1oci
From Proteopedia
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[3.2.0]BCANA:DNA
Overview
[3.2.0]bcANA is a D-arabino-configured bicyclic nucleotide with a, 2'-O,3'-C-methylene bridge. We here present the high-resolution NMR, structure of a [3.2.0]bcANA modified dsDNA nonamer with one modified, nucleotide incorporated. NOE restraints were obtained by analysis of NOESY, cross peak intensities using a full relaxation matrix approach, and, subsequently these restraints were incorporated into a simulated annealing, scheme for the structure determination. In addition, the furanose ring, puckers of the deoxyribose moieties were determined by analysis of COSY, cross peaks. The modified duplex adopts a B-like geometry with, Watson-Crick base pairing in all base pairs and all glycosidic angles in, the anti range. The stacking arrangement of the nucleobases appears to be, unperturbed relative to the normal B-like arrangement. The, 2'-O,3'-C-methylene bridge of the modified nucleotide is located at the, brim of the major groove where it fits well into the B-type duplex, framework. The sugar pucker of the [3.2.0]bcANA nucleotide is O4'-endo and, this sugar conformation causes a change in the delta backbone angle, relative to the C2'-endo deoxyribose sugar pucker. This change is absorbed, locally by slight changes in the epsilon and zeta angles of the modified, nucleotide. Overall, the [3.2.0]bcANA modifications fits very well into a, B-like duplex framework and only small and local perturbations are, observed relative to the unmodified dsDNA of identical base sequence.
About this Structure
1OCI is a Single protein structure of sequence from [1]. Full crystallographic information is available from OCA.
Reference
NMR solution structure of dsDNA containing a bicyclic D-arabino-configured nucleotide fixed in an O4'-endo sugar conformation., Tommerholt HV, Christensen NK, Nielsen P, Wengel J, Stein PC, Jacobsen JP, Petersen M, Org Biomol Chem. 2003 May 21;1(10):1790-7. PMID:12926371
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