2O81
The Structure of Tandem GA RNA Pairs When Flanking Pairs are isoG-isoC Pairs
Summary for 2O81
| Entry DOI | 10.2210/pdb2o81/pdb |
| Related | 2O83 |
| Descriptor | 5'-R(*GP*CP*(IG)P*GP*AP*(IC)P*GP*CP*A)-3' (1 entity in total) |
| Functional Keywords | rna, thermodynamics, secondary structure prediction, sheared ga pair, isoguanosine, isocytidine |
| Total number of polymer chains | 2 |
| Total formula weight | 5819.65 |
| Authors | Chen, G.,Turner, D.H. (deposition date: 2006-12-11, release date: 2007-07-10, Last modification date: 2023-12-27) |
| Primary citation | Chen, G.,Kierzek, R.,Yildirim, I.,Krugh, T.R.,Turner, D.H.,Kennedy, S.D. Stacking Effects on Local Structure in RNA: Changes in the Structure of Tandem GA Pairs when Flanking GC Pairs are Replaced by isoG-isoC Pairs J.Phys.Chem.B, 111:6718-6727, 2007 Cited by PubMed Abstract: The Watson-Crick-like isoG-isoC (iGiC) pair, with the amino and carbonyl groups transposed relative to the Watson-Crick GC pair, provides an expanded alphabet for understanding interactions that shape nucleic acid structure. Here, thermodynamic stabilities of tandem GA pairs flanked by iGiC pairs are reported along with the NMR structures of the RNA self-complementary duplexes (GCiGGAiCGCA)2 and (GGiCGAiGCCA)2. A sheared GA pairing forms in (GCiGGAiCGCA)2, and an imino GA pairing forms in (GGiCGAiGCCA)2. The structures contrast with the formation of tandem imino and sheared GA pairs flanked by GC pairs in the RNA self-complementary duplexes (GCGGACGC)2 and (GGCGAGCC)2, respectively. In both iGiC duplexes, Watson-Crick-like hydrogen bonds are formed between iG and iC, and iGiC substitutions result in less favorable loop stability. The results provide benchmarks for testing computations of molecular interactions that shape RNA three-dimensional structure. PubMed: 17411085DOI: 10.1021/jp068732m PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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