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 1

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 2

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 3

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

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 5

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 6

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

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. 8

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 9

10. Time Schedule 10

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 11

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 12

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

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_ch annels 14

15. Nanopore Insertion 15

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

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

18. DNA Passing 18

19. Resistance Zoomed 19

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

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23. 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 23

24. 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 0.5Â um CMOS foundry process. Nanotechnology. IOPScience, 31 October 2013. Web. 2 July 2014. 24

25. Thank You! We would like to thank NSF for funding our research [Grant ID No.: DUE – 0756921] 25

26. Questions? 26