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| | <StructureSection load='5bxw' size='340' side='right'caption='[[5bxw]], [[Resolution|resolution]] 2.15Å' scene=''> | | <StructureSection load='5bxw' size='340' side='right'caption='[[5bxw]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5bxw]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BXW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BXW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5bxw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BXW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BXW FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5bz7|5bz7]], [[5bz9|5bz9]], [[5bzy|5bzy]]</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=5bxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bxw OCA], [https://pdbe.org/5bxw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bxw RCSB], [https://www.ebi.ac.uk/pdbsum/5bxw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bxw ProSAT]</span></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=5bxw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bxw OCA], [http://pdbe.org/5bxw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bxw RCSB], [http://www.ebi.ac.uk/pdbsum/5bxw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bxw 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: Paukstelis, P J]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Saoji, M]] | + | [[Category: Paukstelis PJ]] |
| - | [[Category: 14mer dna]] | + | [[Category: Saoji M]] |
| - | [[Category: 3d dna lattice]]
| + | |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Self assembly]]
| + | |
| Structural highlights
Publication Abstract from PubMed
DNA has proved to be a remarkable molecule for the construction of sophisticated two-dimensional and three-dimensional architectures because of its programmability and structural predictability provided by complementary Watson-Crick base pairing. DNA oligonucleotides can, however, exhibit a great deal of local structural diversity. DNA conformation is strongly linked to both environmental conditions and the nucleobase identities inherent in the oligonucleotide sequence, but the exact relationship between sequence and local structure is not completely understood. This study examines how a single-nucleotide addition to a class of self-assembling DNA 13-mers leads to a significantly different overall structure under identical crystallization conditions. The DNA 13-mers self-assemble in the presence of Mg(2+) through a combination of Watson-Crick and noncanonical base-pairing interactions. The crystal structures described here show that all of the predicted Watson-Crick base pairs are present, with the major difference being a significant rearrangement of noncanonical base pairs. This includes the formation of a sheared A-G base pair, a junction of strands formed from base-triple interactions, and tertiary interactions that generate structural features similar to tandem sheared G-A base pairs. The adoption of this alternate noncanonical structure is dependent in part on the sequence in the Watson-Crick duplex region. These results provide important new insights into the sequence-structure relationship of short DNA oligonucleotides and demonstrate a unique interplay between Watson-Crick and noncanonical base pairs that is responsible for crystallization fate.
Sequence-dependent structural changes in a self-assembling DNA oligonucleotide.,Saoji M, Paukstelis PJ Acta Crystallogr D Biol Crystallogr. 2015 Dec 1;71(Pt 12):2471-8. doi:, 10.1107/S1399004715019598. Epub 2015 Nov 26. PMID:26627654[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Saoji M, Paukstelis PJ. Sequence-dependent structural changes in a self-assembling DNA oligonucleotide. Acta Crystallogr D Biol Crystallogr. 2015 Dec 1;71(Pt 12):2471-8. doi:, 10.1107/S1399004715019598. Epub 2015 Nov 26. PMID:26627654 doi:http://dx.doi.org/10.1107/S1399004715019598
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