NMR CHARACTERIZATION OF CALICHEAMICIN GAMMA(1)(I) BOUND TO DNA

Calicheamicin gamma(1)(I) is a diyne-ene antitumor antibiotic that binds preferentially to pyrimidine-rich sequences of DNA such as TCCT, ACCT, TCTC, AND TTTT. We are using NMR spectroscopy to study the structure of calicheamicin bound to different DNA duplex octamers in order to shed light on the molecular basis for selective recognition. We have found that calicheamicin forms a unique and stable 1:1 complex with a duplex containing an ACCT recognition site. The tetrasaccharide-aryl tail is centered over the CpC step of the recognition sequence and the aglycone is positioned to abstract hydrogen atoms from the presumptive cleavage sites on this duplex. Binding induced significant conformational changes in the DNA but not, evidently, in the drug. The conformational changes appear to be larger in the pyrimidine strand than the purine strand. One possible explanation for this is that the bound drug, which does not lie symmetrically in the minor groove, exerts greater steric pressure on the pyrimidine strand than the purine strand. Calicheamicin also forms a unique 1:1 complex with a duplex containing a TTTT recognition site, and an analysis of the spectral data shows that it binds to the TTTT recognition site in the same orientation as it does to the ACCT recognition site. Moreover, it induces similar conformational changes in the pyrimidine strand. On the basis of the NMR results, we have proposed that the binding site selectivity of calicheamicin is due to the ability of pyrimidine/purine runs to adapt more readily than other sequences to the particular shape of the drug.