3v07: Difference between revisions

Line 1:

[[~~Image~~:~~3v07~~.~~jpg~~|~~left~~|~~200px~~]]

==Crystal structure of R-6'-Me-3'-fluoro hexitol nucleic acid==

== Structural highlights ==

<table><tr><td colspan='2'>[[3v07]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V07 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V07 FirstGlance]. <br>

</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=F6H:3,7-ANHYDRO-1,5,6-TRIDEOXY-5-FLUORO-6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2-O-PHOSPHONO-D-GLYCERO-L-ALLO-HEPTITOL'>F6H</scene></td></tr>

<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3v06|3v06]]</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=3v07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v07 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v07 RCSB], [http://www.ebi.ac.uk/pdbsum/3v07 PDBsum]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Locked nucleic acid (LNA) analogues with 2',4'-bridged sugars show promise in antisense applications. S-5'-Me-LNA has high RNA affinity, and modified oligonucleotides show weakened immune stimulation in vivo. Conversely, an R-5'-methyl group dramatically lowers RNA affinity. To test the effects of S- and R-6'-methyl groups on 3'-fluoro hexitol nucleic acid (FHNA) stability, we synthesized S- and R-6'-Me-FHNA thymidine and incorporated them into oligo-2'-deoxynucleotides. As with LNA, S-6'-Me is stabilizing whereas R-6'-Me is destabilizing. Crystal structures of 6'-Me-FHNA-modified DNAs explain the divergent consequences for stability and suggest convergent origins of these effects by S- and R-6'-Me (FHNA) [-5'-Me (LNA and RNA)] substituents.

<!--

Insights from crystal structures into the opposite effects on RNA affinity caused by the s- and R-6'-methyl backbone modifications of 3'-fluoro hexitol nucleic Acid.,Pallan PS, Yu J, Allerson CR, Swayze EE, Seth P, Egli M Biochemistry. 2012 Jan 10;51(1):7-9. Epub 2011 Dec 29. PMID:22229409<ref>PMID:22229409</ref>

~~The line below this paragraph~~, ~~containing "STRUCTURE_3v07"~~, ~~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_3v07| PDB=3v07 | SCENE= }}~~

~~===Crystal structure~~ of ~~R-6'-Me-3'-fluoro hexitol nucleic acid===~~

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

</div>

== References ==

~~<!--~~

~~The line below this paragraph, {{ABSTRACT_PUBMED_22229409}}, adds the Publication Abstract to~~ the ~~page~~

__TOC__

~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22229409 is the PubMed ID number~~.

</StructureSection>

-->

[[Category: Egli, M]]

~~{{ABSTRACT_PUBMED_22229409}}~~

[[Category: Pallan, P S]]

~~==About this Structure==~~

~~[[3v07]] is a 2 chain structure. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3V07 OCA].~~

==~~Reference~~==

<~~ref group="xtra">PMID:022229409<~~/~~ref~~><~~references group="xtra"~~/>

[[Category: Egli, M.]]

[[Category: Pallan, P S.]]

[[Category: 3'-fluoro hexitol nucleic acid]]

[[Category: A-form dna]]

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-[[Image:3v07.jpg|left|200px]]
+==Crystal structure of R-6'-Me-3'-fluoro hexitol nucleic acid==
+<StructureSection load='3v07' size='340' side='right' caption='[[3v07]], [[Resolution|resolution]] 1.24&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3v07]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V07 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V07 FirstGlance]. <br>
+</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=F6H:3,7-ANHYDRO-1,5,6-TRIDEOXY-5-FLUORO-6-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2-O-PHOSPHONO-D-GLYCERO-L-ALLO-HEPTITOL'>F6H</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3v06|3v06]]</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=3v07 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v07 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v07 RCSB], [http://www.ebi.ac.uk/pdbsum/3v07 PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Locked nucleic acid (LNA) analogues with 2',4'-bridged sugars show promise in antisense applications. S-5'-Me-LNA has high RNA affinity, and modified oligonucleotides show weakened immune stimulation in vivo. Conversely, an R-5'-methyl group dramatically lowers RNA affinity. To test the effects of S- and R-6'-methyl groups on 3'-fluoro hexitol nucleic acid (FHNA) stability, we synthesized S- and R-6'-Me-FHNA thymidine and incorporated them into oligo-2'-deoxynucleotides. As with LNA, S-6'-Me is stabilizing whereas R-6'-Me is destabilizing. Crystal structures of 6'-Me-FHNA-modified DNAs explain the divergent consequences for stability and suggest convergent origins of these effects by S- and R-6'-Me (FHNA) [-5'-Me (LNA and RNA)] substituents.
-<!--
+Insights from crystal structures into the opposite effects on RNA affinity caused by the s- and R-6'-methyl backbone modifications of 3'-fluoro hexitol nucleic Acid.,Pallan PS, Yu J, Allerson CR, Swayze EE, Seth P, Egli M Biochemistry. 2012 Jan 10;51(1):7-9. Epub 2011 Dec 29. PMID:22229409<ref>PMID:22229409</ref>
-The line below this paragraph, containing "STRUCTURE_3v07", 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_3v07|  PDB=3v07  |  SCENE=  }}
-===Crystal structure of R-6'-Me-3'-fluoro hexitol nucleic acid===
+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_22229409}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 22229409 is the PubMed ID number.
+</StructureSection>
--->
+[[Category: Egli, M]]
-{{ABSTRACT_PUBMED_22229409}}
+[[Category: Pallan, P S]]
-==About this Structure==
-[[3v07]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V07 OCA].
-==Reference==
-<ref group="xtra">PMID:022229409</ref><references group="xtra"/>
-[[Category: Egli, M.]]
-[[Category: Pallan, P S.]]
 [[Category: 3'-fluoro hexitol nucleic acid]]
 [[Category: A-form dna]]