Motion of single long DNA molecules through arrays of magnetic columns

Abstract

We present a videomicroscopy study of T4 DNA (169 kbp) in microfluidic arrays of posts formed by the self-assembly of magnetic beads. We observe DNA moving through an area of 10 000 microm(2), typically containing 100-600 posts. We determine the distribution of the contact times with the posts and the distribution of passage times across the field of view for hundreds of DNA per experiment. The contact time is well approximated by a Poisson process, scaling like the inverse of the field strength, independent of the density of the array. The distribution of passage times allows us to estimate the mean velocity and dispersivity of the DNA during its motion over distances long compared to our field of view. We compare these values with those computed from a lattice Monte Carlo model and geometration theory. We find reasonable quantitative agreement between the lattice Monte Carlo model and experiment, with the error increasing with increasing post density. The deviation between theory and experiment is attributed to the high mobility of DNA after disengaging from the posts, which leads to a difference between the contact time and the total time lost by colliding. Classical geometration theory furnishes surprisingly good agreement for the dispersivity, while geometration theory with a mean free path significantly overestimates the dispersivity.

Collision of a DNA Polymer with a Small Obstacle

“…[23][24][25] In a broader context, similar disentanglement processes occur in polymers flowing over a polymer brush, 45 DNA separations using dilute neutral polymers as a sieving medium, 46 and flows of polymer solutions. 47 Finally, in direct linear analysis, 48,49 DNA collisions with posts may be a useful way of preconditioning DNA configurations before attempting to completely stretch DNA in an elongational flow [48][49][50] or electric field.…”

“…While here we only considered DNA collision with a single post, the various classes of collisions we found should still be present when examining post arrays [12][13][14]25,44 and be considered in future modeling efforts. [23][24][25] In a broader context, similar disentanglement processes occur in polymers flowing over a polymer brush, 45 DNA separations using dilute neutral polymers as a sieving medium, 46 and flows of polymer solutions.…”

“…U and J collisions are the types of ideal collisions described in previous studies. 7,12,25,27 The main distinction is that U collisions (Figure 3a) have nearly symmetric arms so that arm length fluctuations are important to consider when modeling the unhooking time. W collisions ( Figure 3c) are collisions that result in entangled configurations upon impact with the obstacle (see Figure 3c, inset).…”

Nanofluidic structures for single biomolecule fluorescent detection

“…[33][34][35][36] By fixing one end of a fluorescently labeled DNA strand in an elongational flow, it is also possible to observe inhomogenous hydrodynamic stretching, which is a theoretically interesting phenomenon. [36][37][38] A single DNA strand may be visualized as it interacts with pillars in a microfluidic slit, [39][40][41] or as it escapes from a deep well into a thin slit, and it is hoped that the knowledge gained from such studies will lead to faster methods of lab-on-chip DNA sorting. [42][43][44][45][46][47][48] Finally, sequence information may even be obtained from stretched molecules through restriction site mapping or motif mapping using hybridized probes.…”

Microfluidic sorting and multimodal typing of cancer cells in self-assembled magnetic arrays

“…Under moderate external fields (typically 10-30 mTesla), these interactions overcome Brownian motions and induce the formation of chains oriented in the field direction (20). When the suspension is enclosed in a slit-like microchannel (Hele-Shaw cell) with its main walls perpendicular to a uniform field, an array of columns is formed with a hexagonal order on short distances and glass-like order on long distances (21). The average center-to-center distance between two columns, and the distribution of pore sizes and column diameters, result from a complex interplay between the thermodynamics of beadbead interactions, the kinetics of bead chains formation, and the interactions of the chains with the microchannel's walls.…”