Feasibility of a DNA-Based Combinatorial Array Recognition Surface (CARS) in a Polyacrylamide Gel Matrix

We report initial attempts at developing a self-assembled combinatorial DNA biosensor array which may be capable of binding and identifying virtually any soluble analyte that binds the array by pattern recognition, in effect making it a universal biosensor surface. Data are presented for differential binding patterns of various analytes to 1-D arrays of combinatorial deoxyribonucleic acid (DNA) concatamer libraries which are spatially separated according to size and charge by electrophoresis in polyacrylamide gels. These DNA concatamer libraries are essentially composed of single-stranded (ss) random DNA 60 mers, which form a ldquosmearrdquo pattern in gels following electrophoresis. When used to bind and detect various analytes or mixtures of analytes in the gel, we refer to the DNA smear as a ldquocombinatorial array recognition surfacerdquo (CARS). Differences in intrinsic fluorescence scanning patterns of CARS gel strips were compared before and after addition of various analytes to the arrays to detect binding patterns. Scans revealed a high level of reproducibility for individual CARS arrays in a given gel with or without bound analytes. Scan patterns between different CARS gel strips were initially less reproducible, but purification of the DNA library using spin columns prior to electrophoresis improved gel-to-gel reproducibility.