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
