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Dissimilar Kinetic Behavior of Electrically Manipulated Single- and Double-Stranded

DNA Tethered to a Gold SurfaceUlrich Rant,* Kenji Arinaga,* Marc Tornow,* Yong Woon Kim, Roland R. Netz, Shozo Fujita, Naoki Yokoyama, and Gerhard

Abstreiter* *Walter Schottky Institute and Physics Department, Technical University

Munich, 85748 Garching, Germany; and Fujitsu Laboratories, Atsugi 243-

0197, Japan

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Why study DNA Kinetics?•DNA chip technology (Microarrays…)•DNA templated nanostructures•Molecular Mechanics•DNA computing•Structure of Self-Assembled Monolayers•Theoretical Studies

Development of Novel Microarrays with active control

This experiment studies ssDNA & dsDNA stiffness effects on kinetics in an attractive or repulsive E-Field

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Setup:Side View

Single Crystalline Sapphire wafer

10 nm, Ti40 nm, Pt

200 nm, Au

48-mer (~16 nm), ds,ssDNA

3’

5’

Cy3 (565 nm)

Optical Fiber

Ag/Cl

Vapplied

Solution:10 mM Tris, pH=7.3(Low Salinity)

0.5 mm

2 mm

Argon Ion Laser

(515 nm)

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Principle of Distance Measurement: Förster Resonance Energy Transfer (FRET)Decay rate Constant: , Energy Transfer

Thick Film: bET d3

Thin Film: bET d4

For this experiment d2/d1 200 nm/10 nm= 20 --> Thick FilmDistance Related to Fluorescence Intensity by: d F1/3

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Modeling:-Standard model: charged particles connected with elastic bonds-ssDNA modeled as Freely Jointed Chain (FJC)-does not mention model used for dsDNA

Some Different Models Types:

•Freely Jointed Chain (FJC)Fixed Bond Length

•Freely Rotated Chain (FRC)Fixed Bond Length & Angle

•Worm Like Chain (WLC)Continuous Bending of Polymer

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Freely Jointed Chain (FJC)

(Same result as mean quadratic displacement of freely diffusing particle, same underlying process) Though FJC is very simplistic, it can provide accurate results if Kuhn Length, a, is adjusted properly

<re-e>2= Na2= Lca, Lc= Na

*Evan Evans, 2002

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Worm Like Chain (WLC): The WLC is generally used to model a stiff polymer (like dsDNA). In contrast to Freely Jointed Chain, which is flexible between discrete segments, it is continuously flexible.

b is the persistence length, or how long a segment of the chain will have tangent vectors all pointing in nearly the same direction. This is a measure of the bending energy.

LC = Na = Contour Length *Evan Evans, 2002 & Netz, Neutral and Charged Polymers at Interfaces

=

1/21/07 8Single Crystalline Sapphire wafer

3’

5’

Ag/Cl

Vapplied=0

Solution:10 mM Tris, pH=7.3(Low Salinity)

1/21/07 9Single Crystalline Sapphire wafer

Ag/Cl

Vapplied>0

Debye Length, LD~3 nm, LD= єkT/ q2ns ,ns= electrolyte conc.

LD

maxmax

-->~107 V/cm --> DNA “Lies Down”

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Results:

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Results:

I Ion Movement

Double Layer Formed

DNA Up

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Results:

ssDNA “Reeled In”

Upper part of dsDNA pushed by torque on lower part

Thermal Motion Dominates

E - Field Dominates

c

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?s?