Alkylation specificity for a series of distamycin analogues that tether chlorambucil

The sequence specificity of alkylation for a series of pyrrole- and imidazole-containing analogues of distamycin that tether the nitrogen mustard chlorambucil (CHL) was determined using modified sequencing techniques. Examination of the sequence specificity of alkylation for the imidazole-CHL conjugates using a Taq polymerase stop assay revealed that although the doses required to produce similar amounts of damage were at least 10-fold lower, the sequence specificity of alkylation was essentially identical to that seen for CHL. The guanine-N7 alkylation pattern, which consisted of guanines within runs of guanines, was confirmed using a piperidine cleavage assay. The pyrrole-CHL conjugates also produced a similar pattern of alkylation to that seen for CHL, but one exception was a unique site strongly alkylated only by the di- and tripyrrole-CHL conjugates. The unique lesions, at AG for the dipyrrole-CHL conjugate and G for the tripyrrole-CHL conjugate in the sequence 5'-GAAGAT, were confirmed as minor groove adenine- and guanine-N3 lesions using a thermal cleavage assay.