1. 1/21/071 Dissimilar Kinetic Behavior of Electrically Manipulated Single- and Double-Stranded DNA Tethered to a Gold Surface Ulrich 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

2. 1/21/072 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

3. 1/21/073 Setup: Side View Single Crystalline Sapphire wafer 10 nm, Ti 40 nm, Pt 200 nm, Au 48-mer (~16 nm), ds,ssDNA 3’ 5’ Cy3 (565 nm) Optical Fiber Ag/Cl V applied Solution: 10 mM Tris, pH=7.3 (Low Salinity) 0.5 mm 2 mm Argon Ion Laser (515 nm)

4. 1/21/074 Principle of Distance Measurement: Förster Resonance Energy Transfer (FRET) Decay rate Constant:, Energy Transfer   Thick Film:  b ET d 3 Thin Film:  b ET d 4 For this experiment d 2 /d 1  200 nm/10 nm= 20 --> Thick Film  Distance Related to Fluorescence Intensity by: d  F 1/3

5. 1/21/075 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

6. 1/21/076 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 2 = Na 2 = L c a, L c = Na *Evan Evans, 2002

7. 1/21/077 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. L C = Na = Contour Length *Evan Evans, 2002 & Netz, Neutral and Charged Polymers at Interfaces =

8. 1/21/078 Single Crystalline Sapphire wafer 3’ 5’ Ag/Cl V applied =0 Solution: 10 mM Tris, pH=7.3 (Low Salinity)

9. 1/21/079 Single Crystalline Sapphire wafer Ag/Cl V applied >0 Debye Length, L D ~3 nm, L D = єkT/ q 2 n s, n s = electrolyte conc. LDLD  max  max -->  ~10 7 V/cm --> DNA “Lies Down”

10. 1/21/0710 Results:

11. 1/21/0711 Results: I  Ion Movement Double Layer Formed DNA Up

12. 1/21/0712 Results: ssDNA “Reeled In” Upper part of dsDNA pushed by torque on lower part Thermal Motion Dominates E - Field Dominates cc

13. 1/21/0713 ?s?