DNA Electrophoresis on Two-dimensional Arrays of SiO 2 Beads
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DNA Electrophoresis on Two-dimensional Arrays of SiO2 Beads Young-Soo Seo, V.A. Samuilov, J. Sokolov, M. Rafailovich, D. Gersappe, B. Chu1 Department of Materials Science and Engineering and 1Department of Chemistry, SUNY at Stony Brook, NY 11794 ABSTRACT A novel approach of fabricating 2-D arrays of SiO2 beads on a Si surface using the Langmuir-Blodgett (LB) technique is reported. The corrugated surfaces were tested as a separation media for surface electrophoresis of DNA molecules. The measured electrophoretic mobility for λ -DNA is only 20% slower than previously measured on a flat Si wafer. This indicates that the separation mechanism is due to surface friction rather than biased reptation as reported by Tinland in the three dimensional Silica bead matrix where the mobility is two orders of magnitude smaller. INTRODUCTION Electrophoresis has become the most widely used analytical technique today to separate DNA. In solution, DNA fragments cannot be separated under an applied electric field since the electrophoretic mobility of a DNA molecule is related to its charge to friction ratio, a quantity that is independent of chain length. Separation of DNA therefore requires the use of some type of sieving matrix. Current electrophoretic methods assume that only environments with topological constrictions such as crosslinks in a gel [1,3] or entanglements in a polymer melt or solution [2] are suitable as matrices for separation of DNA by length. Since the gel structure can be very complex, recently Meistermann and Tinland [4] and Craighead [5] have proposed new methods for DNA separation that rely on rigid silica matrices with well defined porosity or micropatterned constraints. In order to effectively model the mobility of DNA in these media it is also important to understand the effect of interactions with the silica surface on the DNA mobility. We have recently shown that it is also possible to separate DNA fragments, in the absence of topological constraint, simply by observing the mobility in a constant electric field on a flat native oxide covered Si wafer [6]. For a fixed surface attraction, shorter chains will maximize their entropy and have a larger number of loops or unadsorbed segments, while longer chains will exploit the energetic gains on adsorption and have more trains or adsorbed segments [7]. Consequently, if an electric field were applied in the plane of the surface, the response of the molecule is a function of its conformation on the surface, which is length dependent. In order to separate the effects of confinement form of the surface interaction, we designed a two dimensional analogue of the same silica bead matrix using in ref. 4 where the confinement in the Z direction is removed. In this paper we report on the technique using an ordered monolayer array of Silica beads robustly anchored onto a Si surface and the effect of the surface corrugations on the mobility of λ -DNA. . EXPERIMENTAL PROCEDURE We found that LB technique was most effective in producing highly ordered arrays of silica beads. N
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