lyon, france june 12, 2007 | christophe yamahata electrical & mechanical characteristics of...
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![Page 1: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/1.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
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 TokyoInstitute of Industrial Science
Kagawa UniversityFaculty of Engineering
![Page 2: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/2.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Electrical & Mechanical characteristics of DNA bundlesrevealed by Silicon Nanotweezers
Scope of the research
Working principle & Microfabrication of the Silicon Nanotweezers
DNA trapping by dielectrophoresis
Electrical & Mechanical characterization of DNA bundles
Conclusion & Outlook
![Page 3: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/3.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Scope
of the research
![Page 4: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/4.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
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
![Page 5: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/5.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
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
![Page 6: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/6.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
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
![Page 7: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/7.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
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
![Page 8: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/8.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Working principle
& Microfabrication
of the Silicon Nanotweezers
• Working principle• Microfabrication technology
![Page 9: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/9.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Working principle of the Silicon Nanotweezers
External dimensions:4.5 mm × 5.5 mm
SOI wafer The different elements are:
• Electrically insulated• Mechanically locked with each other
![Page 10: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/10.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Working principle of the Silicon Nanotweezers
![Page 11: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/11.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Working principle of the Silicon Nanotweezers
Differential capacitive sensor
![Page 12: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/12.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Working principle of the Silicon Nanotweezers
Differential capacitive sensor
MS3110 Universal Capacitive Readout™ (Irvine sensors, CA, USA)
![Page 13: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/13.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Working principle
& Microfabrication
of the Silicon Nanotweezers
• Working principle• Microfabrication technology
![Page 14: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/14.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
(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
Microfabrication technology
(5) HF removal of buried oxide
Si
Si3N4
SiO2
(6) Backside etching by deep-RIE (with Al mask)
SOI wafer
• (100)-Si layer: 25 µm
• Oxide layer: 2 µm
• Handling wafer: 380 µm
![Page 15: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/15.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Microfabrication technology
Si
Si3N4
SiO2
(1)
(2)
(3)
(4)
(5)
(6)
SOI wafer
• (100)-Si layer: 25 µm
• Oxide layer: 2 µm
• Handling wafer: 380 µm
![Page 16: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/16.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Microfabrication technology
![Page 17: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/17.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
DNA trapping
by dielectrophoresis
![Page 18: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/18.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
DNA trapping by dielectrophoresis (DEP)
Droplet:
• λ-DNA: 12 nmol/L• DI water: 5 µL
Dielectrophoresis (DEP):
30 sec @ 1 MHz, 40 Vpp (20 µm gap)
![Page 19: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/19.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
λ-DNA bundle20 µm gapdiameter ~ 380 nm
DNA trapping by dielectrophoresis (DEP)
![Page 20: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/20.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Electrical & Mechanical
characterization
of DNA bundles
• Electrical characterization• Mechanical characterization
![Page 21: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/21.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Humidity generator
Ambient air Pump
Gas washing
bottle
Mixer
Temperature and humidity sensor
Glove box
Faraday cage
Keithley 6487 Picoammeter / Voltage Source
chassis
desiccant
saturator
Electrical characterization of DNA bundles
Experimental setup
![Page 22: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/22.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Electrical characterization of DNA bundles
~ 20 GΩ
~ 5 TΩ
Measurements for different DNA bundles diameters
Quasi-ohmic behavior
Measurements on “wet” DNA bundles
(various diameters)
T = 25 °C rh ~ 55% humidity
![Page 23: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/23.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Measurements on “wet” DNA bundles
(various diameters)
Conductivity bundle section
Electrical characterization of DNA bundles
Measurements for different DNA bundles diameters
Effect of DNA bundle diameter
![Page 24: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/24.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
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)
![Page 25: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/25.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
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)
![Page 26: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/26.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Electrical & Mechanical
characterization
of DNA bundles
• Electrical characterization• Mechanical characterization
![Page 27: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/27.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Mechanical characterization of DNA bundles
Displacement: ~ 3 µm Cmax 200 fF
Sensitivity: 2 V/pF 150 mV/µm
Error: ε <1 mV
5 nm resolution
Characterization of empty tweezersMeasurements performed with the MS3110 Universal Capacitive Readout™
![Page 28: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/28.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Sensitivity of the capacitive sensor enables the measurement of few nN forces
(single DNA ~ 80 pN)
Bundle stretching can be observed
Mechanical characterization of DNA bundles
Measurements after DNA bundle trappingMeasurements performed with the MS3110 Universal Capacitive Readout™
![Page 29: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/29.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Conclusion & Outlook
![Page 30: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/30.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Conclusion & Outlook
• 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.
A new type of biophysical tool has been proposed:
![Page 31: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/31.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Acknowledgments
![Page 32: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/32.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
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)
Acknowledgments
![Page 33: Lyon, France June 12, 2007 | Christophe Yamahata Electrical & Mechanical characteristics of DNA bundles revealed by Silicon Nanotweezers C. Yamahata,](https://reader036.vdocuments.net/reader036/viewer/2022062423/56649f315503460f94c4c5ab/html5/thumbnails/33.jpg)
Lyon, France June 12, 2007 | Christophe Yamahata
Thank you for your attention.Thank you for your attention.