A strategy for the broad range detection of compounds with affinity for nucleic acids

A nucleic acid based optical biosensing strategy for the broad range detection of compounds with affinity for nucleic acids is described. The strategy attempts to use the chemical and structural information contained in the DNA helix as a sensing element per se. Detection is based on measuring changes in the fluorescence signal intensity of ToPro-3 complexed with nucleic acids. ToPro-3 is a cationic, planar aromatic fluorescent nucleic acid dye that binds to DNA by intercalation. The fluorescence of the dye is environment dependent and is greatly enhanced upon intercalation. ToPro-3 has a long excitation wavelength of 642 nm with emission occurring at 661 nm. At these wavelengths, spectral interference from organic compounds is dramatically reduced. The sensor is capable of detecting known intercalating and groove binding compounds over a broad range of binding affinities. Detection limits of 200, 20, 95 and 1 nM were obtained for EtBr, DAPI, PI and TOTO1, respectively. The ability of the assay to detect the known mutagens bisbenzidine, 1,2,4-benzenetriamine and proflavin, as well as of unknown compounds in natural product extracts was also investigated. Furthermore, the use of longer wavelengths allows the implementation of solid-state instrumentation which allows stable DC operation, reduces electronic noise and simplifies miniaturization, all of which increase portability. This scheme provides a flexible strategy for detecting compounds with affinity for DNA that can be used in a wide range of application areas. Approaches for expanding the informational content of the scheme are discussed.