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==X-RAY structural analysis of B-DNA decamer D(CCATTAATGG)2 crystal grown in D2O solution== | |||
<StructureSection load='1wqy' size='340' side='right'caption='[[1wqy]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1wqy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WQY 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]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</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=1wqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wqy OCA], [https://pdbe.org/1wqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wqy RCSB], [https://www.ebi.ac.uk/pdbsum/1wqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wqy ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
== | |||
It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the decameric d(CCATTAATGG)2 duplex. Moreover, the D positions in 27 D2O molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 A resolution X-ray and 3.0 A resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in earlier X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules. | It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the decameric d(CCATTAATGG)2 duplex. Moreover, the D positions in 27 D2O molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 A resolution X-ray and 3.0 A resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in earlier X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules. | ||
Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements.,Arai S, Chatake T, Ohhara T, Kurihara K, Tanaka I, Suzuki N, Fujimoto Z, Mizuno H, Niimura N Nucleic Acids Res. 2005 May 24;33(9):3017-24. Print 2005. PMID:15914673<ref>PMID:15914673</ref> | |||
Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements., Arai S, Chatake T, Ohhara T, Kurihara K, Tanaka I, Suzuki N, Fujimoto Z, Mizuno H, Niimura N | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1wqy" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Arai S]] | |||
[[Category: Chatake T]] | |||
[[Category: Fujimoto Z]] | |||
[[Category: Kurihara K]] | |||
[[Category: Mizuno H]] | |||
[[Category: Niimura N]] | |||
[[Category: Ohhara T]] | |||
[[Category: Suzuki N]] | |||
[[Category: Tanaka I]] | |||
Latest revision as of 14:25, 2 August 2023
X-RAY structural analysis of B-DNA decamer D(CCATTAATGG)2 crystal grown in D2O solutionX-RAY structural analysis of B-DNA decamer D(CCATTAATGG)2 crystal grown in D2O solution
Structural highlights
Publication Abstract from PubMedIt has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the decameric d(CCATTAATGG)2 duplex. Moreover, the D positions in 27 D2O molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 A resolution X-ray and 3.0 A resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in earlier X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules. Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements.,Arai S, Chatake T, Ohhara T, Kurihara K, Tanaka I, Suzuki N, Fujimoto Z, Mizuno H, Niimura N Nucleic Acids Res. 2005 May 24;33(9):3017-24. Print 2005. PMID:15914673[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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