DNA site-specifically modified with a photosensitizer (Sens) was synthesized and the charge-separation and charge-recombination dynamics in DNA were studied. We specifically focused on the formation of the long-lived charge-separated state whose lifetime (τ) is longer than 0.1 μs. The quantum yields of the formation of the charge-separated states (Φ) upon the photoexcitation of the Sens, and the τ were measured using the laser flash photolysis technique. We utilized naphthalimide (NI), naphthaldiimide (ND), and anthraquinone (AQ) as a Sens to investigate the mechanism of the formation of the charge-separated state in DNA via rapid positive charge (hole) transfer between adenine and thymine (A-T) base-pairs. By replacing some T bases in the A-T stretch with 5-bromouracil ((br)U), the charge-separation was shown to occur via the photoinduced charge-injection into the second and further neighboring As to the Sens. On the other hand, the generation of a hole on A nearest to Sens ends up with the rapid charge-recombination within a contact ion pair. A long-lived charge-separated state was also generated in DNA when a commonly used fluorophore such asTAMRA, Alexa 532, and ATTO 655, which can only oxidize guanine-cytosine (G-C) base-pair, but not A-T, was used as a Sens. These results suggested that the charge-separation in DNA is a general phenonmenon for fluorescent dyes which fluorescence is quenched only by G-C.