2rmq
From Proteopedia
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| - | + | ==Solution structure of fully modified 4'-thioDNA with the sequence of d(CGCGAATTCGCG)== | |
| - | + | <StructureSection load='2rmq' size='340' side='right'caption='[[2rmq]]' scene=''> | |
| - | + | == Structural highlights == | |
| - | + | <table><tr><td colspan='2'>[[2rmq]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RMQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RMQ 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=C4S:2-DEOXY-4-THIOCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>C4S</scene>, <scene name='pdbligand=S4A:2-DEOXY-4-THIOADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>S4A</scene>, <scene name='pdbligand=S4G:2-DEOXY-4-THIOGUANOSINE+5-(DIHYDROGEN+PHOSPHATE)'>S4G</scene>, <scene name='pdbligand=T49:S4-2DEOXYTHYMIDINE+5-MONOPHOSPHATE'>T49</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=2rmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rmq OCA], [https://pdbe.org/2rmq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rmq RCSB], [https://www.ebi.ac.uk/pdbsum/2rmq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rmq ProSAT]</span></td></tr> | |
| - | + | </table> | |
| - | ''' | + | <div style="background-color:#fffaf0;"> |
| - | + | == Publication Abstract from PubMed == | |
| - | + | ||
| - | == | + | |
Fully modified 4'-thioDNA, an oligonucleotide only comprising 2'-deoxy-4'-thionucleosides, exhibited resistance to an endonuclease, in addition to preferable hybridization with RNA. Therefore, 4'-thioDNA is promising for application as a functional oligonucleotide. Fully modified 4'-thioDNA was found to behave like an RNA molecule, but no details of its structure beyond the results of circular dichroism analysis are available. Here, we have determined the structure of fully modified 4'-thioDNA with the sequence of d(CGCGAATTCGCG) by NMR. Most sugars take on the C3'-endo conformation. The major groove is narrow and deep, while the minor groove is wide and shallow. Thus, fully modified 4'-thioDNA takes on the A-form characteristic of RNA, both locally and globally. The only structure reported for 4'-thioDNA showed that partially modified 4'-thioDNA that contained some 2'-deoxy-4'-thionucleosides took on the B-form in the crystalline form. We have determined the structure of 4'-thioDNA in solution for the first time, and demonstrated unexpected differences between the two structures. The origin of the formation of the A-form is discussed. The remarkable biochemical properties reported for fully modified 4'-thioDNA, including nuclease-resistance, are rationalized in the light of the elucidated structure. | Fully modified 4'-thioDNA, an oligonucleotide only comprising 2'-deoxy-4'-thionucleosides, exhibited resistance to an endonuclease, in addition to preferable hybridization with RNA. Therefore, 4'-thioDNA is promising for application as a functional oligonucleotide. Fully modified 4'-thioDNA was found to behave like an RNA molecule, but no details of its structure beyond the results of circular dichroism analysis are available. Here, we have determined the structure of fully modified 4'-thioDNA with the sequence of d(CGCGAATTCGCG) by NMR. Most sugars take on the C3'-endo conformation. The major groove is narrow and deep, while the minor groove is wide and shallow. Thus, fully modified 4'-thioDNA takes on the A-form characteristic of RNA, both locally and globally. The only structure reported for 4'-thioDNA showed that partially modified 4'-thioDNA that contained some 2'-deoxy-4'-thionucleosides took on the B-form in the crystalline form. We have determined the structure of 4'-thioDNA in solution for the first time, and demonstrated unexpected differences between the two structures. The origin of the formation of the A-form is discussed. The remarkable biochemical properties reported for fully modified 4'-thioDNA, including nuclease-resistance, are rationalized in the light of the elucidated structure. | ||
| - | + | Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance.,Matsugami A, Ohyama T, Inada M, Inoue N, Minakawa N, Matsuda A, Katahira M Nucleic Acids Res. 2008 Apr;36(6):1805-12. Epub 2008 Feb 5. PMID:18252770<ref>PMID:18252770</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | [[Category: | + | <div class="pdbe-citations 2rmq" style="background-color:#fffaf0;"></div> |
| - | [[Category: Inada | + | == References == |
| - | [[Category: Katahira | + | <references/> |
| - | [[Category: Matsugami | + | __TOC__ |
| - | [[Category: Ohyama | + | </StructureSection> |
| - | + | [[Category: Large Structures]] | |
| - | + | [[Category: Inada M]] | |
| - | + | [[Category: Katahira M]] | |
| + | [[Category: Matsugami A]] | ||
| + | [[Category: Ohyama T]] | ||
Current revision
Solution structure of fully modified 4'-thioDNA with the sequence of d(CGCGAATTCGCG)
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