E lectrical & M echanical characteristics of DNA bundles revealed by S ilicon N anotweezers

1. 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

2.  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    

3. Scope of the research 

4.  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

5.  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

6.  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

7.  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

8. Working principle • & Microfabrication • of the Silicon Nanotweezers • Working principle • Microfabrication technology 

9.  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

10.  Working principle of the Silicon Nanotweezers

11.  Working principle of the Silicon Nanotweezers Differential capacitive sensor

12.  Working principle of the Silicon Nanotweezers Differential capacitive sensor MS3110 Universal Capacitive Readout™ (Irvine sensors, CA, USA)

13. Working principle • & Microfabrication • of the Silicon Nanotweezers • Working principle • Microfabrication technology 

14. 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

15. 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)

16.  Microfabrication technology

17. DNA trapping by dielectrophoresis 

18.  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

19.  DNA trapping by dielectrophoresis (DEP) λ-DNA bundle 20 µm gap diameter ~ 380 nm

20. Electrical & Mechanical • characterization • of DNA bundles • Electrical characterization • Mechanical characterization  

21. 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

22.  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

23.  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

24.  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)

25.  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)

26. Electrical & Mechanical • characterization • of DNA bundles • Electrical characterization • Mechanical characterization  

27.  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

28.  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

29. Conclusion & Outlook 

30.  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.

31.     Acknowledgments 

32. 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)

33. Thank you for your attention. Thank you for your attention.