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[[Image:1okf.gif|left|200px]] | [[Image:1okf.gif|left|200px]] | ||
'''NMR STRUCTURE OF AN ALPHA-L-LNA:RNA HYBRID''' | {{Structure | ||
|PDB= 1okf |SIZE=350|CAPTION= <scene name='initialview01'>1okf</scene> | |||
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'''NMR STRUCTURE OF AN ALPHA-L-LNA:RNA HYBRID''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1OKF is a [ | 1OKF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OKF OCA]. | ||
==Reference== | ==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:[http:// | 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:[http://www.ncbi.nlm.nih.gov/pubmed/14530434 14530434] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Nielsen, J T.]] | [[Category: Nielsen, J T.]] | ||
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[[Category: rnase h]] | [[Category: rnase h]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:12:07 2008'' | ||
Revision as of 11:12, 20 March 2008
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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
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