The ability to inhibit an enzyme in a specific tissue with high spatial resolution combined with a readily available antidote should find many biomedical applications. We have accomplished this by taking advantage of the cis-trans photoisomerization of azobenzene molecules. Specifically, we positioned azobenzene moieties within the DNA sequence complementary to a 15-base-long thrombin aptamer and then linked the azobenzene-modified cDNA to the aptamer by a polyethylene glycol (PEG) linker to make a unimolecular conjugate. During the photoisomerization of azobenzene by visible light, the inhibition of thrombin is disabled because the probe hybridizes with the cDNA in the trans-azobenzene conformation so that the aptamer cannot bind its target thrombin. However, when UV light is applied, melting of the hairpin structure (duplex) is induced via trans-to-cis conversion, thereby changing conformation of the aptamer and making the aptamer free to bind to and inhibit its target thrombin. By using standard clotting assays, we measured the IC 200 of various probe designs in both states and concluded the feasibility of using photon energy to temporally and spatially regulate these enzymatic reactions. Thus, we can report the development of DNA probes in the form of photon-controllable (thrombin) inhibitors, termed PCIs, and we expect that this approach will be highly beneficial in future biomedical and pharmaceutical applications.anticoagulation ͉ aptamer ͉ enzyme inhibitor ͉ photo controllable ͉ thrombine O ver the last decade, extensive research has been devoted to the study of phototransformable molecules based on photochromism chemistry. This science has been applied to photooptical technology and such photomodulated devices as eyeglasses called Transitions (1-4). A photochromic compound has 2 molecular states: stable and relatively unstable. The 2 states are interchangeable by the effect of irradiation using different wavelengths and differ from one another in terms of both physical and chemical properties. The photoconversion mechanism can largely be divided into 3 transformation types: photochromic tautomerism, cis-trans isomerization, and photocyclization. Briefly, photoisomerization is a process in which molecular structural change between isomers is caused by photoexcitation. Therefore, because isomerization causes a conformational change that can change the overall structure of a molecule, cis-trans isomerization is an intriguing mechanism that can be used to regulate mechanical devices and biological reactions (5-8).As one of the most popular phototransformable molecules in use today, azobenzene and its derivatives belong to the cis-trans isomerization category and are composed of 2 phenyl rings linked by a NAN double bond (Fig. 1) (9). The 2 isomers can be switched with particular wavelengths of light: UV light at 365 nm, corresponding to the trans-to-cis conversion, and visible light at 465 nm, corresponding to the cis-to-trans isomerization. There are reports that demonstrate the possible applications of su...