Molecular Computation with

Automated Microfluidic Sensors(MCAMS)

Laura Landweber*

Princeton University

Princeton UniversityL. L. Sohn†M. SinghA. SahaiR. Weiss

Stanford UniversityC. WebbR. Davis

UC BerkeleyA. P. Alivisatos

*DARPA Biocomp PI †NSF ITR PI

Molecular Computation with Automated Microfluidic Sensors Molecular Computation with Automated Microfluidic Sensors (MCAMS)(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

Sensing Single Molecules of DNA Saleh & Sohn

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

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)

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

Res

ervo

ir

Pore Reservoir

Measuring DNA

•Each downward spike=single DNA molecule

•Pore: diameter~300 nm, 4 m long

•Why does peak size vary? Varying DNA conformation?

selection principle: DNA input and transport principle

selection principle: DNA input and transport principle

negative selection: DNA input and transport principle

selection principle: logical operations

selection principle: logical NOT operation

selection principle: logical AND operation

a b

selection principle: logical OR operation

a b

(h f) a

3x3 knight problem

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

silicon surfaceNHS-LC-biotin

streptavidin

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

biotinylated single DNA strands

silicon surfaceNHS-LC-biotin

streptavidin

Nanocrystal-labeled DNA

Alivisatos and Schultz , Nature 382 p. 609 1996; Angew. Chemie 38 p. 1808 1999related work by (Mirkin and Letsinger,) (Silvan and Braun)

1

111

1

0

00

Isolating gold nanocrystals bearing discrete numbers of oligonucleotides

read-out: gold particles

electrodes

Au nanocrystals

library strand

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 computationExplore ways to make the chip versatile for different

computing algorithmsDesign microfluidic chip with reaction wells and switching valvesIdentify methods to detect 15-nt bits in RNA computationSolve an instance of a SAT problem using microfluidic device

Year 1 Year 2

Molecular Computation with

Automated Microfluidic Sensors

Princeton UniversityL. F. Landweber (15%)*L. L. Sohn (10%) †M. SinghA. Sahai (5%)R. WeissDanny van Noort (100%)Omar A. Saleh (30%)Zhao Huang (50%)

Stanford UniversityC. Webb (10%)R. Davis (1%)W. Tongparsit (50%)

UC BerkeleyA. P. Alivisatos (10%)Christine Micheel (40%)Teresa Pelelgrino (20%)

*DARPA Biocomp PI †NSF ITR PI