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Title page for ETD etd-07272007-162434

Type of Document Master's Thesis
Author Vargis, Elizabeth Ann
Author's Email Address e.vargis@vanderbilt.edu
URN etd-07272007-162434
Title Virus Detection with DNA Logic Tags
Degree Master of Science
Department Biomedical Engineering
Advisory Committee
Advisor Name Title
F. R. Haselton Committee Chair
  • logical operations
  • DNA computing
  • antibody-based detection
  • Viruses -- Identification
  • Biosensors -- Design and construction
  • Polymerase chain reaction -- Diagnostic use
  • Molecular computers
  • Algebra Boolean
Date of Defense 2007-09-15
Availability unrestricted
Non-specific antibody binding limits the sensitivity of antibody-based detection technologies. We explore the use of logical operations among DNA logic tags associated with antibodies to increase specificity and sensitivity. DNA sequences were developed to perform a logical NOT operation to subtract non-specific binding prior to PCR amplification. Antibody-associated tags A and A' were designed to be partially complementary and contain a restriction enzyme site. Tag A is associated with a specific antibody; tag A' is associated with an isotype matched control antibody. If the concentration of A is greater than A', hybridized AA' is enzymatically cleaved and remaining tag A is subsequently amplified during real-time PCR. Quartz crystal microbalance (QCM), DNA agarose gels, and PCR were used to experimentally characterize components of the NOT operation in respiratory syncytial virus (RSV) detection. QCM showed gold nanoparticles functionalized with both tag DNA and antibody can bind virus. Successful enzymatic cleavage of AA' was visualized on a DNA agarose gel. After cleavage, remaining tag A was amplified by the addition of primers and standard real-time PCR. In the presence of RSV, magnetic pulldown led to the delivery of both tag A and A'. When PCR was run after enzymatic cleavage, the PCR Ct was increased, indicating a decrease in initial tag A. Our results suggest that combining the careful design of DNA logic tags, their association with antibodies, and standard molecular biology techniques is a promising approach to increase the specificity and sensitivity of antibody-based detection methods.
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