Alkylation of DNA has been found to cause cancer and also to serve as its treatment. Quinone methides (QMs) are highly electrophilic molecules implicated in numerous metabolism processes. Studies of QM's reversible reaction with nucleophiles of DNA are important to understand the mechanism of its biological activity.

Reversible alkylation of QMs can extend their lifetime under aqueous conditions. The repeated capture and release of QM from dA adduct can help QM equivalents escape the irreversible trapping and extend QM's lifetime by 100-fold. This effect of dA saturates at a concentration of about 6 mM. In contrast, dG, dC, and dT do not have the ability to preserve QM under aqueous conditions.

Oligonucleotides can also preserve QM equivalents by forming labile intrastrand adducts. An oligonucleotide has now been shown to transfer bisQM to its complementary sequences to form interstrand crosslinking. Non-complementary sequences can not be alkylated by bisQM-oligonucleotide adducts. The nucleotide composition of oligonucleotides affects their ability to transfer QM as well. A G rich sequence showed a strong ability for crosslinking a complementary sequence. However, C rich and A rich sequences did not have such an ability. Excess alkylation of C rich and A rich oligonucleotides relative to that of G rich oligonucleotide may interrupt the hybridization of complementary sequences and suppress the formation of DNA crosslinking.

The reversibility of crosslinking by QM within duplex DNA has been demonstrated by a strand displacement system. The reversible QM-DNA bond does not prevent strand displacement and allows bisQM to migrate within a series of changing DNA structures by forming crosslinking. The reactivity of bisQM is preserved beyond 11 days in duplex DNA by forming labile DNA cross-links under aqueous conditions. The migration of QM is found to be under thermodynamic control and bisQM preferentially retain cross-links in the most stable DNA duplexes.