Nanopores and Nanofluidics for Single DNA Studies Derek Stein Department of Physics Brown University

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1 Nanopores and Nanofluidics for Single DNA Studies Derek Stein Department of Physics Brown University

2 Overview Motivation: biological, physical, and technological The program: develop and characterize new tools apply these to the study of biological systems Nanofluidic devices Solid-state nanopores

3 The importance of biomolecules The machinery of life the structure and function of biomolecules like DNA, RNA, and proteins tell us how living systems work Biomolecules contain information The distribution of biomolecules within the cell indicates identity, activity, disease, etc. Sensitivity to different biomolecules is the basis of medical diagnostics Where a physicist fits in Developing new tools, and exploring the fundamental science

4 Studying biomolecules at the nanoscale Perhaps best way to study a molecule is the most direct: grab it and look at it! 25 nm Microtubule/kinesin ~10 nm 2 nm α-hemolysin 2 nm F1 ATP-ase ~20 µm DNA

5 Motivation for nano-biophysics Biomoleculesoperate 2 nm Under water At micro- and nanometre length scales Nanofabricationallows... The realization of ultra-smalldevices The handling of tinyamounts of fluid Micro- and nanofluidics Seemnaturallysuited to studyingbiologicalsystems!

6 Silicon-based nano-biophysics (The lab-on-a-chip" concept) Borrows the IC s smaller, cheaper, faster paradigm, and its fabrication technology Computation on a chip Chemistry & biology on a chip

7 A vision for nanofluidic technology The vision is to manipulate and analyze every component of a cell in molecular detail! We need to explore what is possible Current leading research is focusing on Any analysis! Applications: Protein crystallization Protein detection and recognition Molecular separations Haplotyping DNA sequencing Science: Single-molecule dynamics (polymers, enzymes, molecular motors) Materials science Fluid dynamics and electrokinetic phenomena

8 Nanofluidic devices Confine and transport tiny quantities of fluid and molecules Nanochannels are the wires of a lab-on-a-chip SEM image of a 28 nm high nanochannel cross-section What are their transport properties?

9 DNA in a pressure-driven flow Pressure-driven λ-dna motion in a 500 nm high channel Pressure gradient applied using water columns 50µm Nanochannel

10 Length dependent DNA transport u max 2 p h = L 8η h h u average = 2 3 u max We define the pressure-driven mobility, ν, using V =ν p

11 Length dependent DNA transport There are two distinct regimes for pressure-driven DNA in channels Length-dependent regime Length-independent regime

12 DNA as a random flight polymer Equilibrium DNA conformations can be modeled using random flight statistics In our experiments: R R g 0.29µm, 0.46µm, and 0.73µm g The Edwards diffusion equation b 6 2 (, ) ( ) 2, P z s = P z s s Hard wall boundary conditions h P z = ±, s = 0 2 The average density of DNA segments across the channel is given by: L 1 ρ = L ( z) P ( z, s) P ( z, L s) 0

13 Modeling DNA transport What is the pressure-driven mobility of DNA? Equilibrium DNA conformations and Poisseuille fluid flow should apply in the low-shear limit. h / 2 h / 2 V U ( z) ρ( z) dz ρ( z) dz = x h / 2 h / 2 fluid flow profile average DNA segment density

14 Pressure-driven DNA mobility Length-independent mobility in thin channels Length-dependent mobility in large channels ρ 2 ( z) sin ( π z h) ( ) 2 ( ) ( ) ρ z tanh π z h / 2 2R g D. Stein, F. v.d. Heyden, W. Koopmans, and C. Dekker, PNAS (2006).

