1g3a: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==STRUCTURE OF RNA DUPLEXES (CIGCGICG)2== | ==STRUCTURE OF RNA DUPLEXES (CIGCGICG)2== | ||
<StructureSection load='1g3a' size='340' side='right'caption='[[1g3a | <StructureSection load='1g3a' size='340' side='right'caption='[[1g3a]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1g3a]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G3A FirstGlance]. <br> | <table><tr><td colspan='2'>[[1g3a]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G3A FirstGlance]. <br> | ||
</td></tr><tr id=' | </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=IC:ISOCYTIDINE-5-MONOPHOSPHATE'>IC</scene>, <scene name='pdbligand=IG:ISOGUANOSINE-5-MONOPHOSPHATE'>IG</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=1g3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g3a OCA], [https://pdbe.org/1g3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g3a RCSB], [https://www.ebi.ac.uk/pdbsum/1g3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g3a ProSAT]</span></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=1g3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g3a OCA], [https://pdbe.org/1g3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g3a RCSB], [https://www.ebi.ac.uk/pdbsum/1g3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g3a ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| Line 21: | Line 22: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Chen | [[Category: Chen X]] | ||
[[Category: Kierzek | [[Category: Kierzek R]] | ||
[[Category: Turner | [[Category: Turner DH]] | ||
Latest revision as of 21:36, 29 November 2023
STRUCTURE OF RNA DUPLEXES (CIGCGICG)2STRUCTURE OF RNA DUPLEXES (CIGCGICG)2
Structural highlights
Publication Abstract from PubMedIsoguanosine (iG) and isocytidine (iC) differ from guanosine (G) and cytidine (C), respectively, in that the amino and carbonyl groups are transposed. The thermodynamic properties of a set of iG, iC containing RNA duplexes have been measured by UV optical melting. It is found that iG-iC replacements usually stabilize duplexes, and the stabilization per iG-iC pair is sequence-dependent. The sequence dependence can be fit to a nearest-neighbor model in which the stabilities of iG--iC pairs depend on the adjacent iG--iC or G--C pairs. For 5'-CG-3'/3'-GC-5' and 5'-GG-3'/3'-CC-5' nearest neighbors, the free energy differences upon iG-iC replacement are smaller than 0.2 kcal/mol at 37 degrees C, regardless of the number of replacements. For 5'-GC-3'/3'-CG-5', however, each iG--iC replacement adds 0.6 kcal/mol stabilizing free energy at 37 degrees C. Stacking propensities of iG and iC as unpaired nucleotides at the end of a duplex are similar to those of G and C. An NMR structure is reported for r(CiGCGiCG)(2) and found to belong to the A-form family. The structure has substantial deviations from standard A-form but is similar to published NMR and/or crystal structures for r(CGCGCG)(2) and 2'-O-methyl (CGCGCG)(2). These results provide benchmarks for theoretical calculations aimed at understanding the fundamental physical basis for the thermodynamic stabilities of nucleic acid duplexes. Stability and structure of RNA duplexes containing isoguanosine and isocytidine.,Chen X, Kierzek R, Turner DH J Am Chem Soc. 2001 Feb 21;123(7):1267-74. PMID:11456697[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
| ||||||||||||||||||