1oci
From Proteopedia
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[[Image:1oci.gif|left|200px]] | [[Image:1oci.gif|left|200px]] | ||
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| - | + | {{STRUCTURE_1oci| PDB=1oci | SCENE= }} | |
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'''[3.2.0]BCANA:DNA''' | '''[3.2.0]BCANA:DNA''' | ||
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==About this Structure== | ==About this Structure== | ||
| - | 1OCI is a [[Single protein]] structure | + | 1OCI is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OCI OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Tommerholt, H V.]] | [[Category: Tommerholt, H V.]] | ||
[[Category: Wengel, J.]] | [[Category: Wengel, J.]] | ||
| - | [[Category: | + | [[Category: Arabino nucleic acid]] |
| - | [[Category: | + | [[Category: Dna]] |
| - | [[Category: | + | [[Category: Nmr]] |
| - | [[Category: | + | [[Category: Rnase h]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 03:39:58 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 00:40, 3 May 2008
[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. 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 Page seeded by OCA on Sat May 3 03:39:58 2008
