4roy
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 4roy is ON HOLD Authors: Saoji, M.M., Paukstelis, P.J. Description: Sequence and structure of a self-assembled 3-D DNA crystal: D(GGACGATCGGGAG)) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Sequence and structure of a self-assembled 3-D DNA crystal: D(GGACGATCGGGAG)== | |
| + | <StructureSection load='4roy' size='340' side='right'caption='[[4roy]], [[Resolution|resolution]] 2.09Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[4roy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ROY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ROY FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.09Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4roy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4roy OCA], [https://pdbe.org/4roy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4roy RCSB], [https://www.ebi.ac.uk/pdbsum/4roy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4roy ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | DNA is a widely used biopolymer for the construction of nanometer-scale objects due to its programmability and structural predictability. One long-standing goal of the DNA nanotechnology field has been the construction of three-dimensional DNA crystals. We previously determined the X-ray crystal structure of a DNA 13-mer that forms a continuously hydrogen bonded three-dimensional lattice through Watson-Crick and non-canonical base pairs. Our current work sets out to understand how the sequence of the Watson-Crick duplex region influences crystallization of this 13-mer. We screened all possible self-complementary sequences in the hexameric duplex region and found 21 oligonucleotides that crystallized. Sequence analysis showed that one specific Watson-Crick pair influenced the crystallization propensity and the speed of crystal self-assembly. We determined X-ray crystal structures for 13 of these oligonucleotides and found sequence-specific structural changes that suggests that this base pair may serve as a structural anchor during crystal assembly. Finally, we explored the crystal self-assembly and nucleation process. Solution studies indicated that these oligonucleotides do not form base pairs in the absence of cations, but that the addition of divalent cations leads to rapid self-assembly to higher molecular weight complexes. We further demonstrate that crystals grown from mixtures of two different oligonucleotide sequences contain both oligonucleotides. These results suggest that crystal self-assembly is nucleated by the formation of the Watson-Crick duplexes initiated by a simple chemical trigger. This work provides new insight into the role of sequence for the assembly of periodic DNA structures. This article is protected by copyright. All rights reserved. | ||
| - | + | Probing the role of sequence in the assembly of three-dimensional DNA crystals.,Saoji M, Zhang D, Paukstelis PJ Biopolymers. 2015 May 26. doi: 10.1002/bip.22688. PMID:26015367<ref>PMID:26015367</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 4roy" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Paukstelis PJ]] | ||
| + | [[Category: Saoji MM]] | ||
Current revision
Sequence and structure of a self-assembled 3-D DNA crystal: D(GGACGATCGGGAG)
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