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

Abstract

Free energies for stacking of unpaired nucleotides (dangling ends) at the termini of oligoribonucleotide Watson-Crick helixes (Δ G 37,stack 0) depend 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 spectroscopy. Stacking involving GA pairs is considered separately. A base is categorized as stacked by its distance from (⩽4.0 Å), angle with (⩽30 °), 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 Δ G 37,stack 0 more favorable than −0.7 kcal/mol, 30 (83 %) are stacked on the adjacent base-pair, indicating a propensity for such sequences to stack in the 3D structure. Structures containing the strongly stacked sequence CU G ← (Δ G 37,stack 0 = −1.2 kcal/mol) show that the amino group of C closely overlaps the carbonyl-4 of U. Thermodynamic measurement of U stacking on a 2-pyrimidinone-guanine base-pair, where the amino group of C is replaced by hydrogen, suggests that interactions with the cytosine amino group contribute ∼0.5 kcal/mol to Δ G 37,stack 0. For GA mismatches at helix termini, the nucleotide at the 3′ helix end is always stacked, and the nucleotide at the 5′ end is stacked in almost 90 % of occurrences. In available structures, non-Watson-Crick paired bases 3′ to an imino-hydrogen bonded GA are also always stacked; the GA provides a large platform for favorable stacking. For the 56 sequences associated with Δ G 37,stack 0 less favorable than −0.4 kcal/mol, 19 (34 %) are stacked; these sequences have a propensity for not stacking on adjacent base-pairs. Phylogenetic conservation of weakly stacking sequences at 3′ ends may be a predictor of a backbone turn.