Binding of CC‐1065 to poly‐ and oligonucleotides

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Abstract
The binding of the antitumor agent CC‐1065 to a variety of poly‐ and oligonucleotides was studied by electronic absorption, CD, and resistance to removal by Sephadex column chromatography. Competitive binding experiments between CC‐1065 and netropsin were carried out with calf‐thymus DNA, poly(dI‐dC) · poly(dI‐dC), poly(dI) · poly(dC), poly(rA) · poly(dT), poly(dA‐ dC) · poly(dG‐dT), and poly(dA) · 2poly(dT). CC‐1065 binds to polynucleotides by three mechanisms. In the first, CC‐1065 binds only weakly, as judged by the induction of zero or very weak CD spectra and low resistance to extraction of drug from the polynucleotide by Sephadex chromatography. In the second and third mechanisms, CC‐1065 binds strongly, as judged by the induction of two distinct, intense CD spectra and high resistance to extraction of drug from the polynucleotide, by Sephadex chromatography in both cases. The species bound by the second mechanism converts to that bound by the third mechanism with varying kinetics, which depend both on the base‐pair sequence and composition of the polynucleotide. Competitive binding experiments with netropsin show that CC‐1065 binds strongly in the minor groove of DNA by the second and third mechanisms of binding. Netropsin can displace CC‐1065 that is bound by the second mechanism but not that bound by the third mechanism. CC‐1065 binds preferentially to B‐form duplex DNA and weakly (by the first binding mechanism) or not at all to RNA, DNA, and RNA–DNA polynucleotides which adopt the A‐form conformation or to single‐strand DNA. This correlation of strong binding of CC‐1065 to B‐form duplex DNA is consistent with x‐ray data, which suggest an anomalous structure for poly(dI) · poly(rC), as compared with poly(rI) · poly(dC) (A‐form) and poly(dI) · poly(dC) (B‐form). The binding data indicate that poly(rA) · poly(dU) takes the B‐form secondary structure like poly(rA) · poly(dT). Triple‐stranded poly(dA) · 2poly(dT) and poly(dA) · 2poly(dU), which are considered to adopt the A‐form conformation, bind CC‐1065 strongly. Netropsin, which also shows a binding preference for B‐form polynucleotides, also binds to poly(dA) · 2poly(dT) and occupies the same binding site as CC‐1065. These binding studies are consistent with results of x‐ray studies, which suggest that A‐form triplex DNA retains some structural features of B‐form DNA that are not present in A‐form duplex DNA; i.e., the axial rise per nucleotide and the base tilt. Triple‐stranded poly(dA) · 2poly(rU) does not bind CC‐1065 strongly but has nearly the same conformation as poly(dA) · 2poly(dT) based on x‐ray analysis. This suggests that the 2′‐OH group of the poly(rU) strands interferes with CC‐1065 binding to this polynucleotide. The same type of interference may occur for other RNA and DNA–RNA polynucleotides that bind CC‐1065 weakly.