1okf

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[[Image:1okf.gif|left|200px]]
[[Image:1okf.gif|left|200px]]
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{{Structure
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|PDB= 1okf |SIZE=350|CAPTION= <scene name='initialview01'>1okf</scene>
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The line below this paragraph, containing "STRUCTURE_1okf", creates the "Structure Box" on the page.
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=ATL:[(1S,3R,4S,7R)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>ATL</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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{{STRUCTURE_1okf| PDB=1okf | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1okf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1okf OCA], [http://www.ebi.ac.uk/pdbsum/1okf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1okf RCSB]</span>
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'''NMR STRUCTURE OF AN ALPHA-L-LNA:RNA HYBRID'''
'''NMR STRUCTURE OF AN ALPHA-L-LNA:RNA HYBRID'''
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==About this Structure==
==About this Structure==
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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].
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1OKF is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OKF OCA].
==Reference==
==Reference==
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[[Category: Petersen, M.]]
[[Category: Petersen, M.]]
[[Category: Stein, P C.]]
[[Category: Stein, P C.]]
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[[Category: alpha-l-lna]]
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[[Category: Alpha-l-lna]]
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[[Category: lna]]
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[[Category: Lna]]
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[[Category: locked nucleic acid]]
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[[Category: Locked nucleic acid]]
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[[Category: nmr]]
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[[Category: Nmr]]
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[[Category: rna]]
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[[Category: Rna]]
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[[Category: rnase h]]
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[[Category: Rnase h]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 03:57:59 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:46:38 2008''
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Revision as of 00:58, 3 May 2008

Image:1okf.gif

Template:STRUCTURE 1okf

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. 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 Sat May 3 03:57:59 2008

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