Sorting by diffusion: An asymmetric obstacle course for continuous molecular separation

Abstract

A separation technique employing a microfabricated sieve has been demonstrated by observing the motion of DNA molecules of different size. The sieve consists of a two-dimensional lattice of obstacles whose asymmetric disposition rectifies the Brownian motion of molecules driven through the device, causing them to follow paths that depend on their diffusion coefficient. A nominal 6% resolution by length of DNA molecules in the size range 15-30 kbp may be achieved in a 4-inch (10-cm) silicon wafer. The advantage of this method is that samples can be loaded and sorted continuously, in contrast to the batch mode commonly used in gel electrophoresis.DNA fractionation ͉ Brownian motion ͉ microfabricated array T he separation of DNA fragments from restriction enzyme digests plays a central role in molecular biology (1), and there is a growing realization that new and faster methods are needed to accelerate and simplify genomic analysis. One route to this goal is the exploitation of technologies in the microfabrication industry to create miniature silicon-based devices in which sample preparation, separation, and analysis are integrated in a single microenvironment (2-5). The task is complicated by the fact that, when forced to move by a flow or by the application of an electric field, DNA molecules of different sizes all migrate at the same speed. Traditionally, a sieving medium such as a gel or a solution of polymers has been used to alter the mobility. Recently, however, Duke and Austin (6) and Ertas (7) proposed an alternative approach that takes advantage of the fact that, as the molecules migrate, they also diffuse-and this they do at a size-dependent rate. On theoretical grounds, they showed how a two-dimensional obstacle course could be constructed to sort the swift diffusers from the slow. The basic concept is to use a regular lattice of asymmetric obstacles to rectify the lateral Brownian motion of the molecules so that species of different sizes follow different trajectories through the device. A mixture of molecules injected in a fine stream would be sorted continuously.We have implemented this idea by using a microfabricated silicon array. That such a device works in principle has been demonstrated by making microscopic observations of the dynamics of fluorescently labeled latex beads and DNA molecules † † and also by the recent work of van Oudenaarden and Boxer (8) with lipids. The experiments are technically demanding, however, and the resolution of different species has not yet been achieved. Progression from a demonstration of principle to practical continuous stream sorting of molecules requires perfection of the technology. In the work reported here, our aim has been to conduct a systematic, quantitative study of the separation process, using molecules of a well-defined size and experimental conditions that are close to optimal. The close correspondence of the results with theoretical predictions permits us to predict, with some confidence, how to construct a device that will work well in practice. Ma...

Artificial Brownian motors: Controlling transport on the nanoscale

“…A micromachined silicon-chip device that transports rhodamine-labeled fragments of DNA in water has been demonstrated with a flashing on-off Brownian motor scheme by Bader et al ͑1999͒. Yet other devices are based on ideas and experimental realizations of entropic ratchets ͑Slater et al Duke and Austin, 1998;Ertas, 1998;Chou et al, 1999;van Oudenaarden and Boxer, 1999;Tessier and Slater, 2002͒ which make use of asymmetry within geometric sieve devices to transport and separate polyelectrolytes.…”

A patterned anisotropic nanofluidic sieving structure for continuous-flow separation of DNA and proteins

“…While significantly more efficient than gels in terms of separation speed and resolution, these regular sieving structures still largely resemble gels in the sense that separation is achieved by repeated sieving through multiple, identical "pores". More recently, microfabricated asymmetric obstacle courses were used to continuously separate macromolecules either by diffusion 16,17 or by asymmetric bifurcation of laminar flow 18 . This later work took advantage of asymmetric interaction of macromolecules with the device geometries, which enabled these novel separation mechanisms.…”

Brownian Motion of Boomerang Colloidal Particles

“…Our experimental observations show that the mean displacements are biased towards the center of hydrodynamic stress (CoH), and that the mean-square displacements exhibit a crossover from short time faster to long time slower diffusion with the short-time diffusion coefficients dependent on the points used for tracking. A model based on Langevin theory elucidates that these behaviors are ascribed to a superposition of two diffusive modes: the ellipsoidal motion of the CoH and the rotational motion of the tracking point with respect to the CoH.Brownian motion as a general phenomenon of the diffusion processes has inspired extensive research [1][2][3][4][5][6][7][8][9][10][11][12] due to both its interesting physics and practical applications such as in microrheology [13][14][15][16], selfpropelled microswimmers [17] and particle and molecular separation [18][19][20]. Inspired by the diverse geometric shapes of biological macromolecules, Brenner and others have extended the hydrodynamic theory of Brownian motion to particles with irregular shapes [21][22][23][24][25][26].…”