Premium
Thermodynamic Examination of Small Symmetric and Asymmetric Loops Containing A•C and G•U Base Pairs in the Context of Group I Intron
Author(s) -
Shishkova Evgenia,
Grover Neena
Publication year - 2012
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.26.1_supplement.946.4
Subject(s) - ribozyme , intron , context (archaeology) , rna , chemistry , crystallography , protonation , group ii intron , rna splicing , base pair , stereochemistry , biology , ion , biochemistry , dna , gene , organic chemistry , paleontology
Group I introns are large ribozymes capable of performing transesterification reactions to splice themselves out of an rRNA. Proper 3D assembly of the intron is crucial for its activation and formation of a correctly spliced product. Divalent metal ions, Mg 2+ in particular, facilitate folding of the intron and are necessary for catalysis. Studies of RNA crystal structures report presence of metal ions in vicinity of highly conserved loops and bulges, suggesting that these regions play key role in functioning of the intron. We are examining the thermodynamic stability and metal ion binding properties of non‐canonical base pairs in the context of group I intron of Tetrahymena thermophile using small RNA as model constructs. An asymmetric adenosine‐rich tetranucleotide, a 4×1 A•C loop construct, and a symmetric 4×4 A•C loop construct were equally stable in 1 M KCl at various pHs. The 4×4 A•C loop gained more stability upon addition of Mg 2+ , as compared to 4×0 and 4×1 constructs. Protonation of A and consequent formation of A+•C base pair is expected at pH 5.5, and corresponding increase of 0.8 kcal/mol in stability of the 4×4 A•C construct was observed at pH 5.5 over pH 7. In 1M KCl at pH 5.5 and pH 7, a symmetric 4×4 G•U construct was 3 kcal/mol more stable than an asymmetric 4×2 G•U construct. The G•U containing RNA gained no additional stability in 9.5 mM Mg 2+ . This work was funded by NSF Grant MCB‐0950582 to NG.