The majority of
DNA-binding small molecules known thus far stabilize duplex
DNA against heat denaturation. A high,
drug-induced increase in the melting temperature (Tm) of
DNA is generally viewed as a good criterion to select
DNA ligands and is a common feature of several anticancer drugs such as
intercalators (e.g.,
anthracyclines) and
alkylators (e.g.,
ecteinascidin 743). The reverse situation (destabilization of
DNA to facilitate its denaturation) may be an attractive option for the identification of therapeutic agents acting on the
DNA structure. We have identified the
tumor-active benzoacronycine derivative
S23906-1 [(+/-)-cis-1,2-diacetoxy-6-methoxy-3,3,14-trimethyl-1,2,3,14-tetrahydro-7H-benzo[b]pyrano[3,2]acridin-7-one] as a potent
DNA alkylating agent endowed with a helicase-like activity. Using complementary molecular approaches, we show that covalent binding to
DNA of the diacetate compound
S23906-1 and its monoacetate analogue S28687-1 induces a marked destabilization of the double helix with the formation of alkylated ssDNA. The
DNA-bonding properties and effects on
DNA structure of a series of benzoacronycine derivatives, including the dicarbamate analogue S29385-1, were studied using complementary biochemical (electromobility shift assay, nuclease S1 mapping) and spectroscopic (fluorescence and Tm measurements) approaches. Alkylation of guanines in
DNA by S28687-1 leads to a local denaturation of
DNA, which becomes susceptible to cleavage by nuclease S1 and significantly decreases the Tm of
DNA. The
drug also directly alkylates single-strand
DNA, but mass spectrometry experiments indicate that guanines in duplexes are largely preferred over single-stranded structures. This molecular study expands the repertoire of
DNA-binding mechanisms and provides a new dimension for
DNA recognition by small molecules.