Alkylation of DNA by a variety of small molecules has been found to be both a cause of cancer and a treatment of the disease. One class of alkylating agent is the quinone methides (QMs). These highly electrophilic molecules are the reactive intermediates of a variety of natural products, such as mitomycin C. Investigation of the reactivity and selectivity of QMs is important in understanding their mechanism of action.

Competition studies with a model QM have been undertaken to investigate the reversibility of the nucleoside adducts formed, as well as their product profile. From these initial studies, it has been found that there are three terminal sites of alkylation, the N1 and N2 of dG and the N6 of dA, as well as two reversible sites, the N1 of dA and the N3 of dC. The N7 adduct of dG was found to deglycosylate over time. Further studies into the reversibility of the N7 adduct of dG found that the adduct regenerated QM and deglycosylated at approximately the same rates. Thus, these studies have identified a third reversible QM adduct of the 2'-deoxynucleosides.

An oxidative quench of labile QM adducts has been developed. The methodology utilizes [bis(trifluoroacetoxy)]iodobenzene to convert convert the nucleoside adducts to a stable derivative. Use of the oxidative quench will allow for the analysis of the observation of labile QM-DNA adducts and determination of the inherent QM selectivity with duplex DNA.

Studies of substituent effects on the reactivity of QMs were also undertaken. Addition of an electron donating group to the aromatic ring increases the rate of QM generation from the precursor and nucleoside adducts. Conversely, addition of an electron withdrawing group to the aromatic ring results in a destabilized QM, which decreases the rate of generation from both the precursor and the nucleoside adducts.

Model reactions of QM with a new sequence-specific DNA binding agent were performed to investigate the possibility of using a QM-TRIPside conjugate for sequence-selective alkylation of DNA. Unfortunately, the major product of reaction was irreversible; however, further changes to the QM or the TRIPsides may result in the formation of a reversible adducts TRIPside adducts, which should allow for sequence-selective DNA alkylation.