Label-Free Detection of DNA

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Eydgahi, Hoda
Abshire, Pamela
In recent years, developing more efficient DNA detection methods has been the center of interest in the growing field of molecular biology. Improved DNA detection methods can benefit the fields of forensic science, risk assessment, medical diagnostics, and genetics, along with a multitude of other technological fields. <p> We are striving to detect the presence of a strand of DNA without the use of any labels. To do so, we must first be able to place DNA on a chiphich is the goal of my summer research project. This project is an excellent example of how the fields of microelectronics and biology are quickly merging into one. The success of this project will result in the creation of a parallel system that will allow us to analyze of various characteristics of a particular strand of DNA at the same time. <p> The standard method currently used in molecular biology studies to analyze DNA binding involves fluorescent labeling. Basically, once the strand of DNA in question is labeled with the proper fluorescent tag, it is added to the chip surface, where it binds with the capture, or known strand of DNA that is bound to the surface. If the oligonucleotide in question is complimentary to the capture DNA, hybridization will occur and they will bind to one another. Fluorescence will be observed when the substrate surface is viewed under a fluorescence microscope. Although highly sensitive and widely available, fluorescence markers are photochemically unstable and require expensive optical devices for analysis. In addition, they can provide researchers with a false-positive result. For instance, a 25 mer oligonucletide that is complimentary to the capture DNA with the exception of one or two base pairs will still bind to the DNA on the substrate even though it will result in a mismatch error. Fluorescence will be observed regardlesseading the scientist to believe that the two strands are complimentary. <p> Since both the chemical and electrical characteristics of the substrate will change upon binding of the DNA strand in question, we propose to approach the problem from an electrical standpoint by using Mr. Som Prakash capacitance sensor to measure the amount of binding between the two strands. <p> We will initially follow the current protocol that uses fluorescence to measure the presence of DNA. We plan to test fully complementary and non-complementary DNA strands as well as strands containing 1, 5, or 10 mismatches. We will then measure fluorescence and capacitance levels. The fluorescence method is used purely as a control in this experiment. The purpose of this experiment is to determine whether or not the label-free, electrical approach is more accurate than the current chemical approach. We hope that the capacitance sensor will be able to detect changes in the strength of the bonds present between the purines and the pyrimidines of the double helix formed. Even if the proposed method is just as accurate as the chemical method, it could be used as the method of choice in the future since it is more efficient and will remove the need for optical instruments and fluorescent labeling.