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==A rare nucleotide base tautomer in the structure of an asymmetric DNA junction==
==A rare nucleotide base tautomer in the structure of an asymmetric DNA junction==
<StructureSection load='3igt' size='340' side='right' caption='[[3igt]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='3igt' size='340' side='right'caption='[[3igt]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3igt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IGT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IGT FirstGlance]. <br>
<table><tr><td colspan='2'>[[3igt]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IGT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IGT FirstGlance]. <br>
</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=3igt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3igt OCA], [http://pdbe.org/3igt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3igt RCSB], [http://www.ebi.ac.uk/pdbsum/3igt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3igt ProSAT]</span></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]] 1.9&#8491;</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=3igt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3igt OCA], [https://pdbe.org/3igt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3igt RCSB], [https://www.ebi.ac.uk/pdbsum/3igt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3igt ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The single-crystal structure of a DNA Holliday junction assembled from four unique sequences shows a structure that conforms to the general features of models derived from similar constructs in solution. The structure is a compact stacked-X form junction with two sets of stacked B-DNA-type arms that coaxially stack to form semicontinuous duplexes interrupted only by the crossing of the junction. These semicontinuous helices are related by a right-handed rotation angle of 56.5 degrees, which is nearly identical to the 60 degree angle in the solution model but differs from the more shallow value of approximately 40 degrees for previous crystal structures of symmetric junctions that self-assemble from single identical inverted-repeat sequences. This supports the model in which the unique set of intramolecular interactions at the trinucleotide core of the crossing strands, which are not present in the current asymmetric junction, affects both the stability and geometry of the symmetric junctions. An unexpected result, however, is that a highly wobbled A.T base pair, which is ascribed here to a rare enol tautomer form of the thymine, was observed at the end of a CCCC/GGGG sequence within the stacked B-DNA arms of this 1.9 A resolution structure. We suggest that the junction itself is not responsible for this unusual conformation but served as a vehicle for the study of this CG-rich sequence as a B-DNA duplex, mimicking the form that would be present in a replication complex. The existence of this unusual base lends credence to and defines a sequence context for the "rare tautomer hypothesis" as a mechanism for inducing transition mutations during DNA replication.
A rare nucleotide base tautomer in the structure of an asymmetric DNA junction.,Khuu P, Ho PS Biochemistry. 2009 Aug 25;48(33):7824-32. PMID:19580331<ref>PMID:19580331</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3igt" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ho, P S]]
[[Category: Large Structures]]
[[Category: Khuu, P]]
[[Category: Ho PS]]
[[Category: Dna]]
[[Category: Khuu P]]
[[Category: Dna four-stranded junction]]

Latest revision as of 13:05, 21 February 2024

A rare nucleotide base tautomer in the structure of an asymmetric DNA junctionA rare nucleotide base tautomer in the structure of an asymmetric DNA junction

Structural highlights

3igt is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

3igt, resolution 1.90Å

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