SPECTROSCOPIC STUDIES ON BINDING OF BERENIL TO DOUBLE HELIX OF D(GCTTAAGC)(2) AND D(GCAATTGC)(2)

Thermodynamic parameters for double helix formation of d(GCTTAAGC)(2), d(GCAATTGC)(2) and their complexes with berenil were obtained by obse rving absorbance at 260 nm during the DNA melting process. Two oligode oxynucleotides are self-complementary and have identical base pairing but different base sequence in the central four bases. From the CD spe ctral and UV melting data, they revealed noticeable difference in thei r conformation as well as thermodynamic property. The melting transiti on of d(GCTTAAGC)2 was more or less enthalpic, but rather entropic for that of d(GCAATTGC)(2). And berenil bound to d(GCAATTGC)(2) more tigh tly and increased the melting temperature of the oligodeoxynucleotide from 30 degrees C to 38 degrees C, but the overall conformation was ma intained. Binding of berenil to the d(GCTTAAGC)2 duplex did not increa se melting temperature of the oligodeoxynucleotide, but caused a confo rmational change. The experimental results showed that Delta H-o and D elta S-o could be used to explain the sequence specificity appeared in the binding interaction between each model oligodeoxynucleotide and b erenil.