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17 Modeling the free energy landscape for DNA Confinement free energy Top view a a d Self-exclusion energy L s l s Entropic elasticity L p,1 L p,2 Viscous energy (work) Side view h H Fixed contour length

18 Modeling DNA transport: single-pit occupancy F - P Increasing pressure l s

19 Modeling DNA transport: double-pit occupancy F Increasing pressure - P l s - P - P

20 The predicted transition from stochastic to deterministic transport was observed Low pressure Po osition 2 µm 2 µm of fluid flow Direction High pressure Time [minutes] Time [seconds]

21 Electro-fluidics manipulating charged molecules with electrostatic fields

22 The electric double layer charged surface Debye electrostatic screening length λ D positive ion negative ion Screenin g length: λ D ~ 1 nm (0.1M) 10 nm (1mM) compact layer (Stern layer) diffuse layer neutral fluid 100nm (10µm) (for monovalent salt)

23 Measuring repulsive electrostatic forces on a single molecule in solution confined DNA molecule increase steric confinement increase λ D (lower salt)

24 A charged rod near a charged wall Our simple model of DNA interacting with a charged nanochannel wall follows the method described by Onsager for colloidal particles: The energy of a charged rod at a given distance and angle is: The excluded width due to electrostatics incorporates the Boltzmann factor follows: This can be integrated, and is well approximated by: We expect an excluded region near each wall that is a few times the Debye screening length.

25 Confinement induces reproducible changes in the size of a polymer D.J. Bonthuis, C. Meyer, D. Stein, and C. Dekker PRL 101, (2008). Confinement(2*R bulk /h)

26 Solid-state nanopores

27 Basic principles of nanopore sensing A biological nanopore as an electronic molecule sensor Low resolution RNA sequencing M. Akeson, D. Branton, J. J. Kasianowicz, E. Brandin, D. W. Deamer, Biophysical Journal 77, (1999).

28 Fabricating nanopores in a transmission electron microscope

29 Single-DNA detection using a solid-state nanopore J. Li, D. Stein, C. McMullan, D. Branton, M.J. Aziz and J.A. Golovchenko, Nature 412, 166 (2001).

30 DNA length discrimination by singlemolecule electrophoresis The translocation time is a measure of molecular length

31 The nanopore senses molecular folds!

32 Extracting sequence information using sequence-specific binding MIZF is a zinc finger protein that binds to dsdna in a sequence-specific manner

33 Controlling the translocation of DNA using optical tweezers Our goal is to generate a DNA barcode that contains sequence information in the electrical signal Optical tweezers & nanopores first demonstrated by: U. F. Keyser et al, Nature Physics2, 473 (2006)

34 Electrostatically gated nanopores (mimicking biology by opening and closing a pore) Open pore Closed pore

35 Probing DNA by transverse electronic tunneling Perhaps metallic carbon nanotubes would make the ideal tunneling electrodes?

36 Nanopores milled through CNT s embedded in a silicon nitride membrane TEM of buried CNT TEM of buried CNT with nanopore (12 nm gap) with nanopore (9 nm gap) CNT CNT

37 Idea: Sequence DNA by combining nanopores with mass spectrometry Appeal: 1) Contrast; 2) Single-ion sensitivity; 3) Bandwidth; 4) Robustness

38 Conclusions Individual molecules can be manipulated and studied in new ways thanks to Lab-on-a-chip -style nanostructures. Certain physical phenomena become particularly important to the behavior of devices at the nanoscale: Statistical properties Electrostatic effects Molecular size exclusion Exciting opportunities for science and technology still await at the nanoscale

39 Acknowledgements Brown University Dr. Walter Reisner Zhijun Jiang Yongqiang Ren Travis Del Bonis-O Donnell Simon Buttrick Stefan Schaffer Nick Hagerty Jason Chan Charles Wood TU Delft Cees Dekker Wiepke Koopmans Frank van derheyden Serge Lemay DouweBonthuis Marc Zuiddam Harvard University JeneGolovchenko Daniel Branton Micheal Aziz Jiali Li Ciaran McMullan Marc Gershow Eric Brandin

40 Ion beam sculpting a nanopore Idea: gain nanometre control by incorporating feedback The feedback-controlled ion beam sculpting apparatus

41 Discovery of a new matter transport phenomenon

42 A surface diffusion model of ion beam sculpting A cartoon of ion-induced surface diffusion The surface diffusion model predicts the flux dependence of nanopore formation J. Li, D. Stein, C. McMullan, D. Branton, M.J. Aziz and J.A. Golovchenko, Nature 412, 166 (2001).

43 Information from a nanopore signal The duration and the amplitude of an event provide information about the translocating molecule

44 DNA translocation distributions

45 A study of individual translocation events reveals two distinct populations