motif being expandable at any position but before the G. Thermodynamic measurements of nucleotide-analogue-substituted oligonucleotides revealed pairwise-coupling free energies ranging from weak to strong. When coupling free energies were remeasured in the background of changes at a third site, they remained essentially unchanged even though all of the sites were coupled to each other. This type of coupling, referred to as "direct", is peculiar to the RNA loop. The data suggest that, for small stable loops, folding of RNA obeys a model with nearest-neighbor interactions, while folding of DNA follows a more concerted process in which the stabilizing interactions are linked through a conformational change. The lesser cooperativity in RNA loops may provide a more robust loop that can withstand mutations without a severe loss in stability. These differences may enhance the ability of RNA to evolve.
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