DNA Mobility through 20 nm Nanoslits

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DNA Mobility through 20 nm Nanoslits

• Georgette Salieb-Beugelaar
• Juliane Teapal
• Jonas Tegenfeldt
• Jan Eijkel
• Fred Lisdat
• Albert van den Berg
• University of Twente, University of Wildau and
  University of Lund

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Introduction, Experimental, Results, Conclusions,
Outlook
Nano2Life
We Nanoslit device in which we electrically
pulled DNA Jonas O. Tegenfeldt Technical
experience and physical knowledge with DNA inside
nanoslits and channels Thanks to Nano2Life we
were able to collaborate - student received an
introduction in Lund - combination of technical
experience and theoretical background
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Introduction, Experimental, Results, Conclusions,
Outlook
Introduction

• Why these fundamental DNA studies
• study the structure and physics of DNA
• develop new nanofluidic devices for DNA analysis
• improve DNA diagnostics
• develop tools to study DNA-protein interactions

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Introduction, Experimental, Results, Conclusions,
Outlook
DNA in sub 20 nm nanoslits
3d DNA blob
In slit 2d DNA pancake
Mannion and Craighead, Biopolymers 85 (2006) 131
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Introduction, Experimental, Results, Conclusions,
Outlook
DNA in sub 20 nm nanoslits
qE
Study DNA movement under the influence of an
applied electrical field
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DNA and buffer inlet
Introduction, Experimental, Results, Conclusions,
Outlook
Nanoslit device
Outlets
qE
Nanoslit array ( between microchannels)
Microchannels
Buffer inlet
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Introduction, Experimental, Results, Conclusions,
Outlook
Nanoslit device
Fused Silica sandwich
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Introduction, Experimental, Results, Conclusions,
Outlook
Surface roughness nanoslit
7.7 nm
0.0 nm
y 500 nm
x 500 nm
Etched surface AFM scan tip-radius 2 nm 1 nm rms
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Introduction, Experimental, Results, Conclusions,
Outlook
Experimental conditions

• YOYO-1 - ? -DNA (1/5 bp), length 20 µm
• Tris-Borate-Na-EDTA buffer, pH 8.3
• ß-MercaptoEthanol 3 against photobleaching and
  photoknicking
• Polyvinylpyrrolidone MW 10.000, 2.5 against
  electroosmotic flow

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Introduction, Experimental, Results, Conclusions,
Outlook
YOYO-1 ?-DNA in a 20 nm nanoslit high field
qE
Electrical field 200 kV/m
50 µm
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Introduction, Experimental, Results, Conclusions,
Outlook
High field ?-DNA movement
Stop Go movement
Electrical field 200 kV/m
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Introduction, Experimental, Results, Conclusions,
Outlook
High field ? -DNA movement

• Mobility in go phase 1 of bulk mobility!
• On average 10 of time go, 90 stop
• Overall mobility 0.1 of bulk

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Introduction, Experimental, Results, Conclusions,
Outlook
YOYO-1 ?-DNA in a 20 nm nanoslit low field
qE
Electrical field 20 kV/m
50 µm
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Introduction, Experimental, Results, Conclusions,
Outlook
Low field ?-DNA movement
Fluent movement
Mobility 10 of bulk mobility
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Introduction, Experimental, Results, Conclusions,
Outlook
Field-strength dependent mobility
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Introduction, Experimental, Results, Conclusions,
Outlook
Previous studies no mobility dependence on
E-field
Tegenfeldt 2004 100x200 nm 0.5 kV/m Mannion
2006 100 nm cylinders 2.1 kV/m Cross 2007 19
and 70 nm slits 3.3 kV/m we 12 and 20 nm
slits 2-200 kV/m
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Introduction, Experimental, Results, Conclusions,
Outlook
Possible theoretical description
Describe data with a field-dependent mobility
f(E) determined by a field-dependent retardation
effect
Possible effects - steric trapping -
dielectrophoretic trapping - combination of
both -
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Introduction, Experimental, Results, Conclusions,
Outlook
Steric trapping
Roughness defects
Height 20 nm
Width 3 ?m
Retardation by a series of trapping events
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Introduction, Experimental, Results, Conclusions,
Outlook
Dielectrophoretic trapping
e.g. Ajdari and Prost, PNAS 88 (1991) 4468
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Introduction, Experimental, Results, Conclusions,
Outlook
Conclusions

• DNA mobility measured in 20 nm slits
• Mobility depends strongly on applied E-field
• Stop- and go movements at high fields

Outlook
Extension of dataset 5 and 50 nm high
nanoslits Theoretical understanding
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• Acknowledgements

Jan van Nieuwkasteele Daniël Wijnperlé Martin
Siekman Jeroen Huijben NanoNed Nano2Life
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Thanks for your attention!!
Questions?
(DNA in droplet)