Date of Award

Fall 2008

Document Type

Thesis

Degree Name

Master of Science in Biomedical Engineering - (M.S.)

Department

Biomedical Engineering

First Advisor

Dentcho V. Ivanov

Second Advisor

William Corson Hunter

Third Advisor

Treena Livingston Arinzeh

Abstract

The primary focus of this research work was on the design and development of a molecular scale (nano-scale) capacitive sensing mechanism for the highly sensitive and label-free detection of Nucleic Acid hybridization. These novel capacitive sensors with nano-scale electrode spacing offer solutions to many problems suffered by the conventional signal transduction mechanisms, thereby immensely improving the sensitivity of the biomolecular detection processes. Reducing the separation between the capacitive electrodes to the same scale as the Debye length of the sample solution, results in the overlapping of the electrical double layers of the two electrodes, thereby confining them to occupy a major fraction of the dielectric volume. This decreases the potential drop across the electrodes and thus dielectric measurements at low frequencies are made possible. The dielectric properties during hybridization reaction were measured using 10- mer nucleotide sequences. A 30-40% change in relative permittivity (capacitance) was observed due to DNA hybridization at 10Hz, which is much more sensitive than the previously reposted detection measurements (2-8% signal change).

In parallel to the above work, a second label-free sensing mechanism based on field effect capacitive sensors with Metal-Oxide-Semiconductor (MOS) structure has been developed and its ability to provide real-time monitoring of oligonucleotide immobilization and hybridization events are studied. The immobilization of probe oligomers on the sensor surface and their hybridization with the target oligomers of complimentary sequences has produced significant shifts (140mV and 73mV respectively) in the Capacitance-Voltage characteristics measured across the device. In an attempt to utilize the individual merits of the nano-scale electrochemical capacitive sensor and the field effect MOS capacitive structure, a novel dual parametric sensing architecture comprising of both these transducing elements on a single sensor is designed. The detection scheme based on the combined analysis of the two parameters- Dielectric property and intrinsic molecular charge- of Nucleic acid molecules has found to reveal complimentary information of significance about the analyte-probe interactions.

As a separate experiment the applications and promises of a novel technique of enhancing the speed and selectivity of the molecular detection processes by the application of an external electric field of precisely controlled intensity was studied. Experiments were conducted with 10-mer sequences and proved the feasibility of this technique in inducing in providing a faster and selective immobilization and hybridization reactions. The research work in this direction has been in collaboration with the Rational Affinity Devices, LLC, a New Jersey based corporation. The above mentioned biosensing mechanisms and detection techniques have the advantage of simplifying the readout and increasing the speed and ease of nucleic acid assays, which is especially desirable for characterizing infectious agents, scoring sequence polymorphism and genotypes, and measuring mRNA or miRNA levels during expression profiling. Once fully optimized and well assembled they have great potential to be developed in to a commercial full-scale biosensor capable of providing high-value diagnostic testing at the point of patient care places.

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