481d

<StructureSection load='481d' size='340' side='right' caption='[[481d]], [[Resolution|resolution]] 1.60&Aring;' scene=''>

<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=481D FirstGlance]. <br>

</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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>

<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=481d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=481d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=481d RCSB], [http://www.ebi.ac.uk/pdbsum/481d PDBsum]</span></td></tr>

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.

 

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:11829600<ref>PMID:11829600</ref>

 

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<references/>

[[Category: Declercq, R.]]

[[Category: Meervelt, L Van.]]

[[Category: Dna]]

[[Category: Hexitol nucleic acid]]