[Illinois] ECE 416 Next Gen Sequencing II

By Brian Cunningham1, NanoBio Node1

1. University of Illinois at Urbana-Champaign

Published on

Abstract

           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.

Bio

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

Cite this work

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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Time

Location

University of Illinois, Urbana-Champaign, IL

[Illinois] ECE 416 Lecture 35: Next Gen Sequencing II
  • Bridge Amplification 1. Bridge Amplification 0
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  • Illumina Colonies (called 2. Illumina Colonies (called "pol… 56.032732654304866
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  • Illumina 3. Illumina 88.263950552798818
    00:00/00:00
  • Illumina Products 4. Illumina Products 181.85844868111778
    00:00/00:00
  • Helicos 5. Helicos 257.72577696526508
    00:00/00:00
  • ECE/BioE 416 Lecture 24 6. ECE/BioE 416 Lecture 24 469.9559502045791
    00:00/00:00
  • Helicos Images 7. Helicos Images 533.42665622007485
    00:00/00:00
  • Heliscope Images 8. Heliscope Images 547.434839383651
    00:00/00:00
  • Helicos Images 9. Helicos Images 558.34386698006438
    00:00/00:00
  • Heliscope Images 10. Heliscope Images 606.93862627317844
    00:00/00:00
  • ECE/BioE 416 Lecture 24 11. ECE/BioE 416 Lecture 24 638.17811439018021
    00:00/00:00
  • Helicos Products 12. Helicos Products 668.30190650300335
    00:00/00:00
  • Pacific Biosciences 13. Pacific Biosciences 722.599112039697
    00:00/00:00
  • Pacific Biosciences 14. Pacific Biosciences 916.978149212153
    00:00/00:00
  • Pacific Biosciences 15. Pacific Biosciences 1097.472969443719
    00:00/00:00
  • Pacific Biosciences 16. Pacific Biosciences 1165.6543919213025
    00:00/00:00
  • DNA Sequencing with Zero Mode Waveguides 17. DNA Sequencing with Zero Mode … 1211.7698267606861
    00:00/00:00
  • DNA Sequencing with Zero Mode Waveguides 18. DNA Sequencing with Zero Mode … 1214.1251849917298
    00:00/00:00
  • DNA Sequencing with Zero Mode Waveguides 19. DNA Sequencing with Zero Mode … 1253.4224775833552
    00:00/00:00
  • Pacific Bioscience Example Data 20. Pacific Bioscience Example Dat… 1330.0336032036216
    00:00/00:00
  • Pacific Biosciences Products 21. Pacific Biosciences Products 1509.0408287629496
    00:00/00:00
  • Ion Torrent Single Molecule Sequencing 22. Ion Torrent Single Molecule Se… 1540.2803168799512
    00:00/00:00
  • Ion Torrent Sequencing 23. Ion Torrent Sequencing 1745.4444154261339
    00:00/00:00
  • Ion Torrent Sequencing 24. Ion Torrent Sequencing 1788.5846609210412
    00:00/00:00
  • Ion Torrent Products 25. Ion Torrent Products 1899.5344302254723
    00:00/00:00
  • Putting all the short sequences together 26. Putting all the short sequence… 2419.5727343954036
    00:00/00:00