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 thermo-stability of nucleic acid duplexes by up to ～4 ℃ 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 modifiednucleotides. 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 ℃ relative to the corresponding DNA:RNA hybrid, retains the global structure of this hybrid. To our knowledge, this is the first example of such as 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.