Kinetic and equilibrium binding studies of actinomycin D with some d(TGCA)-containing dodecamers

Comparative kinetic, melting, and equilibrium binding studies of actinomycin D (ACTD) with d(ATATACGTATAT), four d(TGCA)-containing dodecamers, and poly(dG-dC).poly(dG-dC) revealed that (1) the affinity of ACTD for the dC-dG sequence is much less than for the dG-dC sequence; (2) ACTD forms 1:1 and 2:1 drug-duplex complexes with d(TATATGCATATA) and d(TATGCATGCATA), respectively, and their SDS driven dissociations exhibit single-exponential characteristics with rates (approximately 5 X 10(-4)s-1 at 20 degrees C) slightly slower than that of poly(dG-dC).poly(dG-dC); (3) although the melting temperature of d(CATGCATGCATG) is 8-9 deg higher than that of d(TATGCATGCATA), the rates of ACTD dissociation from these two oligomers are not greatly different and binding constants of (1-5) X 10(7) M-1 have been estimated for both; (4) a 3:1 stoichiometry is exhibited by ACTD binding to duplex d(TGCATGCATGCA) and the complex dissociates with two characteristic times, the fast component (1/k = approximately 100 s) comprising 2/3 of the contribution and the slow process (approximately 2000 s) contributing the other 1/3; and (5) the slow dissociation kinetics of an oligomer appears to be correlated to the higher percentage of slow association kinetics detectable by non-stop-flow techniques. These results indicate that the d(TGCA) sequence is a stronger binding and a slower dissociation site than the d(CGCG) sequence and suggest that base pairs flanking the dG-dC intercalative site may modulate interactions of the pentapeptide rings of ACTD with the DNA minor groove.(ABSTRACT TRUNCATED AT 250 WORDS)