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Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface
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10.1063/1.3366725
/content/aip/journal/apl/96/12/10.1063/1.3366725
http://aip.metastore.ingenta.com/content/aip/journal/apl/96/12/10.1063/1.3366725

Figures

Image of FIG. 1.
FIG. 1.

(a) Molecular visualization of ssDNA in water film on PEG-silane grafted surface. The surface lies along the -plane. The snapshot was rendered with (Visual Molecular Dynamics, Ref. 23). The red ball is the oxygen atom, white is the hydrogen atom, blue is the nitrogen atom, cyan is the carbon atom, and tan is the phosphorus atom; (b) Structure of PEG-silane molecule; (c) Density plots of water and PEG for the thick water film; (d) Density plots of water and PEG for the thin water film. For the examples considered here, water density was not significantly influenced by the DNA type.

Image of FIG. 2.
FIG. 2.

Temporal variation of the -position of the monomers in ssDNA and the typical DNA conformation in equilibrium state: (a) , long 12-base ssDNA. Red and blue lines represent the and -end monomers, respectively. The green lines are the middle monomers in the DNA; (b) , short 6-base ssDNA; (c) water density of thick film; (d) , long 12-base ssDNA; (e) , short 6-base ssDNA; (f) water density of thin film.

Image of FIG. 3.
FIG. 3.

Comparison of the interaction energy between monomer in ssDNA and surface: (a) total interaction; (b) LJ interaction; (c) electrostatic interaction. -axis is the index of the monomer in ssDNA.

Tables

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Table I.

Diffusion coefficient of ssDNA .

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/content/aip/journal/apl/96/12/10.1063/1.3366725
2010-03-24
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Water film thickness-dependent conformation and diffusion of single-strand DNA on poly(ethylene glycol)-silane surface
http://aip.metastore.ingenta.com/content/aip/journal/apl/96/12/10.1063/1.3366725
10.1063/1.3366725
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