3knc

From Proteopedia

(Difference between revisions)

Revision as of 06:34, 19 July 2023

Crystal structure of the CeNA-RNA hybrid octamer ce(GCGTAGCG):r(CGCUACGC)

Structural highlights

3knc is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Cyclohexenyl nucleic acids (CeNA) are characterised by the carbon-carbon double bond replacing the O4'-oxygen atom of the natural D-2'-deoxyribose sugar ring in DNA. CeNAs exhibit a high conformational flexibility, are stable against nuclease activity and their hybridisation is RNA selective. Additionally, CeNA has been shown to induce an enhanced biological activity when incorporated in siRNA. This makes CeNA a good candidate for siRNA and synthetic aptamer applications. The crystal structure of the synthetic CeNA:RNA hybrid ce(GCGTAGCG):r(CGCUACGC) has been solved with a resolution of 2.50 A. The CeNA:RNA duplex adopts an anti-parallel, right-handed double helix with standard Watson-Crick base pairing. Analyses of the helical parameters revealed the octamer to form an A-like double helix. The cyclohexenyl rings mainly adopt the (3) H(2) conformation, which resembles the C3'-endo conformation of RNA ribose ring. This C3'-endo ring puckering was found in most of the RNA residues and is typical for A-family helices. The crystal structure is stabilised by the presence of hexahydrated magnesium ions. The fact that the CeNA:RNA hybrid adopts an A-type double helical conformation confirms the high potential of CeNAs for the construction of efficient siRNAs which can be used for therapeutical applications.

The Crystal Structure of the CeNA:RNA Hybrid ce(GCGTAGCG):r(CGCUACGC).,Ovaere M, Herdewijn P, Van Meervelt L Chemistry. 2011 Jul 4;17(28):7823-30. doi: 10.1002/chem.201003594. Epub, 2011 May 26. PMID:21618623^[1]

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

References

↑ Ovaere M, Herdewijn P, Van Meervelt L. The Crystal Structure of the CeNA:RNA Hybrid ce(GCGTAGCG):r(CGCUACGC). Chemistry. 2011 Jul 4;17(28):7823-30. doi: 10.1002/chem.201003594. Epub, 2011 May 26. PMID:21618623 doi:10.1002/chem.201003594

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3knc"

Categories: Large Structures | Ovaere M | Van Meervelt L

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[3knc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KNC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KNC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=XAR:[(1R,4S,6S)-4-(6-AMINO-9H-PURIN-9-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>XAR</scene>, <scene name='pdbligand=XCR:[(1R,4S,6S)-4-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>XCR</scene>, <scene name='pdbligand=XGR:[(1R,4S,6S)-4-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>XGR</scene>, <scene name='pdbligand=XTR:[(1R,4S,6S)-6-HYDROXY-4-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOHEX-2-EN-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>XTR</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XAR:[(1R,4S,6S)-4-(6-AMINO-9H-PURIN-9-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>XAR</scene>, <scene name='pdbligand=XCR:[(1R,4S,6S)-4-(4-AMINO-2-OXOPYRIMIDIN-1(2H)-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>XCR</scene>, <scene name='pdbligand=XGR:[(1R,4S,6S)-4-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>XGR</scene>, <scene name='pdbligand=XTR:[(1R,4S,6S)-6-HYDROXY-4-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOHEX-2-EN-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>XTR</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=3knc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3knc OCA], [https://pdbe.org/3knc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3knc RCSB], [https://www.ebi.ac.uk/pdbsum/3knc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3knc ProSAT]</span></td></tr>
 </table>
@@ Line 22: / Line 22: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Meervelt, L Van]]
+[[Category: Ovaere M]]
-[[Category: Ovaere, M]]
+[[Category: Van Meervelt L]]
-[[Category: Cyclohexene]]
-[[Category: Rna]]
-[[Category: Rna-cyclohexene-rna hybrid complex]]
-[[Category: Sugar modification]]

3knc

From Proteopedia

Revision as of 06:34, 19 July 2023

Crystal structure of the CeNA-RNA hybrid octamer ce(GCGTAGCG):r(CGCUACGC)

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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