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Thermodynamic Comparison of Dinucleotide bulges in DNA and RNA
Author(s) -
Lockwood W Charles,
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.946.5
Subject(s) - rna , dna , chemistry , intron , metal ions in aqueous solution , crystallography , ion , biophysics , stereochemistry , biochemistry , biology , gene , organic chemistry
Bulges are non‐helical regions in RNA that provide sites for protein, ligand and metal ion interactions. In crystal structures, non‐canonical interactions of bulges are often the sites for interactions with metal ions. To fully elucidate RNA interaction in the bulge regions, we are also examining the corresponding DNA analogs. Dinucleotide bulges in DNA and RNA were modeled from Group II intron and HIV‐2 TAR RNA to understand the sequence and ion binding properties. Thermal denaturation experiments were performed on the wild type and modified constructs containing dinucleotide sequences in 1 M KCl and various concentrations of Mg2+ ions. DNA analogs typically are less stable than the RNA analogs in 1 M KCl and do not gain additional stability upon binding to Mg2+ ions. Comparative thermodynamic analysis will be presented for various DNA and RNA constructs. This work was funded by NSF Grant MCB‐0950582 to NG.