A three-dimensional waveguide structure as a support for genomic and proteomic microarrays

Stephan K. Dertinger; Marco Kluehr; Christian A. Elsner; Alexander Sauermann; Kristin Rueffer; Petra M. Nicklaus; Kerstin Thein

doi:10.1117/12.578532

8 December 2004 A three-dimensional waveguide structure as a support for genomic and proteomic microarrays

Stephan K. Dertinger, Marco Kluehr, Christian A. Elsner, Alexander Sauermann, Kristin Rueffer, Petra M. Nicklaus, Kerstin Thein

Author Affiliations +

Proceedings Volume 5591, Lab-on-a-Chip: Platforms, Devices, and Applications; (2004) https://doi.org/10.1117/12.578532
Event: Optics East, 2004, Philadelphia, Pennsylvania, United States

Abstract

In this paper we present a three-dimensional waveguide structure with unique optical and fluidic properties and demonstrate its application as a substrate for DNA microarrays. The structure is fabricated by thermal oxidation of a macroporous silicon membrane with a periodic pattern of discrete pores running perpendicular through the substrate. Partial oxidation generates a SiO₂ membrane, but leaves a rectangular grid of silicon walls dividing the membrane into compartments. We show that the SiO₂ walls act as optical waveguides and characterize their optical properties; modes can be launched using Koehler illumination. The silicon walls optically isolate adjacent compartments and prevent light from spreading laterally in the membrane. In a DNA hybridization experiment, the detection of 100 attomol of a Cy-3 labeled DNA fragment (17 oligonucleotides) has been achieved with a signal to noise ratio of > 3:1. We believe that even lower detection limits can be achieved by further tuning the optical parameters of the three-dimensional waveguide structure.

Citation Download Citation

Stephan K. Dertinger, Marco Kluehr, Christian A. Elsner, Alexander Sauermann, Kristin Rueffer, Petra M. Nicklaus, and Kerstin Thein "A three-dimensional waveguide structure as a support for genomic and proteomic microarrays", Proc. SPIE 5591, Lab-on-a-Chip: Platforms, Devices, and Applications, (8 December 2004); https://doi.org/10.1117/12.578532

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