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 d etection of compounds with affinity for nucleic acids is described. Th e strategy attempts to use the chemical and structural information con tained in the DNA helix as a sensing element per se. Detection is base d 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 f luorescence of the dye is environment dependent and is greatly enhance d upon intercalation. ToPro-3 has a long excitation wavelength of 642 nm with emission occurring at 661 nm. At these wavelengths, spectral i nterference from organic compounds is dramatically reduced, The sensor is capable of detecting known intercalating and groove binding compou nds over a broad range of binding affinities. Detection limits of 200, 20, 95 and 1 nM were obtained for EtBr, DAPI, PI and TOTO-1, respecti vely. The ability of the assay to detect the known mutagens bisbenzidi ne, 1,2,4-benzenetriamine and proflavin, as well as of unknown compoun ds in natural product extracts was also investigated. Furthermore, the use of longer wavelengths allows the implementation of solid-state in strumentation which allows stable DC operation, reduces electronic noi se 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.