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Figure 3 (a) Fluoresence intensity for  -Hind III Digest as a function of time in a confocal microscope positioned at a fixed distance from the injection point (5-10 mm). Applied electric field = 5 V/cm. (insets) -, T2, and S. Pombe DNA. The labeled peaks correspond to -Hind III Digest (1-124 bp, 2-564 bp, 3-2,027 bp, 4-2,322 bp, 5-4,361 bp, 6-6,557 bp, 7-9,416 bp, 8-23,130 bp), -DNA (48.5 kbp), T2 DNA (164 kbp), or chromosomal S. Pombe DNA (1-3.5 Mbp, 2-4.7 Mbp, and 3-5.7 Mbp). (b) Mobility of double stranded DNA,  , as a function of the number of base pairs, N. The dashed line at the top of the figure corresponds to the mobility of free draining DNA. Inset: Fractional resolution versus number of base pairs. The dashed line indicates (t/t) = 0.018 as a guide line. |
Figure 1 Surface image of Ni nanopattern on Si wafer using SEM. Inset (a) shows schematic etching process fabricating Ni nanopattern from surface micelle array. Inset (b) Topography of Ni nanopattern was measured using SEM where the height of the dots was 11-13 nm and center-to-center distance, 250-300 nm.Inset (c) A chemical map of the surface was obtained by using fluorescence with elemental dispersion analysis (EDAX) where the Ni peak intensity was much higher when a electron beams indicated by circle are focused on the Ni dots. thus the bare wall is more attractive than the patch. (g) SPM image in air of a  -DNA chain adsorbed from buffer solution onto the nano-patterened surface described in Figure 1. |
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Figure 2 Mobility of DNA calculated by MD simulations. (A) Plot of mobility of DNA on a hexagonal patch surface where the patches are less attractive than the bare wall. (B) Plot of the mobility of DNA on a square patch surface where the patches are more attractive than the bare wall. In (A) the dimensionless electric field was fixed at E = 0.02 and in (B) E = 0.25 |
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Figure 4 Surface electrophoresis experimental setup
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Surface Electrophoresis(Chu):
The project is a collaborative effort among the research groups of D. Gersappe, M. Rafailovich, and B. Chu. Surface electrophoresis is a new approach to electrophoresis that takes advantage of unique surface characteristics to separate DNA fragments over a wide range from several hundreds of base pairs (bps) to genomic megabase pair sizes without substantial loss of resolution. It provides the possibility to satisfy specific applications by using engineered reusable surfaces, instead of conventional polymer separation matrices. [Pernodet, N. et al. Phys. Rev. Lett. 2000, 85, 5651].
A possible scheme is to introduce a nanopattern on the substrate surface [Fig 1] where the effects on chain conformation can be amplified by partial adsorption from tuning the relative interaction strength of the polymer chains with surface domains [Seo, Y. et al. Nano Lett. 2004, 4, 659.] Both molecular dynamics simulations [Fig 2] and experimental studies [Fig 3] were carried out for a pattened surface, using setup shown in Fig 4.
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