1g3a
From Proteopedia
(New page: 200px<br /><applet load="1g3a" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g3a" /> '''STRUCTURE OF RNA DUPLEXES (CIGCGICG)2'''<br ...) |
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| - | [[Image:1g3a.gif|left|200px]]<br /><applet load="1g3a" size=" | + | [[Image:1g3a.gif|left|200px]]<br /><applet load="1g3a" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1g3a" /> | caption="1g3a" /> | ||
'''STRUCTURE OF RNA DUPLEXES (CIGCGICG)2'''<br /> | '''STRUCTURE OF RNA DUPLEXES (CIGCGICG)2'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Isoguanosine (iG) and isocytidine (iC) differ from guanosine (G) and | + | Isoguanosine (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. |
==About this Structure== | ==About this Structure== | ||
| - | 1G3A is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1G3A is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G3A OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Chen, X.]] | [[Category: Chen, X.]] | ||
[[Category: Kierzek, R.]] | [[Category: Kierzek, R.]] | ||
| - | [[Category: Turner, D | + | [[Category: Turner, D H.]] |
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:45:35 2008'' |
Revision as of 10:45, 21 February 2008
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STRUCTURE OF RNA DUPLEXES (CIGCGICG)2
Overview
Isoguanosine (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.
About this Structure
1G3A is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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
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