Yiliang Zhao

In Situ Synthesis of Peptide Nucleic Acids in Porous Silicon for Drug Delivery and Biosensing

Peptide nucleic acids (PNA) are a unique class of synthetic molecules that have a peptide backbone and can hybridize with nucleic acids. Here, a versatile method has been developed for the automated, in situ synthesis of PNA from a porous silicon (PSi) substrate for applications in gene therapy and biosensing. Nondestructive optical measurements were performed to monitor single base additions of PNA initiated from (3-aminopropyl)triethoxysilane attached to the surface of PSi films, and mass spectrometry was conducted to verify synthesis of the desired sequence. Comparison of in situ synthesis to postsynthesis surface conjugation of the full PNA molecules showed that surface mediated, in situ PNA synthesis increased loading 8-fold. For therapeutic proof-of-concept, controlled PNA release from PSi films was characterized in phosphate buffered saline, and PSi nanoparticles fabricated from PSi films containing in situ grown PNA complementary to micro-RNA (miR) 122 generated significant anti-miR activity in a Huh7 psiCHECK-miR122 cell line. The applicability of this platform for biosensing was also demonstrated using optical measurements that indicated selective hybridization of complementary DNA target molecules to PNA synthesized in situ on PSi films. These collective data confirm that we have established a novel PNA–PSi platform with broad utility in drug delivery and biosensing.

Effect of DNA-Induced Corrosion on Passivated Porous Silicon Biosensors

This work examines the influence of charge density and surface passivation on the DNA-induced corrosion of porous silicon (PSi) waveguides in order to improve PSi biosensor sensitivity, reliability, and reproducibility when exposed to negatively charged DNA molecules. Increasing the concentration of either DNA probes or targets enhances the corrosion process and masks binding events. While passivation of the PSi surface by oxidation and silanization is shown to diminish the corrosion rate and lead to a saturation in the changes by corrosion after about 2 h, complete mitigation can be achieved by replacing the DNA probe molecules with charge-neutral PNA probe molecules. A model to explain the DNA-induced corrosion behavior, consistent with experimental characterization of the PSi through Fourier transform infrared spectroscopy and prism coupling optical measurements, is also introduced.

Comparative Kinetic Analysis of Closed-Ended and Open-Ended Porous Sensors

Efficient mass transport through porous networks is essential for achieving rapid response times in sensing applications utilizing porous materials. In this work, we show that open-ended porous membranes can overcome diffusion challenges experienced by closed-ended porous materials in a microfluidic environment. A theoretical model including both transport and reaction kinetics is employed to study the influence of flow velocity, bulk analyte concentration, analyte diffusivity, and adsorption rate on the performance of open-ended and closed-ended porous sensors integrated with flow cells. The analysis shows that open-ended pores enable analyte flow through the pores and greatly reduce the response time and analyte consumption for detecting large molecules with slow diffusivities compared with closed-ended pores for which analytes largely flow over the pores. Experimental confirmation of the results was carried out with open- and closed-ended porous silicon (PSi) microcavities fabricated in flow-through and flow-over sensor configurations, respectively. The adsorption behavior of small analytes onto the inner surfaces of closed-ended and open-ended PSi membrane microcavities was similar. However, for large analytes, PSi membranes in a flow-through scheme showed significant improvement in response times due to more efficient convective transport of analytes. The experimental results and theoretical analysis provide quantitative estimates of the benefits offered by open-ended porous membranes for different analyte systems.

Resonant photonic structures in porous silicon for biosensing

The formation of resonant photonic structures in porous silicon leverages the benefit of high surface area for improved molecular capture that is characteristic of porous materials with the advantage of high detection sensitivity that is a feature of resonant optical devices. This review provides an overview of the biosensing capabilities of a variety of resonant porous silicon photonic structures including microcavities, Bloch surface waves, ring resonators, and annular Bragg resonators. Detection sensitivities > 1000 nm/RIU are achieved for small molecule detection. The challenge of detecting molecules that approach and exceed the pore diameter is also addressed.

Understanding and mitigating DNA induced corrosion in porous silicon based biosensors

Porous silicon structures have been demonstrated as effective biosensors due to their large surface area, size-selective filtering capabilities, and tunable optical properties. However, porous silicon surfaces are highly susceptible to oxidation and corrosion in aqueous environments and solutions containing negative charges. In DNA sensing applications, porous silicon corrosion can mask the DNA binding signal as the typical increase in refractive index that results from a hybridization event can be countered by the decrease in refractive index due to corrosion of the porous silicon matrix. Such signal ambiguity should be eliminated in practical devices. In this work, we carefully examined the influence of charge density and surface passivation on the corrosion process in porous silicon waveguides in order to control this process in porous silicon based biosensors. Both increased DNA probe density and increased target DNA concentration enhance the corrosion process, leading to an overall blueshift of the waveguide resonance. While native porous silicon structures degrade upon prolonged exposure to solutions containing negative charges, porous silicon waveguides that are sufficiently passivated to prevent oxidation/corrosion in aqueous solution exhibit a saturation effect in the corrosion process, which increases the reliability of the sensor. For practical implementation of porous silicon DNA sensors, the negative charges from DNA must be mitigated. We show that a redshift of the porous silicon waveguide resonance results from either replacing the DNA target with neutral charge PNA or introducing Mg2+ ions to shield the negative charges of DNA.

Enhancing the sensitivity of slow light MZI biosensors through multi-hole defects

We demonstrate enhanced detection sensitivity of a slow light Mach-Zehnder interferometer (MZI) sensor by incorporating multi-hole defects (MHDs). Slow light MZI biosensors with a one-dimensional photonic crystal in one arm have been previously shown to improve the performance of traditional MZI sensors based on the increased lightmatter interaction that takes place in the photonic crystal region of the structure. Introducing MHDs in the photonic crystal region increases the available surface area for molecular attachment and further increases the enhanced lightmatter interaction capability of slow light MZIs. The MHDs allow analyte to interact with a greater fraction of the guided wave in the MZI. For a slow light MHD MZI sensor with a 16 μm long sensing arm, a bulk sensitivity of 151,000 rad/RIU-cm is demonstrated experimentally, which is approximately two-fold higher than our previously reported slow light MZI sensors and thirteen-fold higher than traditional MZI biosensors with millimeter length sensing regions. For the label-free detection of nucleic acids, the slow light MZI with MHDs also exhibits a two-fold sensitivity improvement in experiment compared to the slow light MZI without MHDs. Because the detection sensitivity of slow light MHD MZIs scales with the length of the sensing arm, the tradeoff between detection limit and device size can be appropriately mitigated for different applications. All experimental results presented in this work are in good agreement with finite difference-time domain-calculations. Overall, the slow light MZI biosensors with MHDs are a promising platform for highly sensitive and multiplexed lab-on-chip systems.

A smartphone compatible colorimetric biosensing system based on porous silicon

A colorimetric biosensing system based on a porous silicon (PSi) rugate filter is demonstrated. Using an imaged-based technique that monitors RGB intensity, a spectral shift less than 0.25nm can be reliably detected. The porous silicon rugate filter demonstrates a sensitivity of 310 nm/RIU, which corresponds to a detection limit near 7×10-4 RIU. In this work, an external light source and camera are employed for proof-of-concept demonstration. By utilizing a smartphone camera LED and smartphone camera as the light source and detector, respectively, this system could serve as an effective, low-cost, point-of-care diagnostic tool.