A flow injection analysis (FIA) system for the detection of the compounds that intercalate within DNA is reported. A derivative of 9,10-anthraquinone has been used as the reference compound for photoelectrochemical detection. The sodium salts of 9,10-anthraquinone-2,6-disulfonic acid and 9,10-anthraquinone-2-sulfonic acid are photochemically activated and then reduced in the presence of an electron donor (glucose). The electrochemical signal is based on the measurement of the anodic current resulting from the oxidation of the reduced form of 9,10-anthraquinone. The reduced form of the 9,10-anthraquinone is oxidized through a mediated mechanism at the surface of a tetracyanoquinodimethane-(TCNQ)-modified graphite paste electrode covered by a Nucleopore membrane. TCNQ acts as an efficient mediator for the oxidation of reduced 9,10-anthraquinone. Cyclic voltammetry, photocyclic voltammetry, and the photoelectrochemical FIA response of 9,10-anthraquinone are reported. Experimental results show that these anthraquinones can be intercalated within the helix of double-stranded calf thymus DNA. The anthraquinone molecules that are intercalated within DNA cannot be oxidized due to their limited transport to the modified electrode surface. This results in a decrease in the anodic current at a constant concentration of anthraquinone after intercalation. There is a linear relation between the decrease in electrochemical response and the DNA concentration at a constant concentration of anthraquinone. The intercalated anthraquinone molecules can be completely replaced by another intercalating agent (i.e., ethidium bromide) that is more strongly intercalated within DNA, thereby regenerating the electrochemical response.(ABSTRACT TRUNCATED AT 250 WORDS)