NMR structure of an α‐L‐LNA:RNA hybrid: structural implications for RNase H recognition

摘要

α‐L‐LNA (α‐L‐ribo configured locked nucleic acid) is a nucleotide analogue that raises the thermostability of nucleic acid duplexes by up to ～4°C per inclusion. We have determined the NMR structure of a nonamer α‐L‐LNA:RNA hybrid with three α‐L‐LNA modifications. The geometry of this hybrid is intermediate between A‐ and B‐type, all nucleobases partake in Watson–Crick base pairing and base stacking, and the global structure is very similar to that of the corresponding unmodified hybrid. The sugar–phosphate backbone is rearranged in the vicinity of the modified nucleotides. As a consequence, the phosphate groups following the modified nucleotides are rotated into the minor groove. It is interesting that the α‐L‐LNA:RNA hybrid, which has an elevation in melting temperature of 17°C relative to the corresponding DNA:RNA hybrid, retains the global structure of this hybrid. To our knowledge, this is the first example of such a substantial increase in melting temperature of a nucleic acid analogue that does not act as an N‐type (RNA) mimic. α‐L‐LNA:RNA hybrids are recognised by RNase H with subsequent cleavage of the RNA strand, albeit with slow rates. We attempt to rationalise this impaired enzyme activity from the rearrangement of the sugar–phosphate backbone of the α‐L‐LNA:RNA hybrid.