University of Illinois Urbana-Champaign

Multiplexed label-free electrical detection of DNA amplification using field effect transistors

Duarte Guevara, Carlos

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DUARTEGUEVARA-DISSERTATION-2016.pdf

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https://hdl.handle.net/2142/90717

Description

Title
Multiplexed label-free electrical detection of DNA amplification using field effect transistors
Author(s)
Duarte Guevara, Carlos
Issue Date
2016-02-09
Director of Research (if dissertation) or Advisor (if thesis)
Bashir, Rashid
Doctoral Committee Chair(s)
Bashir, Rashid
Committee Member(s)
  • Cunningham, Brian
  • Liu, Logan
  • Adesida, Ilesanmi
Department of Study
Electrical & Computer Eng
Discipline
Electrical & Computer Engr
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Date of Ingest
2016-07-07T20:26:47Z
Keyword(s)
  • Field effect transistors (FET) biosensor
  • Complementary metal-oxide semiconductor (CMOS)-compatible
  • Ion-sensitive field effect transistors (ISFET)
  • Loop-mediated isothermal amplification
  • Food safety
Abstract
The objective of this research project was to develop a miniaturized DNA amplification biosensor for the detection and identification of pathogenic bacteria. Using tailored loop-mediated isothermal amplification (LAMP) and field effect transistors, we developed a microchip platform for multiplexed screening of samples querying the presence of multiple pathogenicity genes. In our platform, ion-sensitive field effect transistors (ISFETs) detect the incorporation of nucleotides during LAMP by monitoring changes in the solution's acidity. Employing transistors as biosensors enables label-free detection of the reaction, simple multiplexing, and seamless integration with required electronics for data acquisition. These characteristics of the detection system and protocols that we developed will make genotyping analysis simple and readily available for different applications that would benefit from low cost, portability, and ease-of-use. Here, we present a series of studies performed in three experimental setups that are related to the multiplexed electrical detection of LAMP and culminate in a large ISFET sensor array microchip that monitors DNA amplification reactions. A first chip consisted of 30 nL silicon oxide wells that were prepared with dried nucleic acid primers for multiplexed on-chip amplification. This initial study demonstrated the high specificity and low limit of detection of on-chip parallel LAMP when used for the detection of E.coli O157, S.enterica, L. monocytogenes, and non O157 Shiga-toxin producing E.coli of the `big six' group. Then, a second chip with novel individually addressable dual-gated ISFETs was fabricated in collaboration with Taiwan Semiconductor Manufacturing Company (TSMC). These devices were used to evaluate and optimize their pH sensing ability, develop methods to do label-free detection of LAMP, and study the sensor performance when biased with polypyrrole quasi-reference electrodes. The last platform, that demonstrates the impressive scalability of the semiconductor technology, is a chip with over a million ISFET sensors distributed in a 7x7 mm2 area. The use of on-chip decoding and routing circuits enables the parallel operation of 1024x1024 sensors in an array for massively multiplexed biosensing. In this platform we applied methods and systems developed previously to perform parallel electrical detection of foodborne pathogens by monitoring DNA amplification reactions in micro-chambers of 250 nL detecting down to 25 copies/reaction in less than 60 min. We demonstrate that the intrinsic redundancy of the high density ISFET array enabled clear identification of electrical signals resulting from the amplification reaction. This microchip for the detection of DNA and the related protocols on reaction miniaturization, parallelism, and electrical detection are poised to be the basis of new detection systems that bring the impressive advances of the semiconductor industry into biological applications.
Graduation Semester
2016-05
Type of Resource
text
Permalink
http://hdl.handle.net/2142/90717
Copyright and License Information
Copyright 2016 Carlos Eduardo Duarte-Guevara

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