Nanogap capacitive biosensor for label-free aptamer-based protein detection

Namhil, Zahra Ghobaei

Abstract

Recent advances in nanotechnology offer a new platform for the label free detection of biomolecules at ultra-low concentrations. Nano biosensors are emerging as a powerful method of improving device performance whilst minimizing device size, cost and fabrication times. Nanogap capacitive biosensors are an excellent approach for detecting biomolecular interactions due to the ease of measurement, low cost equipment needed and compatibility with multiplex formats.

This thesis describes research into the fabrication of a nanogap capacitive biosensor and its detection results in label-free aptamer-based protein detection for proof of concept. Over the last four decades many research groups have worked on fabrication and applications of these type of biosensors, with different approaches, but there is much scope for the improvement of sensitivity and reliability. Additionally, the potential of these sensors for use in commercial markets and in everyday life has yet to be realized.

Initial work in the field was limited to high frequency (>100 kHz) measurements only, since at low frequency there is significant electronic thermal noise (<V2>=4kBTR) from the electrical double layer (EDL). This was a significant drawback since this noise masked most of the important information from biomolecular interactions of interest. A novel approach to remove this parasitic noise is to minimize the EDL impedance by reducing the capacitor electrode separation to less than the EDL thickness. In the case of aptamer functionalized electrodes, this is particularly advantageous since device sensitivity is increased as the dielectric volume is better matched to the size of the biomolecules and their binding to the electrode surface. This work has demonstrated experimentally the concepts postulated theoretically.

In this work we have fabricated a large area (100 x 5 μm x 5 μm) vertically oriented capacitive nanogap biosensor with a 40 nm electrode separation between two gold electrodes. A silicon dioxide support layer separates the two electrodes and this is partially etched (approximately 800 nm from both sides of each 5 μm x 5 μm capacitor), leaving an area of the gold electrodes available for thiol-aptamer functionalization.

AC impedance spectroscopy measurements were performed with the biosensor in the presence of air, D.I. water, various ionic strength buffer solutions and aptamer/protein pairs inside the nanogap. Applied frequencies were from 1Hz to 500 kHz at 20 mV AC voltage with 0 DC. We obtained relative permittivity results as a function of frequency for air (ɛ=1) and DI water (ɛ~80) which compares very favorably with previous works done by different research groups.

The sensitivity and response of the sensors to buffer solution (SSC buffer) with various ionic strengths (0.1x SSC, 0.2x SSC, 0.5x SSC and 1x SSC) was studied in detail. It was found that in the low frequency region (<1 kHz) the relative permittivity (capacitance) was broadly constant, that means it is independent from the applied frequency in this range. With increasing buffer concentration, the relative permittivity starts to increase (from ɛ=170 for 0.1x SSC to ɛ=260 for 1x SSC).

The sensor performance was further investigated for aptamer-based protein detection, human alpha thrombin aptamers and human alpha thrombin protein pairs were selected for proof of concept. Aptamers were functionalized into the gold electrode surface with the Self-Assembly-Monolayer (SAM) method and measurements were performed in the presence of 0.5x SSC buffer solution (ɛ=180). Then the hybridization step was carried out with 1 μM of human alpha thrombin protein followed by measurements in the presence of the same buffer (ɛ=130). The response of the sensors with different solutions inside the nanogap was studied at room temperature (5 working devices were tested for each step). The replacement of the buffer solution (ɛ=250) with lower relative permittivity biomolecules (aptamer ɛ=180) and further binding proteins to immobilized aptamer (ɛ=130) was studied. To validate these results, a control experiment was carried out using different aptamers, in this case which are not able to bind to human alpha thrombin protein. It was found that the relative permittivity did not change after the hybridization step compared to the aptamer functionalization step, which indicates that the sensors performance is highly sensitive and reliable.

This work serves as a proof of concept for a novel nanogap based biosensor with the potential to be used for many applications in environmental, food industry and medical industry. The fabrication method has been shown to be reliable and consistent with the possibility of being easily commercialized for mass production for use in laboratories for the analysis of a wide range of samples.

Citation

Namhil, Z. G. (2018). Nanogap capacitive biosensor for label-free aptamer-based protein detection. (Thesis). University of Hull. Retrieved from https://hull-repository.worktribe.com/output/4220514

• Thesis Type: Thesis
• Deposit Date: Aug 9, 2018
• Publicly Available Date: Feb 23, 2023
• Keywords: Physics
• Public URL: https://hull-repository.worktribe.com/output/4220514
• Additional Information: School of Mathematics and Physical Sciences, The University of Hull
• Award Date: Jan 1, 2018