Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges.

Ultraviolet absorption techniques were used to study the thermodynamics of duplex formation for a DNA decamer, d(GCGAAAAGCG).d(CGCTTTTCGC), and a series of related duplexes, each of which contains a bulged base centered in the A.T tract. Thermodynamic parameters were obtained from nonlinear least-squares fits of the melting curves and the concentration dependences of the melting temperatures. Duplexes containing a localized single-base bulge were found to be 3.5-4.6 kcal/mol less stable than the decamer at 37 degrees C. These results indicate that both the identity of the bulged base and the strand in which it is located may influence the amount by which the duplex is destabilized. Bulged bases located in the T-strand, d(CGCTTYTTCGC), in position Y, were observed to be slightly more destabilizing than those located in the A-strand, d(GCGAAXAAGCG), in position X. Bulged purines may be more destabilizing than bulged pyrimidines.