INTERACTION OF MINOR-GROOVE LIGANDS TO AN AAATT AATTT SITE - CORRELATION OF THERMODYNAMIC CHARACTERIZATION AND SOLUTION STRUCTURE/

A combination of circular dichroism spectroscopy, titration calorimetr y, and optical melting has been used to investigate the association of the minor groove ligands netropsin and distamycin to the central A(3) T(2) binding site of the DNA duplex d(CGCAAATTGGC).d(GCCAATTTGCG). For the complex with netropsin at 20 degrees C, a ligand/duplex stoichiom etry of 1:1 was obtained with K-b similar to 4.3 x 10(7) M(-1), Delta H-b similar to -7.5 kcal mol(-1), Delta S-b similar to 9.3 cal K-1 mol (-1), and Delta C-p similar to 0. Previous NMR studies characterized t he distamycin complex with A(3)T(2) at saturation as a dimeric side-by -side complex. Consistent with this result, we found a ligand/duplex s toichiometry of 2:1. In the current study, the relative thermodynamic contributions of the two distamycin ligands in the formation of this s ide-by-side complex (2:1 Dst.A(3)T(2)) were evaluated and compared wit h the thermodynamic characteristics of netropsin binding. The associat ion of the first distamycin molecule of the 2:1 Dst.A(3)T(2) complex y ielded the following thermodynamic profile: K-b similar to 3.1 X 10(7) M(-1), Delta H-b = -12.3 kcal mol(-1), Delta S-b = -8 cal K-1 mol(-1) , and Delta C-p = -42 cal K-1 mol(-1). The binding of the second dista mycin molecule occurs with a lower K-b of similar to 3.3 x 10(6) M(-1) , a more favorable Delta H-b of -18.8 kcal mol(-1), a more unfavorable Delta S-b of -34 cal K-1 mol(-1), and a higher Delta C-p of -196 cal K-1 mol(-1). The latter term indicates an ordering of electrostricted and structural water molecules by the complexes. These results correla te well with the NMR titrations and are discussed in context of the so lution structure of the 2:1 Dst.A(3)T(2) complex.