Quantitative Microfluidic Separation of DNA in Self-Assembled Magnetic Matrixes

Abstract

We present an experimental study of the microfluidic electrophoresis of long DNA in self-assembling matrixes of magnetic bead columns. Results are presented for the rapid separation of lambda-phage, 2lambda-DNA, and bacteriophage T4 DNA, where separation resolutions greater than 2 between lambda and T4 are achieved in times as short as 150 s. The use of a computer-piloted flow control system and injection results in high reproducibility between separations. We compare the experimentally measured mobility and dispersion with an exactly solvable lattice Monte Carlo model. The theory predicts that the mean velocity scales linearly with the field, the band broadening scales with the inverse of the field, and the resolution is independent of the field for intermediate fields-all of which are in accord with the experimental results. Moreover, reasonable quantitative agreement is achieved for band broadening for longer DNA (2lambda and T4) when the average postengagement time is measured experimentally. This work demonstrates the possibility of achieving fast microfluidic separation of large DNA on a routine basis.

Magnetic bead handling on-chip: new opportunities for analytical applications

“…Figure 11d is a separation of k-phage DNA concatemers at a field of 3.2 V/cm at conditions identical to those in Figure 11c. Experimental separations using the SPS matrix have been combined with theoretical modeling and, recently, computer-piloted flow control and injection of the experiment resulted in a quantitative and reproducible separation of long DNA by an SPS matrix (Minc et al 2004). …”

Collision of a DNA Polymer with a Small Obstacle

“…The first experimental work to separate O[10-100 kbp] DNA by length using hooking collisions was by Doyle et al 3 Followup work was performed in slightly more dense obstacle courses at higher fields 21 and in extremely dense courses, 22 though as the obstacle density increases, the separation mode switches from unhooking to pore sieving characteristic of gels. Motivated by these experiments, macroscale separation models were proposed to explain the dependence of the average mobility and dispersivity in an obstacle array on the DNA length.…”

Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning

“…10,11 Collisions with microfabricated obstacles have also been shown to linearize DNA. [12][13][14] But a very practical method for simple, inexpensive, high-throughput devices is using field gradients to deform the molecules. 15,16 In DLA devices, the molecules are typically stretched by field gradients in microcontractions.…”