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Why study DNA Kinetics? DNA chip technology (Microarrays…) DNA templated nanostructures

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Why study DNA Kinetics? DNA chip technology (Microarrays…) DNA templated nanostructures

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  1. 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

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

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

  4. Principle of Distance Measurement: Förster Resonance Energy Transfer (FRET) Decay rate Constant: , Energy Transfer   Thin Film:  bET d4 Thick Film:  bET d3 • For this experiment d2/d1  200 nm/10 nm= 20 --> Thick Film • Distance Related to Fluorescence Intensity by: d  F1/3

  5. 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. Freely Jointed Chain (FJC) <re-e>2= Na2= Lca, Lc= Na *Evan Evans, 2002 (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

  7. 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

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

  9. Debye Length, LD~3 nm, LD= єkT/ q2ns ,ns= electrolyte conc. -->~107 V/cm --> DNA “Lies Down” Ag/Cl LD max max Vapplied>0 Single Crystalline Sapphire wafer

  10. Results:

  11. Results: Double Layer Formed I  Ion Movement DNA Up

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

  13. ?s?

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