Faculty Advisor or Committee Member

Hong Susan Zhou, Advisor

Faculty Advisor or Committee Member

David DiBiasio

Identifier

etd-043007-170242

Abstract

DNA arrays, capable of detecting specific DNA sequences from a sample have become widely used. They rely on DNA heterogeneous hybridization, which is the binding between a single strand of DNA immobilized on a surface (probe) and its complementary strand present in the bulk (target). In order to improve the hybridization time in DNA arrays, it is crucial to understand the kinetics of DNA hybridization. The study of the Damkohler number that compares the DNA supply by diffusion to the DNA consumption by reaction (hybridization) shows that in many cases we can expect DNA hybridization to be a diffusion limited process. This is verified by a finite element study, where a whole microfluidic chamber (bulk and reacting surface) is simulated. In these cases, the formation of a depletion zone above the sensing zone is observed. The reaction rate is much lower than in the ideal case where the reaction would be reaction rate limited. A better DNA transport could be a solution to overcome the diffusion barrier. Therefore, the influence of convection on DNA hybridization was studied. Finite element simulation shows that even a small DNA velocity (10 ƒ�m/s) can greatly enhance the overall reaction rate and help preventing the formation of a depletion zone. These observations are valid when one kind of probe reacts with one kind of target. In reality, non specific hybridization can happen between a probe and a non complementary target. We show that in some cases, non specific hybridization can slow down the kinetics and reduce the fraction of specifically hybridized probes at equilibrium. The fraction of non specific hybrids can reach a maximum before decreasing and reaching equilibrium, suggesting that a longer hybridization time would lead to a better specificity. The addition of convective transport does not affect the equilibrium, but allows to reach it faster and with a better ratio between specific and non specific hybrids during the process. Therefore, convective transport of DNA appears to be beneficial. Another possibility is to act on the DNA itself to focus it near the sensing zone. Our study of the different electrokinetic forces leads us to derive the expression of the dielectrophoretic force in a field resulting from the combination of a DC field and an AC field. This could be a novel way to act on polarizable particles like DNA.

Publisher

Worcester Polytechnic Institute

Degree Name

MS

Department

Chemical Engineering

Project Type

Thesis

Date Accepted

2007-04-30

Accessibility

Unrestricted

Subjects

DNA, hybridization, microfluidics, kinetics, DNA microarrays, Hybridization, Molecular aspects

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