Numerical model for DNA loading in microdevices: Stacking and autogating effects

Abstract

Many electrophoresis-based DNA sequencing and genotyping microdevices rely on field-driven effects to load and preconcentrate the sample. A quantitative model is developed for a broad class of electrophoresis-based microfabricated sample injectors. Quantitative predictions of DNA preconcentration are compared with experimental data and are shown to qualitatively reproduce the detailed time-evolving sample distribution in the injector. The model provides practical guidance on device and protocol design, in order to optimize this critical aspect of microfluidic devices.

AOTF-based multicolor fluorescence detection for short tandem repeat (STR) analysis in an electrophoretic microdevice

“…While 5 lL sample aliquots were used for the majority of this work, the intensity of the product peaks was observed to scale with the amount of sample initially loaded onto the spin-column, increasing linearly from 1 to 10 lL. Consistent with previous reports relating the injection conditions to the relative concentrations of injected DNA fragments, 20 it was observed that a 30 s injection at 500 V cm −1 resulted in increased product being introduced into the analysis channel. This was due to stacking at the DNA-buffer interface.…”

Scaling of nucleic acid assays on microelectrophoresis array devices: High‐dynamic range multi‐gene readout from less than ten transcripts

“…1). The first of these [1] is at the “gel” interface in the sample well (analogous to CAE). The second [2,7,8] is at the parting intersection of the loading arm and the separation channel, where a second conductivity discontinuity can be induced using ion depletion with pre-loading currents and low-conductivity buffer.…”

“…Even without high injection voltages Aborn [3] showed that careful conditioning of the first and second interfaces using pre-loading currents could be used to achieve routine injections into a 768-lane microdevice sequencer with a factor of eight reduction in required sample mass relative to contemporary CAE Sanger sequencing. Stacking and autogating effects at the first interface, which confound the experimental reproducibility, were reproduced accurately by a numerical model [1]. In practice, the uniform conditioning of both the first and second stacking interfaces is among the very most important aspects needed to get uniform results out of an cross-injected array microdevice [3].…”

“…Micromachined glass microdevices at various complexity were fabricated as described previously [1–5]. Plates of 1.1-mm-thick alumina silicate glass (Corning 1730, Corning Co., Corning NY) were patterned by photolithography, HF etching and laser drilling.…”

“…Channel surfaces were coated with linear polyacrylamide (LPA) using a modified Hjerten procedure. More details can be found in the cited references [1–5]. Traditional injections used platinum electrodes of 0.5-mm diameter.…”