Dynamic DNA Hybridization on a Chip Using Paramagnetic Beads

Abstract

Dynamic DNA hybridization is presented as an approach to perform gene expression analysis. The method is advantageous because of its dynamic supplies of both DNA samples and probes. The approach was demonstrated on a microfluidic platform by incorporating paramagnetic beads as a transportable solid support. A glass chip was fabricated to allow simultaneous interrogation of eight DNA target samples by DNA probes. DNA targets were immobilized on beads via streptavidin-biotin conjugation or base pairing between oligonucleotide residues. The DNA/bead complex was introduced into the device in which hybridization took place with a complementary probe. The hybridized probe was then removed by heat denaturation to allow the DNA sample to be interrogated again by another probe with a different sequence of interest. A pneumatic pumping apparatus was constructed to transport DNA probes and other reagents into the microfluidic device while hydrostatic pumping was used for the introduction of paramagnetic beads with samples. After investigating three types of paramagnetic beads, we found Dynabeads Oligo(dT)25 best suited this application. Targets on the beads could be sequentially interrogated by probes for 12 times, and the hybridization signal was maintained within experimental variation. Demonstration of specific hybridization reactions in an array format was achieved using four synthesized DNA targets in duplicate and five probes in sequence, indicating the potential application of this approach to gene expression analysis.

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

“…Dynamic DNA hybridization was demonstrated by immobilizing DNA targets on magnetic beads via streptavidin-biotin conjugation or base pairing between oligonucleotide residues (Fan et al 1999). The DNA/ bead complex was introduced into the device, after which, hybridization took place with a complimentary probe.…”

Optically programming DNA computing in microflow reactors

“…A practical implementation is under construction to ascertain the limits posed by these and other potential problems and will be reported elsewhere. Some basic experiments on hybridization to beads in microflow reactors have been reported (Fan et al, 1999), indicating that DNA hybridization in flow can indeed be more rapid and efficient than in bulk solution.…”

PEGylation of magnetic poly(glycidyl methacrylate) microparticles for microfluidic bioassays

“…The boom in microfluidics, which began about 20 years ago, brought with it ideas about incorporating magnetic particles into various microfluidic devices [6][7][8][9] . This offers additional benefits compared to batchtype processes, such as reduced sample and reagent volumes, faster reaction times, the possibility to engineer the design of a chip to control particle mobility, and integration of various processes into a unified system 5 .…”