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1oci

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[[Image:1oci.gif|left|200px]]
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{{Seed}}
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[[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'''
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===[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.
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(as it appears on PubMed at http://www.pubmed.gov), where 12926371 is the PubMed ID number.
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{{ABSTRACT_PUBMED_12926371}}
==About this Structure==
==About this Structure==
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1OCI is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OCI OCA].
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1OCI is a [[Single protein]] structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OCI OCA].
==Reference==
==Reference==
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[[Category: Nmr]]
[[Category: Nmr]]
[[Category: Rnase h]]
[[Category: Rnase h]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 03:39:58 2008''
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''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

Image:1oci.png

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

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