We have constructed a compact, all solid state, time correlated single photon counting device for sensitive measurement of the time resolved behavior of DNA fragments passing through a capillary tube. The instrument consists of a pulsed diode laser PDL, a single photon avalanche diode SPCM-211 and a PC board containing all TCPC electronics. We achieved an overall instrument response function of the system of less than 300 ps. This is fast enough for measurement of fluorescence lifetimes. We demonstrated the utility and the sensitivity of the instrument; dynamic measurements of fluorescence decays for NIR dye-labelled nucleotide bases were measured during capillary electrophoresis. The results indicate that in a two-dye experiment the characteristic lifetime of the probe could be used to identify the terminal nucleotide base. The lifetimes of the tow dyes bound to DNA fragments were determined to be 670 ps and 530 ps.