481d: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:481d.jpg|left|200px]]


<!--
==CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 1.6A RESOLUTION==
The line below this paragraph, containing "STRUCTURE_481d", creates the "Structure Box" on the page.
<StructureSection load='481d' size='340' side='right'caption='[[481d]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[481d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=481D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=481D FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6HA:1,5-ANHYDRO-2,3-DIDEOXY-2-(ADENIN-9-YL)-6-O-PHOSPHORYL-D-ARABINO-HEXITOL'>6HA</scene>, <scene name='pdbligand=6HC:1,5-ANHYDRO-2,3-DIDEOXY-2-(CYTOSIN-1-YL)-6-O-PHOSPHORYL-D-ARABINO-HEXITOL'>6HC</scene>, <scene name='pdbligand=6HG:1,5-ANHYDRO-2,3-DIDEOXY-2-(GUANIN-9-YL)-6-O-PHOSPHORYL-D-ARABINO-HEXITOL'>6HG</scene>, <scene name='pdbligand=6HT:1,5-ANHYDRO-2,3-DIDEOXY-2-(THYMIN-1-YL)-6-O-PHOSPHORYL-D-ARABINO-HEXITOL'>6HT</scene></td></tr>
{{STRUCTURE_481d|  PDB=481d  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=481d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=481d OCA], [https://pdbe.org/481d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=481d RCSB], [https://www.ebi.ac.uk/pdbsum/481d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=481d ProSAT]</span></td></tr>
 
</table>
'''CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 1.6A RESOLUTION'''
__TOC__
 
</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Declercq R]]
A huge variety of chemically modified oligonucleotide derivatives has been synthesized for possible antisense applications. One such derivative, hexitol nucleic acid (HNA), is a DNA analogue containing the standard nucleoside bases, but with a phosphorylated 1',5'-anhydrohexitol backbone. Hexitol nucleic acids are some of the strongest hybridizing antisense compounds presently known, but HNA duplexes are even more stable. We present here the first high-resolution structure of a double helical nucleic acid with all sugars being hexitols. Although designed to have a restricted conformational flexibility, the hexitol oligomer h(GTGTACAC) is able to crystallize in two different double helical conformations. Both structures display a high x-displacement, normal Watson-Crick base pairing, similar base stacking patterns, and a very deep major groove together with a minor groove with increased hydrophobicity. One of the conformations displays a major groove which is wide enough to accommodate a second HNA double helix resulting in the formation of a double helix of HNA double helices. Both structures show most similarities with the A-type helical structure, the anhydrohexitol chair conformation thereby acting as a good mimic for the furanose C3'-endo conformation observed in RNA. As compared to the quasi-linear structure of homo-DNA, the axial position of the base in HNA allows efficient base stacking and hence double helix formation.
[[Category: Van Meervelt L]]
 
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=481D OCA].  
 
==Reference==
Crystal structure of double helical hexitol nucleic acids., Declercq R, Van Aerschot A, Read RJ, Herdewijn P, Van Meervelt L, J Am Chem Soc. 2002 Feb 13;124(6):928-33. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11829600 11829600]
[[Category: Declercq, R.]]
[[Category: Meervelt, L Van.]]
[[Category: Dna analogue]]
[[Category: Double helix]]
[[Category: Hexitol nucleic acid]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 22:19:54 2008''
Retrieved from "https://proteopedia.org/481d"