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A Synthetic Electronic Nanopore for DNA Sequencing and Stochastic Sensing

A Synthetic Electronic Nanopore for DNA Sequencing and Stochastic Sensing. Mr. Aaron Choi, Computer Science, Sophomore Mr. Davis Sneider, Biomedical Engineering, Sophomore Mr. Saifuddin Aijaz, Chemical Engineering, Pre-Junior Mentors:

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A Synthetic Electronic Nanopore for DNA Sequencing and Stochastic Sensing

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  1. A Synthetic Electronic Nanopore for DNA Sequencing and Stochastic Sensing Mr. Aaron Choi, Computer Science, Sophomore Mr. Davis Sneider, Biomedical Engineering, Sophomore Mr. Saifuddin Aijaz, Chemical Engineering, Pre-Junior Mentors: Dr. David Wendell, Assistant Professor, Environmental Engineering Dr. Vasile Nistor, Assistant Professor, Biomedical Engineering Ms. Elizabeth Wurtzler, Graduate Student, Environmental Engineering

  2. Introduction • Background • Goals & Tasks • Time Schedule • What we’ve done, where we’re going • Inserting DNA • What we’re looking for, what we’ve found • Findings • Conclusion

  3. Current problem • DNA sequencing can cost up to 10,000 dollars and take about a week • Nanopore technology can save a lot of money and reduce the time to one day

  4. Nanopores: What are they? • They are extremely small holes. • They have potential applications for many kinds of developing technology Oxford Nanopore Technologies

  5. Hydraphile Nanopore • A synthetic nanopore, created by Dr. George Gokel at University of Missouri, St. Louis • Lariat Ethers • Excellent cation selectivity • Excellent binding and release kinetics Royal Society of Chemistry http://pubs.rsc.org/en/content/articlehtml/2000/cc/a903825f

  6. Size Comparison • The nanopore is said to be approximately 8 picometers • DNA has been shown to go through the nanopore and single stranded DNA is 1 nm

  7. Applications • We could detect cancer earlier and much more efficiently • DNA sequencing allows us to find many genetic disorders • Ability to detect viruses

  8. Our Goals • To determine which buffer works best • To use the hydraphile nanopore for • DNA sequencing • Norovirus sensing • Help to define the width of the hydraphile nanopore.

  9. Tasks • Use QuB to analyze data from four buffers • Run items through nanopore • Ion Solutions • DNA • Norovirus • Use passages to get an idea of how wide the nanopore is

  10. Time Schedule

  11. Conclusion From Buffers Tests • Out of the four solutions used, it was determined that KCl is the best choice to use for nanopore sequencing as it gives a more stable membrane. apcg.space.noa.gr

  12. Potassium Buffer • 1M KCl Buffer, with 5mM Hepes • Able to get data with ease • Analyzing Data • Clampex • 100< data points • Standard deviation 1.76 nanosiemens Glogster.com

  13. Painting the Membrane • Take in and remove lipid hexane solution • Create air bubble with pipet • Wipe air bubble over membrane

  14. Inserting Nanopores • Once a thin membrane is present, we then insert the hydraphile nanopore • If membrane is too thick, nanopores won’t span length of membrane Wikipedia http://en.wikipedia.org/wiki/Synthetic_ion_channels

  15. Nanopore Insertion

  16. Inserting DNA • Dilute mixture • 2µL of DNA • 18µL of water • Intake .5µL of mixture overtop of hole

  17. Detecting DNA Current Change • Inserting DNA causes resistances in the current across the membrane • Negative charge across membrane www.ks.uiuc.edu

  18. DNA Passing

  19. Resistance Zoomed

  20. What We Measured • 2 major measurements • Blockage % • Dwell Time (ms) • DNA length • 250 BP • 500 BP • 1,000 BP • 2,500 BP

  21. What Does It Mean & What Is It Useful For? • Blockage % • Tells us how much of the nanopore has been blocked • Helps us identify approximate width of DNA/RNA strand • Event Duration • Tells us how long it took the DNA segment to pass through the nanopore • Helps us identify approximate length of the DNA/RNA strand

  22. References • Gokel, George. Hydraphiles: Design, Synthesis and Analysis of a Family of Synthetic, Cation-conducting Channels. Tech. Royal Society of Chemistry, 24 Dec. 1999. Web. 13 June 2014. • "Towards the 15-minute Genome." The Economist. The Economist Newspaper, 12 Mar. 2011. Web. 17 June 2014. • Uddin A, Yemenicioglu S, Chen C-H, Corigliano E, Milaninia K and Theogarajan L. Integration of solid-state nanopores in a 0.5 um CMOS foundry process. Nanotechnology. IOPScience, 31 October 2013. Web. 2 July 2014.

  23. Thank You! • We would like to thank NSF for funding our research [Grant ID No.: DUE – 0756921]

  24. Questions?

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