1gv6
From Proteopedia
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[[Image:1gv6.gif|left|200px]] | [[Image:1gv6.gif|left|200px]] | ||
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| - | + | {{STRUCTURE_1gv6| PDB=1gv6 | SCENE= }} | |
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'''SOLUTION STRUCTURE OF ALFA-L-LNA:DNA DUPLEX''' | '''SOLUTION STRUCTURE OF ALFA-L-LNA:DNA DUPLEX''' | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1GV6 is a [[Single protein]] structure | + | 1GV6 is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GV6 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Petersen, M.]] | [[Category: Petersen, M.]] | ||
[[Category: Wengel, J.]] | [[Category: Wengel, J.]] | ||
| - | [[Category: | + | [[Category: Dna]] |
| - | [[Category: | + | [[Category: Lna]] |
| - | [[Category: | + | [[Category: Locked nucleic acid]] |
| - | [[Category: | + | [[Category: Nmr]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 18:03:01 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 15:03, 2 May 2008
SOLUTION STRUCTURE OF ALFA-L-LNA:DNA DUPLEX
Overview
We have used NMR and CD spectroscopy to study and characterise two alpha-L-LNA:DNA duplexes, a nonamer that incorporates three alpha-L-LNA nucleotides and a decamer that incorporates four alpha-L-LNA nucleotides, in which alpha-L-LNA is alpha-L-ribo-configured locked nucleic acid. Both duplexes adopt right-handed helical conformations and form normal Watson-Crick base pairing with all nucleobases in the anti conformation. Deoxyribose conformations were determined from measurements of scalar coupling constants in the sugar rings, and for the decamer duplex, distance information was derived from 1H-1H NOE measurements. In general, the deoxyriboses in both of the alpha-L-LNA:DNA duplexes adopt S-type (B-type structure) sugar puckers, that is the inclusion of the modified alpha-L-LNA nucleotides does not perturb the local native B-like double-stranded DNA (dsDNA) structure. The CD spectra of the duplexes confirm these findings, as these display B-type characteristic features that allow us to characterise the overall duplex type as B-like. The 1H-1H NOE distances which were determined for the decamer duplex were employed in a simulated annealing protocol to generate a model structure for this duplex, thus allowing a more detailed inspection of the impact of the alpha-L-ribo-configured nucleotides. In this structure, it is evident that the malleable DNA backbone rearranges in the vicinity of the modified nucleotides in order to accommodate them and present their nucleobases in a geometry suitable for Watson-Crick base pairing.
About this Structure
1GV6 is a Single protein structure. Full crystallographic information is available from OCA.
Reference
alpha-L-LNA (alpha-L-ribo configured locked nucleic acid) recognition of DNA: an NMR spectroscopic study., Nielsen KM, Petersen M, Hakansson AE, Wengel J, Jacobsen JP, Chemistry. 2002 Jul 2;8(13):3001-9. PMID:12489231 Page seeded by OCA on Fri May 2 18:03:01 2008
