CORALYNE BINDS TIGHTLY TO BOTH T.A.T-CONTAINING AND C.G.C-CONTAINING DNA TRIPLEXES()

Coralyne is a DNA-binding antitumor antibiotic whose structure contain s four fused aromatic rings. The interaction of coralyne with the DNA triplexes poly(dT).poly(dA).poly(dT) and poly[d(TC)].poly-[d(GA)].poly [d(C+T)] was investigated by using three techniques. First, T(m) value s were measured by thermal denaturation analysis. Upon binding coralyn e, both triplexes showed T(m) values that were increased more than tho se of the corresponding duplexes. A related drug, berberinium, in whic h one of the aromatic rings is partially saturated, gave much smaller changes in T(m). Second, the fluorescence of coralyne is quenched in t he presence of DNA, allowing the measurement of binding parameters by Scatchard analysis. The binding isotherms were biphasic, which was int erpreted in terms of strong intercalative binding and much weaker stac king interactions. In the presence of 2 mM Mg2+, the binding constants to poly(dT).poly-(dA).poly(dT) and poly[d(TC)].poly[d(GA)].poly[d(C+T )] were 3.5 X 10(6) M-1 and 1.5 X 10(6) M-1, respectively, while the a ffinity to the parent duplexes was at least 2 orders of magnitude lowe r. In the absence of 2 mM Mg2+, the binding constants to poly[d(TC)].p oly[d(GA)].poly[d(C+T)] and poly-[d(TC)].poly[d(GA)] were 40 X 10(6) M -1 and 15 X 10(6) M-1, respectively. Thus coralyne shows considerable preference for the triplex structure but little sequence specificity, unlike ethidium, which will only bind to poly(dT).poly(dA)-poly(dT). F urther evidence for intercalation of coralyne was provided by an incre ase in the relative fluorescence quantum yield at 260 nm upon binding of coralyne to triplexes as well as an absence of quenching of fluores cence in the presence of Fe[(CN)6]4-. Third, coralyne promoted intermo lecular triplex formation between plasmids containing a pyr.pur tract and a single-stranded polypyrimidine. The ability of coralyne to bind to triplexes may relate to its in vivo activity and also suggests ways of designing triplex-binding drugs with sequence specificity.