DNA size separation using artificially nanostructured matrix

Abstract

We have demonstrated two types of size separation of biomolecules using a nanostructured matrix artificially fabricated using electron-beam lithography: sieve-type separation using a regular pillar array structure and size exclusion chromatography (SEC) type separation using a structure with narrow and wide gaps. With these devices, samples of double-stranded DNA molecules (2, 5, and 10 k base pairs) were clearly separated into bands; smaller molecules eluted earlier in the sieve type while they eluted later in the SEC type. The nanostructured matrix enables various types of molecular separation by changing the design of the nanostructure. Moreover, it should be easy to integrate the matrix with other biomolecular fluidic devices because it does not require a filling medium.

Electrophoretic collision of a DNA molecule with a small elliptical obstacle

“…The answer to this question depends on the separation mechanism. In size-exclusion [14] and Brownian ratchet [15][16][17][18] devices, the underlying separation mechanisms do not require the DNA to form a hairpin. As a result, it is sensible that successful separations by these mechanisms use high-aspect ratio elliptical obstacles [14][15][16][17][18].…”

“…In size-exclusion [14] and Brownian ratchet [15][16][17][18] devices, the underlying separation mechanisms do not require the DNA to form a hairpin. As a result, it is sensible that successful separations by these mechanisms use high-aspect ratio elliptical obstacles [14][15][16][17][18]. Indeed, the obstacles in the Brownian ratchet device are tilted with respect to the field [15][16][17][18], which we saw further reduces the hooking probability.…”

“…Elliptical obstacles have also been used in the context of electrophoretic separations. For example, size exclusion [14] and Brownian ratchet [15][16][17][18] separation devices feature high-aspect ratio obstacles. In these devices, the ''short'' side of the obstacle is commensurate with the radius of gyration of the DNA.…”

Chemistry in nanochannel confinement

“…For example, photolithography can be used to define nanosized spaces between pillars [76], or silicon or aluminum can be treated electrochemically to achieve a porous layer with random but (if manufactured under the right conditions) vertically aligned pores, with typical pore sizes in the range 2-10 nm for porous silicon [77] and 30-70 nm for porous alumina [78]. Although it is not a trivial task to properly interface these channels to achieve fluid flow through them unless they are designed as membranes with open space on either side of each pore, these porous layers may also be useful for the studies described in this paper, and can actually be designed such that the processes that occur in the pores can be monitored with integrated analysis tools in situ (see below).…”

Fabrication and electroosmotic flow measurements in micro- and nanofluidic channels

“…Reducing the cross-section of microfluidic channels down to the nanometer scale is attractive for detecting, transporting, manipulating and sorting single molecules such as DNA (Foquet et al 2003(Foquet et al , 2004Turner et al 1998). Microfluidic interfaces to nanosized pores, pillars or channels have proven to be useful to separate and fractionate DNA Cao et al 2002a, b;Chou et al 1999;Baba et al 2003). Having a stretched DNA molecule in a nanochannel presents an attractive perspective for linear analysis of DNA (Tegenfeldt et al 2002(Tegenfeldt et al , 2004.…”