1okf
From Proteopedia
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NMR STRUCTURE OF AN ALPHA-L-LNA:RNA HYBRID
Overview
Alpha-L-LNA (alpha-L-ribo configured locked nucleic acid) is a nucleotide, analogue that raises the thermostability of nucleic acid duplexes by up to, approximately 4 degrees C per inclusion. We have determined the NMR, structure of a nonamer alpha-L-LNA:RNA hybrid with three alpha-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 alpha-L-LNA:RNA hybrid, which, has an elevation in melting temperature of 17 degrees 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. alpha-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 alpha-L-LNA:RNA hybrid.
About this Structure
1OKF is a Single protein structure of sequence from [1]. Full crystallographic information is available from OCA.
Reference
NMR structure of an alpha-L-LNA:RNA hybrid: structural implications for RNase H recognition., Nielsen JT, Stein PC, Petersen M, Nucleic Acids Res. 2003 Oct 15;31(20):5858-67. PMID:14530434
Page seeded by OCA on Sun Nov 25 01:01:36 2007
Categories: Single protein | Nielsen, J.T. | Petersen, M. | Stein, P.C. | Alpha-l-lna | Lna | Locked nucleic acid | Nmr | Rna | Rnase h
