[Illinois] ECE 416 Next Gen Sequencing II

By Brian Cunningham1, NanoBio Node1

1. University of Illinois at Urbana-Champaign

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           In this lecture, we start off with a revision of the Illumina company and their DNA sequencing technology. After that we move on to the Helicos Company and their true Single Molecule Sequencing (tSMS). It starts off with a glass surface covered by multiple a "multiT" single stranded DNA. After that the single stranded DNA is capture to be sequenced with DNA prepared with a "multiA" end, so that it will be oriented correctly. After that the the fluoro-tagged nucleotide is added one at a time. After each nucleotide, a fluorescent image is captured. The next company talked about is Pacific Biosensors and their Zero Mode Waveguides methods for reading the genetic sequences. They attach DNA polymerase to their surface and allow the DNA molecules to be set free. The nucleotide brings the fluorescent dye with it and to be detected a fluoro microscope is used and the imaging comes from below. The DNA polymerization is then directly observed with base-pair resolution. Example data from this method is then shown. Last, the ion torrent method is discussed. It requires no fluorescent tags which makes it better than the others discussed. It begins with a single strand DNA sequence and DNA polymerase that can build up a double-stranded molecule one base pair at a time. One nucleotide is flown through at a time. If the nucleotide incorporates, a current pulse is measured and if no match is incorporated, then no pulse occurs. The lecture ends off with a comparison of all the methods through the data they presented.


My research group is focused on the application of sub-wavelength optical phenomena and fabrication methods to the development of novel devices and instrumentation for the life sciences. The group is highly interdisciplinary, with expertise in the areas of microfabrication, nanotechnology, computer simulation, instrumentation, molecular biology, and cell biology. In particular, we are working on biosensors based upon photonic crystal concepts that can either be built from low-cost flexible plastic materials, or integrated with semiconductor-based active devices, such as light sources and photodetectors, for high performance integrated detection systems.

Using a combination of micrometer-scale and nanometer-scale fabrication tools, we are devising novel methods and materials for producing electro-optic devices with nanometer-scale features that can be scaled for low-cost manufacturing. Many of our techniques are geared for compatibility with flexible plastic materials, leading to applications such as low cost disposable sensors, wearable sensors, flexible electronics, and flexible displays. Because our structures manipulate light at a scale that is smaller than an optical wavelength, we rely on computer simulation tools such as Rigorous Coupled Wave Analysis (RCWA) and Finite Difference Time Doman (FDTD) to model, design, and understand optical phenomena within photonic crystals and related devices.

In addition to fabricating devices, our group is also focused on the design, prototyping, and testing of biosensor instrumentation for high sensitivity, portability, and resolution. Advanced instruments enable high resolution imaging of biochemical and cellular interactions with the ability to monitor images of biochemical interactions as a function of time. Using the sensors and instrumentation, we are exploring new applications for optical biosensor technology including protein microarrays, biosensor/mass spectrometry systems, and microfluidics-based assays using nanoliter quantities of reagents. The methods and systems developed in the laboratory are applied in the fields of life science research, drug discovery, diagnostic testing, and environmental monitoring. -From Professor Cunningham's Faculty Profile

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Researchers should cite this work as follows:

  • Brian Cunningham; NanoBio Node (2013), "[Illinois] ECE 416 Next Gen Sequencing II," https://nanohub.org/resources/17704.

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University of Illinois, Urbana-Champaign, IL