1gv6
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(New page: 200px<br /><applet load="1gv6" size="450" color="white" frame="true" align="right" spinBox="true" caption="1gv6" /> '''SOLUTION STRUCTURE OF ALFA-L-LNA:DNA DUPLEX'...)
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Revision as of 23:43, 24 November 2007
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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 of sequence from [1]. 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
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