Dangling ends perturb the stability of RNA duplexes responsive to surrounding conditions

Unpaired terminal nucleotides (dangling ends) occur in various biologically important RNA structures. We studied the thermal stability of RNA duplexes with dangling ends under conditions that mimic those in cells. Dangling ends of one or two nucleotides stabilized a duplex up to approximately 2.7 kcal mol(-1) in the absence of cosolutes. RNA duplexes with dangling purine nucleotides were more stable than those with pyrimidine nucleotides. Interestingly, in the presence of various cosolutes, RNA duplexes with purine dangling ends were significantly destabilized, although those with pyrimidine dangling ends were destabilized slightly. For example, in 30 wt % poly(ethylene glycol), stabilization resulting from adenine dangling ends was reduced by 1.4 kcal mol(-1) . Our quantitative analyses also showed that the number of water molecules bound to the dangling ends in an aqueous solution was independent of the nucleotide type but dependent on the stability of the dangling-end region. It has been considered that dangling ends stabilize helices; however, our results suggest that the stabilization is responsive to the surrounding conditions.