Solution structure of a modified 2 0 ,5 0 -linked RNA hairpin involved in an equilibrium with duplex

The isomerization of phosphodiester functionality of nucleic acids from 30,50- to a less common 20,50-linkage influences the complex interplay of stereoelectronic effects that drive pseudorotational equilibrium of sugar rings and thus affect the conformational pro-pensities for compact or more extended structures. The present study highlights the subtle balance of non-covalent forces at play in structural equilibrium of 20,50-linked RNA analogue, 30-O-(2-methoxyethyl) substituted dodecamer *CG*CGAA*U*U*CG*CG, 30-MOE-20,50-RNA, where all cytosines and uracils are methylated at C5. The NMR and UV spectroscopic stud-ies have shown that 30-MOE-20,50-RNA adopts both hairpin and duplex secondary structures, which are involved in a dynamic exchange that is slow on the NMR timescale and exhibits strand and salt concentra-tionaswellaspHdependence.UnusualeffectofpHover a narrow physiological range is observed for imino pro-ton resonances with exchange broadening observed at lower pH and relatively sharp lines observed at higher pH. The solution structure of 30-MOE-20,50-RNA hairpin displays a unique and well-defined loop, which is sta-bilized by Watson–Crick A5.*U8 base pair and by n!p* stacking interactions of O40 lone-pair electrons of A6 and *U8 with aromatic rings of A5 and *U7, respectively. In contrast, the stem region of 30-MOE-20,50-RNA hairpin ismoreflexible.Ourdatahighlight theimportant feature of backbone modifications that can have pronounced effects on interstrand association of nucleic acids