There are several possible mechanisms of cleavage which the anthraquinone molecule may induce. Two of these such mechanisms include direct cleavage by either abstraction of a hydrogen from the 4' carbon group of deoxyribose in DNA, or indirect cleavage by the anthraquinone intercalating in DNA thus catalyizing an energy transfer reaction. This results in the oxidation of a distant guanine base. Cleavage experiments are currently performed by first allowing the anthraquinone conjugate to bind the radioactively tagged DNA oligo, and then exposing this complex to a ultra violet light source which is specific to anthraquinone's absorbance peak at 330nm. Samples are then treated with piperdine and run on a SDS-PAGE gel.
Direct cleavage is observed by identifying DNA fragments at the spot where cleavage occured.
The goal of these photocleavage experiments is to obtain a high efficiency of direct cleavage and an undetectable amount of indirect cleavage. Continuous experimentation and development of site specific photocleave agents such as these conjugate systems have broad therapeutic applications in rational drug design. For instance, a pathogenic receptor protein could be used to develop a site specific cleavage agent attacking only the pathogen. In addition, there are various types of known binding domains which could be used to develop an even greater number and variety of binding domains by having the ability to alter these domains with mutagenesis techniques, creating flexibility in conjugate design. Experiments with the anthraquinone conjugate may eventually contribute to the path in discovering therapeutic agents with efficient and specific photocleavage abilities.