New potent agents binding to a poly(dT) sequence in double-stranded DNA: bis(Zn(2+)-cyclen) and tris(Zn(2+)-cyclen)...

In an effort to search for mechanistically new and more potent agents than conventional drugs that target AT-rich sequences in double-stranded DNA, we have tested multi(Zn(2+)-cyclen) complexes. Indeed, they selectively bound to poly(dT) sequences to melt the A-T hydrogen bonds; only 2.5 microM or 4 microM of the p-tris(Zn(2+)-cyclen) complex were required to completely melt a 50 microM nucleobase of double-stranded poly(dA) x poly(dT) or poly(dA-dT)(2) at 25 degrees C. The region with seven consecutive T's in native DNA (150 bp) was protected from micrococcal nuclease hydrolysis, as revealed by footprinting assays, with IC(50) values of 2 microM for p-bis(Zn(2+)-cyclen) and 0.5 microM for p-tris(Zn(2+)-cyclen). The high affinity to AT-rich sequences of these Zn(2+)-cyclen complexes matches or surpasses those of the conventional AT-binding drugs distamycin A (IC(50)=2 microM) and DAPI (5 microM). Moreover, the p-tris(Zn(2+)-cyclen) complex selectively binds to the TATA box sequence of the SV40 early promoter to inhibit the binding of the TATA binding protein as effectively as distamycin A, with an IC(50) value of 0.4 microM. In vitro transcription of poly(dA) x poly(dT) using Escherichia coli RNA polymerase was effectively inhibited by p-tris(Zn(2+)-cyclen). The [(3)H]-ATP incorporation into RNA was more strongly blocked (IC(50)=0.8 microM) than the [(3)H]-UTP incorporation (IC(50)=40 microM), a fact indicating that the p-tris(Zn(2+)-cyclen) complex interacts only with the poly(dT) strand in the double-stranded DNA template.