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Thermodynamic stablity and divalent ion interactions of RNA containing purine‐rich bulges
Author(s) -
Strom Shane Fancher,
Grover Neena
Publication year - 2010
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.24.1_supplement.500.4
Subject(s) - rna , uracil , cytosine , nucleotide , chemistry , divalent , biophysics , transcription (linguistics) , crystallography , purine , stereochemistry , biochemistry , biology , dna , enzyme , gene , linguistics , philosophy , organic chemistry
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 microRNA. In HIV‐1 TAR RNA, a trinucleotide bulge interacts with the Tat protein of HIV‐1 to increase its rate of transcription one hundred fold. 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 conditions. 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 bulge size is varied between one and five nucleotides. Thermal denaturation experiments are being performed on varying concentrations of RNA in buffers containing 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. This work was funded by NSF MCB‐0621509 to NG.