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| - | [[Image:1oci.gif|left|200px]] | + | {{Seed}} |
| | + | [[Image:1oci.png|left|200px]] |
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| | {{STRUCTURE_1oci| PDB=1oci | SCENE= }} | | {{STRUCTURE_1oci| PDB=1oci | SCENE= }} |
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| - | '''[3.2.0]BCANA:DNA'''
| + | ===[3.2.0]BCANA:DNA=== |
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| - | ==Overview==
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| - | [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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_12926371}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 12926371 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_12926371}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | 1OCI is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OCI OCA]. | + | 1OCI is a [[Single protein]] structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OCI OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Nmr]] | | [[Category: Nmr]] |
| | [[Category: Rnase h]] | | [[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 Sun Jul 27 12:15:38 2008'' |
Revision as of 09:15, 27 July 2008
Template:STRUCTURE 1oci
[3.2.0]BCANA:DNA
Template:ABSTRACT PUBMED 12926371
About this Structure
1OCI is a Single protein structure. Full experimental 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 Sun Jul 27 12:15:38 2008
