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Thermodynamic Stability and Divalent Ion Interactions of RNA Containing Purine‐Rich Bulges
Author(s) -
Strom Shane
Publication year - 2011
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.25.1_supplement.903.6
Subject(s) - rna , ribozyme , nucleotide , uracil , chemistry , cytosine , crystallography , intron , purine , biophysics , stereochemistry , dna , biochemistry , biology , enzyme , gene
Bulges are a common non‐helical motif found in RNA that play an important role in RNA recognition. Small asymmetrical bulges occur in many different RNA including HIV‐RNA and various micro RNA. In the P5abc region of group I intron, an X nucleotide adenine rich bulge coordinates two Mg 2+ ions in order to allow for the formation of a specific structure necessary for ribozyme catalysis. Previous studies in our lab have shown that TAR RNA containing cytosine‐rich trinucleotide bulges are ~2 kcal/mol more stable than those containing uracil‐rich bulges in 1 M KCl. Magnesium ions stabilize TAR RNA containing uracil‐rich bulges by ~1–2 kcal/mol and cytosine‐rich bulges by ~ 1 kcal/mol, relative to 1 M KCl conditions. In this study, we are examining the differences in RNA stability as the size of a purine bulge is varied between one and five nucleotides. Thermal denaturation experiments are being performed on varying concentrations of RNA in buffers containing either 1 M KCl or varying concentrations of divalent ions. Altering the nucleotide sequence of the bulge alters RNA stability as well as its ion binding properties. A comparison of thermodynamic properties of purine and pyrimidine‐rich bulges will be presented.