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Lawrie, Jenifer
Ph.D. in Interdisciplinary Materials Science, December 2012

Research Information

Ph.D. in Interdisciplinary Materials Science, December 2012

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Dissertation Title
In situ DNA synthesis in porous silicon for biosensing applications

Ph.D. Thesis Advisor
Sharon Weiss (Electrical Engineering)

Ph.D. Committee Members
Richard Haglund (Physics)
Paul Laibinis (Chemical and Biomolecular Engineering)
Deyu Li (Mechanical Engineering)
Michael Stone (Chemistry)

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Abstract.  Porous silicon optical structures have generated significant interest in recent years for biological applications such as drug delivery, environmental monitoring, and chemical sensing. The enormous internal surface area in porous silicon of up to a few hundred square meters per cubic centimeter provides a significant advantage for capturing and detecting gaseous, chemical, and biological species. The pore diameters, the porosity, and the thickness of the porous layers can be carefully controlled by tuning the fabrication conditions in order to produce high quality optical structures. For a waveguide structure, the light is guided in the plane of the thin film, facilitating the integration of such a sensor, along with source and detector components, into lab-on-a-chip devices. Varying the effective porous silicon optical thickness by biorecognition events in the waveguide results in a shift in the reflectance resonance, and allows for quantitative analysis of the target biomolecules.

In an effort to increase the sensitivity of porous silicon waveguide sensors, we have utilized in situ synthesis of DNA oligonucleotide bioreceptors, in contrast to the traditional method of infiltrating and attaching bioreceptor molecules on the internal surfaces of the pores. Applying this commercial, solid-phase synthesis method using phosphoramidite protected nucleic acids, DNA oligos are immobilized in the waveguide in higher densities than allowed via the traditional method. As a result, DNA conformation, flexibility, and length do not play a role in bioreceptor density. The increased sensitivity of in situ prepared porous silicon waveguide sensors has been demonstrated for short oligo targets.

This work demonstrates the use of porous silicon waveguides for label-free detection of target DNA oligos, with the lowest detection limits reported in the nanomolar range. Bioreceptor and target molecule infiltration for a given waveguide porosity has been shown to depend directly on the DNA oligo length. The pore size, DNA bioreceptor density and length, and target size and aspect ratio play a significant role in molecule infiltration and detection sensitivity of porous silicon waveguide sensors. Using synthesized DNA oligos in porous silicon as aptamers, highly selective detection of the small molecule target adenosine and ochratoxin A has also been demonstrated. This first demonstration of DNA aptamer-based sensing within porous silicon may be expanded to other small molecule targets of interest, combining the high selectivity of aptamer detection schemes with the sensitivity and filtering capabilities afforded by mesoporous silicon waveguide sensors.


Selected Publications

Size-Dependent Infiltration and Optical Detection of Nucleic Acids in Nanoscale Pores. Lawrie, JL; Jiao, Y; Weiss, SM, IEEE TRANSACTIONS ON NANOTECHNOLOGY, 9, 596-602 , (2010)

Current status and outlook for silicon-based optical biosensors. Weiss, SM; Rong, G; Lawrie, JL, PHYSICA E-LOW-DIMENSIONAL SYSTEMS & NANOSTRUCTURES, 41, 1071-1075 , (2009)

DNA oligonucleotide synthesis in mesoporous silicon for biosensing applications. Lawrie, JL; Xu, Z; Laibinis, PE; Weiss, SM, PROCEEDINGS - SPIE, 7167, 7167OR , (2009)

Synthesis of DNA oligonucleotides in mesoporous silicon. Lawrie, JL; Xu, Z; Rong, GG; Laibinis, PE; Weiss, SM, PHYSICA STATUS SOLIDI A-APPLICATIONS AND MATERIALS SCIENCE, 206, 1339-1342 , (2009)

 
Vanderbilt University