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E lectrical & M echanical characteristics of DNA bundles revealed by S ilicon N anotweezers C. Yamahata , T. Takekawa, M. Kumemura, M. Hosogi, G. Hashiguchi, D. Collard & Hiroyuki Fujita. . The University of Tokyo Institute of Industrial Science. Kagawa University

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Presentation Transcript

Electrical & Mechanical

characteristics of

DNA bundles

revealed by

Silicon Nanotweezers

C. Yamahata, T. Takekawa,

M. Kumemura, M. Hosogi, G. Hashiguchi,

D. Collard & Hiroyuki Fujita

The University of Tokyo

Institute of Industrial Science

Kagawa University

Faculty of Engineering


Electrical mechanical characteristics of dna bundles

revealed by Silicon Nanotweezers

Electrical & Mechanical characteristics of DNA bundles

Scope of the research

Working principle &Microfabricationof the Silicon Nanotweezers

DNA trapping by dielectrophoresis

Electrical & Mechanicalcharacterization of DNA bundles

Conclusion & Outlook


Scope

of the research


Scope of the research

Biophysical tools used for molecular manipulation

  • Optical tweezers

  • Magnetic tweezers

  • AFM probes

* D. Collard et al., IEEJ Trans 2: 262–271, 2007


Scope of the research

Biophysical tools used for molecular manipulation

  • Optical tweezers

  • Magnetic tweezers

  • AFM probes

* D. Collard et al., IEEJ Trans 2: 262–271, 2007


Scope of the research

Biophysical tools used for molecular manipulation

  • Optical tweezers

  • Magnetic tweezers

  • AFM probes

* D. Collard et al., IEEJ Trans 2: 262–271, 2007


Scope of the research

Biophysical tools used for molecular manipulation

  • Optical tweezers

  • Magnetic tweezers

  • AFM probes

  • and

  • Silicon nanotweezers

* D. Collard et al., IEEJ Trans 2: 262–271, 2007


  • Working principle

  • & Microfabrication

  • of the Silicon Nanotweezers

    • Working principle

    • Microfabrication technology


Working principle of the Silicon Nanotweezers

  • SOI wafer  The different elements are:

    • Electrically insulated

    • Mechanically locked

    • with each other

External dimensions:

4.5 mm × 5.5 mm


Working principle of the Silicon Nanotweezers


Working principle of the Silicon Nanotweezers

Differential capacitive sensor


Working principle of the Silicon Nanotweezers

Differential capacitive sensor

MS3110 Universal Capacitive Readout™ (Irvine sensors, CA, USA)


  • Working principle

  • & Microfabrication

  • of the Silicon Nanotweezers

    • Working principle

    • Microfabrication technology


Si3N4

Si

SiO2

Microfabrication technology

(1) Si3N4 deposition (LPCVD) + patterning

(2) Silicon etching (RIE)

(3) SiO2 oxidation (LOCOS)

(3) SiO2 oxidation (LOCOS)

+Si3N4 removal

(4) KOH anisotropic etching of Silicon

 <111> facets

(5) HF removal of buried oxide

(6) Backside etching by deep-RIE (with Al mask)

  • SOI wafer

  • (100)-Si layer:

  • 25 µm

  • Oxide layer:

    • 2 µm

  • Handling wafer:

  • 380 µm


Si3N4

Si

SiO2

Microfabrication technology

(1)

(4)

(2)

(5)

  • SOI wafer

  • (100)-Si layer:

  • 25 µm

  • Oxide layer:

    • 2 µm

  • Handling wafer:

  • 380 µm

(3)

(6)


Microfabrication technology


DNA trapping

by dielectrophoresis


DNA trapping by dielectrophoresis (DEP)

Dielectrophoresis (DEP):

30 sec @ 1 MHz, 40 Vpp

(20 µm gap)

  • Droplet:

    • λ-DNA: 12 nmol/L

    • DI water:5 µL


DNA trapping by dielectrophoresis (DEP)

λ-DNA bundle

20 µm gap

diameter ~ 380 nm


  • Electrical & Mechanical

  • characterization

  • of DNA bundles

    • Electrical characterization

    • Mechanical characterization


Humidity generator

Glove box

desiccant

Faraday cage

Ambient

air

Pump

Mixer

saturator

Gas washing

bottle

chassis

Temperature and humidity sensor

Keithley 6487Picoammeter / Voltage Source

Electrical characterization of DNA bundles

Experimental setup


Electrical characterization of DNA bundles

Measurements for different DNA bundles diameters

Quasi-ohmic behavior

Measurements on

“wet” DNA bundles

(various diameters)

T = 25 °C

rh ~ 55% humidity

~ 20 GΩ

~ 5 TΩ


Electrical characterization of DNA bundles

Measurements for different DNA bundles diameters

Effect of DNA bundle diameter

  • Measurements on

  • “wet” DNA bundles

  • (various diameters)

  • Conductivity  bundle section


Electrical characterization of DNA bundles

Effect of humidity

Exponential dependence with relative humidity

Transient current

recording for a 5V step.

Data recorded at 21 °C

(1°C overall fluctuation) for different humidity levels

(rh0.2% for each curve)


Electrical characterization of DNA bundles

Effect of humidity

Exponential dependence with relative humidity

Data extracted from previous measurements (5V step)

after 60 sec. (rh was decreased from

75% to 45% in 6 hours)


  • Electrical & Mechanical

  • characterization

  • of DNA bundles

    • Electrical characterization

    • Mechanical characterization


Mechanical characterization of DNA bundles

Characterization of empty tweezers

Measurements performed with the MS3110 Universal Capacitive Readout™

Displacement: ~ 3 µm

Cmax 200 fF

Sensitivity: 2 V/pF

150 mV/µm

Error:ε<1 mV

 5 nm resolution


Mechanical characterization of DNA bundles

Measurements after DNA bundle trapping

Measurements performed with the MS3110 Universal Capacitive Readout™

  • Sensitivity of the

  • capacitive sensor enables the measurement of

  • few nN forces

  • (single DNA  ~ 80 pN)

  • Bundle stretching can

    be observed


Conclusion & Outlook


Conclusion& Outlook

A new type of biophysical tool has been proposed:

  • Efficient trapping of DNA by dielectrophoresis

  • Extensive electrical characterization of DNA bundles

  • Displacement: 2-3 µm range /few nm resolution

  • Force: few nN sensitivity

  •  High potential for biophysical characterization of long macromolecules.

  • e.g.: DNA bundle, microtubules, actin filament, etc.


Acknowledgments


Acknowledgments

Swiss National Science Foundation (SNSF)

Japan Society for the Promotion of Science (JSPS)

Japan Science and Technology Corporation(JST)

Centre National de la Recherche Scientifique (CNRS)


Thank you for your attention.

Thank you for your attention.


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