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==BromoUracil substituted structure of intercalation-locked DNA tetraplex==
==BromoUracil substituted structure of intercalation-locked DNA tetraplex==
<StructureSection load='4rip' size='340' side='right' caption='[[4rip]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='4rip' size='340' side='right'caption='[[4rip]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4rip]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RIP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RIP FirstGlance]. <br>
<table><tr><td colspan='2'>[[4rip]] 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=4RIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RIP FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4rim|4rim]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></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=4rip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rip OCA], [http://pdbe.org/4rip PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rip RCSB], [http://www.ebi.ac.uk/pdbsum/4rip PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rip ProSAT]</span></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=4rip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rip OCA], [https://pdbe.org/4rip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rip RCSB], [https://www.ebi.ac.uk/pdbsum/4rip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rip ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson-Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A-A base pairs between adjacent G-G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H-1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.
An intercalation-locked parallel-stranded DNA tetraplex.,Tripathi S, Zhang D, Paukstelis PJ Nucleic Acids Res. 2015 Jan 27. pii: gkv033. PMID:25628357<ref>PMID:25628357</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4rip" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Paukstelis, P]]
[[Category: Large Structures]]
[[Category: Tripathi, S K]]
[[Category: Synthetic construct]]
[[Category: Zhang, D]]
[[Category: Paukstelis P]]
[[Category: Bromouracil]]
[[Category: Tripathi SK]]
[[Category: Dna]]
[[Category: Zhang D]]
[[Category: Homoduplex]]
[[Category: Intercalation-locked dna tetraplex]]
Retrieved from "https://proteopedia.org/4rip"