Friday, March 09, 2007

New Bedside- Diagnostics Tool

Can microfluidics turn out cheap and powerful alternatives to microarrays?

By Peter Fairley

Customizable particles: These capsule-shaped particles of plastic, roughly a quarter of a millimeter long, are both unique and cheap to produce. Decoding the pattern of dots on each particle reveals the identity of single-stranded DNA probes bound throughout the porous particles’ other half. Credit: Daniel Pregibon

By simultaneously scanning for hundreds or thousands of genes or proteins, geneticists can now detect whether a patient has a propensity toward certain forms of cancer. (See, for example, "TR10: Epigenetics.") However, they commonly do this using DNA or protein microarrays that are costly to produce and require expensive detection equipment, limiting their application. In today's issue of the journal Science, an MIT chemical-engineering doctoral student and his colleagues at MIT and Harvard Medical School offer an elegant cost-cutting solution.

Daniel Pregibon's technique is a one-step process for producing capsule-shaped plastic particles, each packing a graphical ID and one or more biological probes that fluoresce when they detect a specific sequence of DNA or protein in a test sample. The result is a cheap yet sensitive system for producing diagnostics with as many as one million unique particles capable of detecting more than a million distinct biological targets. "For bedside diagnostics, you need to do a lot of tests for a reasonable price," says Pregibon. "With the current technologies, I don't know that the price will ever be low enough. With our system, we think it can."

Microarrays are expensive because their manufacture requires a complex, multistep process, and many designs for producing coded particle probes analogous to Pregibon's suffer from the same drawback. Pregibon's Science paper demonstrates a simpler method for producing coded particles proposed last year by coauthor Patrick Doyle, an MIT chemical-engineering professor and Pregibon's advisor. (See "Printing Press for Biosensors.") Doyle's printing press is a microfluidic device that produces multifunctional particles in plastic by exploiting laminar flow--the tendency of micrometer-width fluid streams to remain distinct rather than mixing.

To produce a basic particle, Doyle's device flows two solutions containing molecular building blocks for the plastic polyethylene glycol down a 200-micrometer-wide channel etched in a silicon-polymer block, where they form parallel, 100-millimeter-wide streams. A 30-millisecond pulse of ultraviolet light projected through a stencil stimulates polyethylene-glycol precursors in both streams to solidify into a single particle, incorporating domains from each stream. Pregibon used this particle press to turn out unique biosensor particles by doping one of the precursor streams with a DNA biotag. He gave each particle a recognizable fingerprint by projecting patterns of dots on the second stream of precursors, producing particles with a unique pattern of holes that is visible with a low-magnification microscope.

UC Berkeley chemist and biosensor developer Jay Groves calls the one-step production system a "clever" step toward low-cost diagnostics. "The idea of inputting only a few liquid reagents into a device that creates indexed arrays of particles ... seems powerful to me," he says.

Pregibon's particle probes may also be more sensitive than existing microarrays and particles because they are porous, rather than solid. With solid microarrays and particles, target molecules such as DNA from a patient's blood bind only on the probe's surface. In contrast, target molecules can diffuse into the porous polyethylene glycol of Pregibon's particles, increasing the number of target molecules that bind and therefore producing a more intense fluorescent signal. "We're able to gather a lot more signal that way," he says.