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| | ==[3.2.0]bcANA:DNA== | | ==[3.2.0]bcANA:DNA== |
| - | <StructureSection load='1oci' size='340' side='right'caption='[[1oci]], [[NMR_Ensembles_of_Models | 40 NMR models]]' scene=''> | + | <StructureSection load='1oci' size='340' side='right'caption='[[1oci]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1oci]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OCI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OCI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1oci]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OCI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OCI FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLB:2-O,3-C-METHYLENE-ARABINOFURANOSYL-THYMINE-5-MONOPHOSPHATE'>TLB</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1oci FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oci OCA], [http://pdbe.org/1oci PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oci RCSB], [http://www.ebi.ac.uk/pdbsum/1oci PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1oci ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TLB:2-O,3-C-METHYLENE-ARABINOFURANOSYL-THYMINE-5-MONOPHOSPHATE'>TLB</scene></td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1oci FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oci OCA], [https://pdbe.org/1oci PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oci RCSB], [https://www.ebi.ac.uk/pdbsum/1oci PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oci ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Christensen, N K]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Jacobsen, J P]] | + | [[Category: Christensen NK]] |
| - | [[Category: Nielsen, P]] | + | [[Category: Jacobsen JP]] |
| - | [[Category: Petersen, M]] | + | [[Category: Nielsen P]] |
| - | [[Category: Stein, P C]] | + | [[Category: Petersen M]] |
| - | [[Category: Tommerholt, H V]] | + | [[Category: Stein PC]] |
| - | [[Category: Wengel, J]] | + | [[Category: Tommerholt HV]] |
| - | [[Category: Arabino nucleic acid]]
| + | [[Category: Wengel J]] |
| - | [[Category: Deoxyribonucleic acid]]
| + | |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Rnase h]]
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| Structural highlights
Publication Abstract from PubMed
[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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Tommerholt HV, Christensen NK, Nielsen P, Wengel J, Stein PC, Jacobsen JP, Petersen M. NMR solution structure of dsDNA containing a bicyclic D-arabino-configured nucleotide fixed in an O4'-endo sugar conformation. Org Biomol Chem. 2003 May 21;1(10):1790-7. PMID:12926371
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