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New page: left|200px<br /><applet load="1cx5" size="450" color="white" frame="true" align="right" spinBox="true" caption="1cx5" /> '''ANTISENSE DNA/RNA HYBRID CONTAINING MODIFIED... |
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== | ==ANTISENSE DNA/RNA HYBRID CONTAINING MODIFIED BACKBONE== | ||
The solution structure of an antisense DNA.RNA hybrid duplex, d(CGCGTT-MMI-TTGCGC).r(GCGCAAAACGCG) (designated R4), containing an MMI | <StructureSection load='1cx5' size='340' side='right'caption='[[1cx5]]' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1cx5]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CX5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CX5 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MMT:5-O-(DIMETHYLAMINO)-THYMIDINE'>MMT</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=1cx5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cx5 OCA], [https://pdbe.org/1cx5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cx5 RCSB], [https://www.ebi.ac.uk/pdbsum/1cx5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cx5 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The solution structure of an antisense DNA.RNA hybrid duplex, d(CGCGTT-MMI-TTGCGC).r(GCGCAAAACGCG) (designated R4), containing an MMI backbone linker [3'-CH(2)N(CH(3))-O5'], is elucidated. The structural details of the MMI linker, its structural effects on the neighboring residues, and the molecular basis of the MMI effects are examined. The lipophilic N-methyl group of MMI is peripheral to the helix, assuming a conformation that is most stable with regard to the N-O torsion angle. The MMI linker promotes a 3'-endo conformation for the sugar moieties at both 3'- and 5'-adjacent positions and a backbone kink involving distant residues along the 3'-direction. Comparison of R4 with other analogous hybrid duplexes previously studied in this laboratory reveals a new family of low-energy helical conformations that can be accommodated in stable duplexes and a common feature of C3'-modified sugars for adopting a C3'-endo pucker. The results of these studies emphasize the interplay of several factors that govern the formation of stable hybrid duplexes and provide a basis for the understanding of the biological role of the MMI modifications, which are important building blocks for a family of promising chimeric antisense oligonucleotides. | |||
NMR structure of an antisense DNA.RNA hybrid duplex containing a 3'-CH(2)N(CH(3))-O-5' or an MMI backbone linker.,Yang X, Han X, Cross C, Bare S, Sanghvi Y, Gao X Biochemistry. 1999 Sep 28;38(39):12586-96. PMID:10504227<ref>PMID:10504227</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 1cx5" style="background-color:#fffaf0;"></div> | ||
[[Category: Cross | == References == | ||
[[Category: Gao | <references/> | ||
[[Category: Han | __TOC__ | ||
[[Category: Sanghvi | </StructureSection> | ||
[[Category: Yang | [[Category: Large Structures]] | ||
[[Category: Cross C]] | |||
[[Category: Gao X]] | |||
[[Category: Han X]] | |||
[[Category: Sanghvi Y]] | |||
[[Category: Yang X]] | |||
Latest revision as of 14:41, 22 November 2023
ANTISENSE DNA/RNA HYBRID CONTAINING MODIFIED BACKBONEANTISENSE DNA/RNA HYBRID CONTAINING MODIFIED BACKBONE
Structural highlights
Publication Abstract from PubMedThe solution structure of an antisense DNA.RNA hybrid duplex, d(CGCGTT-MMI-TTGCGC).r(GCGCAAAACGCG) (designated R4), containing an MMI backbone linker [3'-CH(2)N(CH(3))-O5'], is elucidated. The structural details of the MMI linker, its structural effects on the neighboring residues, and the molecular basis of the MMI effects are examined. The lipophilic N-methyl group of MMI is peripheral to the helix, assuming a conformation that is most stable with regard to the N-O torsion angle. The MMI linker promotes a 3'-endo conformation for the sugar moieties at both 3'- and 5'-adjacent positions and a backbone kink involving distant residues along the 3'-direction. Comparison of R4 with other analogous hybrid duplexes previously studied in this laboratory reveals a new family of low-energy helical conformations that can be accommodated in stable duplexes and a common feature of C3'-modified sugars for adopting a C3'-endo pucker. The results of these studies emphasize the interplay of several factors that govern the formation of stable hybrid duplexes and provide a basis for the understanding of the biological role of the MMI modifications, which are important building blocks for a family of promising chimeric antisense oligonucleotides. NMR structure of an antisense DNA.RNA hybrid duplex containing a 3'-CH(2)N(CH(3))-O-5' or an MMI backbone linker.,Yang X, Han X, Cross C, Bare S, Sanghvi Y, Gao X Biochemistry. 1999 Sep 28;38(39):12586-96. PMID:10504227[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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