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. 2007 Jun 21;111(24):6718-27. doi: 10.1021/jp068732m. Epub 2007 Apr 6.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adenine / chemistry*
  • Base Pairing*
  • Cytidine / chemistry*
  • Guanine / chemistry*
  • Hydrogen Bonding
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • Thermodynamics


  • isocytidine
  • Cytidine
  • Guanine
  • RNA
  • isoguanine
  • Adenine