This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1oci
From Proteopedia
(New page: 200px<br /><applet load="1oci" size="450" color="white" frame="true" align="right" spinBox="true" caption="1oci" /> '''[3.2.0]BCANA:DNA'''<br /> ==Overview== [3.2...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1oci.gif|left|200px]]<br /><applet load="1oci" size=" | + | [[Image:1oci.gif|left|200px]]<br /><applet load="1oci" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1oci" /> | caption="1oci" /> | ||
'''[3.2.0]BCANA:DNA'''<br /> | '''[3.2.0]BCANA:DNA'''<br /> | ||
==Overview== | ==Overview== | ||
| - | [3.2.0]bcANA is a D-arabino-configured bicyclic nucleotide with a | + | [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== | ==About this Structure== | ||
| - | 1OCI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1OCI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OCI OCA]. |
==Reference== | ==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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12926371 12926371] | 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12926371 12926371] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Christensen, N | + | [[Category: Christensen, N K.]] |
| - | [[Category: Jacobsen, J | + | [[Category: Jacobsen, J P.]] |
[[Category: Nielsen, P.]] | [[Category: Nielsen, P.]] | ||
[[Category: Petersen, M.]] | [[Category: Petersen, M.]] | ||
| - | [[Category: Stein, P | + | [[Category: Stein, P C.]] |
| - | [[Category: Tommerholt, H | + | [[Category: Tommerholt, H V.]] |
[[Category: Wengel, J.]] | [[Category: Wengel, J.]] | ||
[[Category: arabino nucleic acid]] | [[Category: arabino nucleic acid]] | ||
| Line 24: | Line 24: | ||
[[Category: rnase h]] | [[Category: rnase h]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:16:04 2008'' |
Revision as of 12:16, 21 February 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 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
Page seeded by OCA on Thu Feb 21 14:16:04 2008
