Sensitivity enhancement of DNA microarray on nano-scale controlled surface by using a streptavidin–fluorophore conjugate

High throughput analysis of DNA in low concentration and small volume is an important issue and a continuing challenge in the field of DNA microarray and sensor. Recently, we have demonstrated that the DNA microarray on nano-scale controlled surface provides ample space for hybridization resulting in the best discrimination efficiency for SNP analysis. Here, we report the utility of the nano-scale controlled surface in conjunction with a multiply tagged protein. Application of streptavidin–fluorophore conjugates in combination with the highly controlled surface that suppresses non-specific binding of DNA allows highly sensitive detection of DNA while maintaining superior SNP discrimination efficiency comparable to our earlier results. The sensitivity of DNA microarray on the mesospaced surface is two orders of magnitude higher than that of the generic surface when a streptavidin–fluorophore conjugate was employed, and the detection limit on the former surface was found to be 50 fM of 15-mer target DNA. Various streptavidin–fluorophore conjugates including streptavidin–Cy3, streptavidin–Cy5, streptavidin–Alexa Flour 555 and streptavidin–phycoerythrin were examined.