Binding specificities of actinomycin D to self-complementary tetranucleotide sequences -XGCY-.

Binding of actinomycin D (ACTD) to self-complementary decamers d(ATA-XGCY-TAT), where XGCY = TGCA, AGCT, CGCG, and GGCC, has been investigated by equilibrium, kinetic, and thermal denaturation studies. The results indicate that despite the presence of a GC dinucleotide sequence, -GGCC- exhibits a much weaker binding affinity toward ACTD than the other three tetranucleotide sequences. Binding constants estimated from Scatchard plots indicate that binding to the -GGCC- site is at least an order of magnitude weaker than binding to -CGCG- and -AGCT-, which in turn is only slightly weaker than binding to the -TGCA- sequence. At 18.5 degrees C and 1% SDS, ACTD dissociates from d-(ATA-TGCA-TAT) with a slow characteristic time of 3300 s, roughly 4 times slower than dissociation from those containing -CGCG- and -AGCT- sequences and more than 2 orders of magnitude slower than that from -GGCC-. An 18.2 degrees C increase in the melting temperature is observed for the -TGCA-containing decamer upon binding of the ACTD, whereas increases of 10.3, 6.7, and 2.0 degrees C are observed for the -CGCG-, -AGCT-, and -GGCC-containing decamers, respectively. The effects observed by changing the adjacent base pair (sequence) may occur as a result of differential stacking and/or peptide ring-DNA groove interactions. Base sequence alterations adjacent to the ACTD binding site may result in differences in the minor groove environment and/or subtle conformational alterations at the intercalation site.(ABSTRACT TRUNCATED AT 250 WORDS)