DNA Oligonucleotide Synthesis in Mesoporous Silicon for Biosensing Applications

We report a method for improving the sensitivity of label-free optical biosensors based on in-situ synthesis of DNA probes within porous silicon structures. The stepwise attachment of up to 15mer probes inside 30 nm mesopores was accomplished through a series of phosphoramidite reactions. In this work, a porous silicon waveguide was utilized as the sensor structure. Synthesis of DNA probe, as well as sensing of target DNA, was verified by monitoring the change in effective refractive index of the porous silicon waveguide through angle-resolved attenuated total reflectance measurements. The average resonance shift per oligo of 0.091° during stepwise synthesis corresponds to surface coverage slightly less than 50%, according to theoretical models. When compared with the traditional method of direct attachment of pre-synthesized oligonucleotide probes, the sequential phosphoramidite method resulted in an approximately four-fold increase in DNA probe attachment. This increased surface coverage by DNA probes increases the likelihood of target molecule binding, leading to improved sensitivity for bio-molecule detection. Exposure to a 50μM solution of target 8-base DNA in deionized water produced a 0.4236° change in the waveguide resonance angle. Nanomolar detection limits for small molecule sensing are realizable with this sensor scheme.