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Thermodynamic examination of the role of the base triple in TAR RNA
Author(s) -
Booth David Scott,
Grover Neena
Publication year - 2007
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.21.5.a280-d
Subject(s) - rna , chemistry , divalent , arginine , crystallography , base pair , tar (computing) , nucleotide , binding site , stereochemistry , biochemistry , biophysics , biology , amino acid , dna , organic chemistry , gene , programming language , computer science
The t rans‐ a ctivating r egion (TAR RNA) of human immunodeficiency virus type‐1 (HIV‐1) contains a conserved tri‐nucleotide bulge region critical for protein recognition. Binding of a single arginine residue changes TAR RNA conformation from bent to straight and allows a base triple to form between U23 in the bulge and A27‐U38 in the upper‐helical stem, which is required for biochemical activity. Divalent metal ions have also been implicated in the straightening of TAR RNA. The crystal structure of Ca 2+ ‐bound TAR RNA indicates that divalent metal ions may prevent the formation of the base triple. The base triple, however, may only form transiently. If base triple formation occurs, then a noticeable increase in RNA stability is expected. We are examining how thermodynamic parameters change when TAR RNA binds to metal ions and arginine, and comparing these parameters to RNA in which the base triple has been disrupted C23 A27‐U38 or alternatively restored as C23 + ·G27‐C38 (at pH 5.5). This comparative analysis of divalent metal ion binding in the presence or absence of arginine will allow us to establish the role of the base triple in binding these ligands and their potential physiological roles.