Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs

Free energies for stacking of unpaired nucleotides (dangling ends) at the t ermini of oligoribonucleotide Watson-Crick helixes (Delta G(37,stack)(o)) d epend on sequence for 3' ends but are always small for 5' ends. Here, these free energies are correlated with stacking at helix termini in a database of 34 RNA structures determined by X-ray crystallography and NMR spectrosco py. Stacking involving GA pairs is considered separately. A base is categor ized as stacked by its distance from (less than or equal to 4.0 Angstrom) a ngle with (less than or equal to 30 degrees), and overlap with the terminal helix base-pair. A base is unstacked if it does not satisfy one or more of these criteria. Of the 36 unpaired bases in sequences with Delta G(37,stack)(o) more favora ble than -0.7 kcal/mol, 30 (83%) are stacked on the adjacent base-pair, ind icating a propensity for such sequences to stack in the 3D structure. Struc tures containing the strongly stacked sequence [GRAPHICS] (Delta G(37,stack)(o) = - 1.2 kcal/mol) show that the amino group of C clos ely overlaps the carbonyl-4 of U. Thermodynamic measurement of U stacking o n a 2-pyrimidinone-guanine base-pair, where the amino group of C is replace d by hydrogen, suggests that interactions with the cytosine amino group con tribute -0.5 kcal/mol to Delta G(37,stack)(o). For GA mismatches at helix termini, the nucleotide at the 3' helix end is a lways stacked, and the nucleotide at the 5' end is stacked in almost 90% of occurrences. Ln available structures, non-Watson-Crick paired bases 3' to an imino-hydrogen bonded GA are also always stacked; the GA provides a larg e platform for favorable stacking. For the 56 sequences associated with Delta G(37,stack)(o) less favorable th an -0.4 kcal/mol, 19 (34%) are stacked; these sequences have a propensity f or not stacking on adjacent base-pairs. Phylogenetic conservation of weakly stacking sequences at 3' ends may be a predictor of a backbone turn. (C) 1 999 Academic Press.