481d: Difference between revisions

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~~{{Seed}}~~

==CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 1.6A RESOLUTION==

[[~~Image~~:481d.~~png|left|200px~~]]

== Structural highlights ==

<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>

<table>

== Publication Abstract from PubMed ==

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>

~~The line below this paragraph~~, ~~containing "STRUCTURE_481d"~~, ~~creates the "Structure Box" on the page~~.

~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)

~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~

~~or leave the SCENE parameter empty for the default display~~.

-->

~~{{STRUCTURE_481d| PDB=481d | SCENE= }}~~

~~===CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 1.6A RESOLUTION===~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

~~<!--~~

~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_11829600}}, adds~~ the ~~Publication Abstract to the page~~

__TOC__

~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 11829600 is the PubMed ID number~~.

</StructureSection>

-->

~~{{ABSTRACT_PUBMED_11829600}}~~

==~~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]]

[[Category: Dna analogue]]

[[Category: Double helix]]

[[Category: Hexitol nucleic acid]]

~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 13:25:41 2008''~~

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@@ Line 1: / Line 1: @@
-{{Seed}}
+==CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 1.6A RESOLUTION==
-[[Image:481d.png|left|200px]]
+<StructureSection load='481d' size='340' side='right' caption='[[481d]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<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>
+<table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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>
-The line below this paragraph, containing "STRUCTURE_481d", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_481d|  PDB=481d  |  SCENE=  }}
-===CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 1.6A RESOLUTION===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_11829600}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 11829600 is the PubMed ID number.
+</StructureSection>
--->
-{{ABSTRACT_PUBMED_11829600}}
-==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]]
 [[Category: Dna analogue]]
 [[Category: Double helix]]
 [[Category: Hexitol nucleic acid]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul  3 13:25:41 2008''