1. Molecular Computation with Automated Microfluidic Sensors (MCAMS) Laura Landweber * Princeton University L. L. Sohn† M. Singh A. Sahai R. Weiss Stanford University C. Webb R. Davis UC Berkeley A. P. Alivisatos *DARPA Biocomp PI †NSF ITR PI

2. Molecular Computation with Automated Microfluidic Sensors (MCAMS) Accelerate the field of molecular-based computing by increasing sensitivity and throughput and enabling “hands-free” molecular computation. Combine microfluidic technology and biophysical methods for detecting nucleic acids with recently-developed algorithms of RNA-based computing to create a compact, automated, scalable, nucleotide-based computational device capable of rapidly and directly detecting the computational output. New Ideas Impact/Relevance

7. Sensing Single Molecules of DNA Saleh & Sohn

8. The sensing device EBL on quartz is time consuming Etched samples have finite lifetimes- after ~5 msmts., too dirty to clean and reuse Solution: Embed pore in PDMS- make one master, cast from it forever… Seal PDMS to glass slip that holds electrodes

9. The master Negative pore: Electron-beam-defined polystyrene line (height, width adjustable 450 nm to <100 nm), or photolith defined etched quartz (1x1  m and bigger) Negative reservoirs: SU-8 photoresist (5  m thick)

10. Saleh and Sohn’s device in PDMS AFM on PDMS shows successful casting down to 200 nm line width Optical image of sealed devices a small and quickly fabricated pore! PDMS Reservoir Pore Reservoir

11. Measuring DNA Each downward spike=single DNA molecule Pore: diameter~300 nm, 4  m long Why does peak size vary? Varying DNA conformation?

12. selection principle: DNA input and transport principle

14. negative selection: DNA input and transport principle

16. selection principle: logical operations

17. selection principle: logical NOT operation

18. selection principle: logical AND operation a  ba  b

19. selection principle: logical OR operation a  ba  b

20. (  h   f)   a 3x3 knight problem

21. Immobilization principle: surface enlargement with streptavidin coated beads, NHS-LC-biotin to aminolated silicon surface silicon surface NHS-LC-biotin streptavidin

22. Immobilization principle: surface enlargement with streptavidin coated beads, NHS-LC-biotin to aminolated silicon surface biotinylated single DNA strands silicon surface NHS-LC-biotin streptavidin

24. Nanocrystal-labeled DNA Alivisatos and Schultz, Nature 382 p. 609 1996; Angew. Chemie 38 p. 1808 1999 related work by (Mirkin and Letsinger,) (Silvan and Braun) 1 1 11 1 0 0 0

25. Isolating gold nanocrystals bearing discrete numbers of oligonucleotides

26. read-out: gold particles electrodes Au nanocrystals library strand

28. Scheduled Milestones/Success Metrics Design prototype microfluidic system Identify methods for sizing and detection of RNA-based computation outputs, such as electrical detection. Develop microfluidic chip to perform RNA-based computation Explore ways to make the chip versatile for different computing algorithms Design microfluidic chip with reaction wells and switching valves Identify methods to detect 15-nt bits in RNA computation Solve an instance of a SAT problem using microfluidic device Year 1Year 2

29. Molecular Computation with Automated Microfluidic Sensors Princeton University L. F. Landweber (15%)* L. L. Sohn (10%) † M. Singh A. Sahai (5%) R. Weiss Danny van Noort (100%) Omar A. Saleh (30%) Zhao Huang (50%) Stanford University C. Webb (10%) R. Davis (1%) W. Tongparsit (50%) UC Berkeley A. P. Alivisatos (10%) Christine Micheel (40%) Teresa Pelelgrino (20%) *DARPA Biocomp PI †NSF ITR PI