1g3a | pdb_00001g3a
STRUCTURE OF RNA DUPLEXES (CIGCGICG)2
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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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