Image courtesy of Dr. Patrick Doyle, Massachusetts Institute of Technology, Cambridge, Massachusetts.Like coupon-cutting bargain hunters, many researchers prefer to stretch their grant money with cost-effective laboratory techniques. Microarray chips can be expensive to produce and are used only once. Pregibon et al. designed particles for high-throughput analysis of genes and proteins in solution that can be produced in house. They report two-dimensional microparticles that contain both oligonucleotide probes and barcodes in a recent article in Science.
The authors used polyethylene glycol to create microparticles. The particles functioned as transparent films that could be viewed with standard fluorescent microscopy. Half of each particle contained an orientation indicator and a dot-encoded barcode capable of identifying over one million entities. The other half contained a site for acrylate-modified fluorescent probes, which were covalently attached by polymerization. The authors conjugated the two halves together with bursts of ultraviolet light. The resulting pill-shaped particles were 180 to 270 
m long, 90 m wide and approximately 30 m thick. This system allowed the authors the flexibility to probe for one gene with many microparticles or thousands of genes with individual microparticles.
The authors tested three sets of particles with oligonucleotide probes in four different solutions containing combinations of probe targets. The probes fluoresced only in the presence of their targets. Fluorescence accumulated on the outer edges of particles, but also spread to their centers, suggesting that target molecules diffused inside the gel-like microparticles, according to the authors. The microparticles had high detection sensitivity: without any amplification, the authors detected 500 attomoles (10-18 moles) of DNA. They also successfully tested microparticles containing several probes (striped across the probe region) and gradients of the same probe.
To enable high-throughput analysis of solutions with multiple probes, the authors created a scanner. They placed solutions containing target DNA that had been incubated with microparticle probes into a chamber that flowed into a 90 m-wide channel, allowing only one particle in at a time. A camera mounted on an inverted fluorescence microscope captured images as microparticles flowed through the channel to a designated detection region. Fluorescence intensity was scanned from each image. Prolonged peaks in fluorescence intensity indicated target detection by microparticle probes, whereas peaks and valleys of fluorescence in the barcode region could be translated to identify each probe.
Although the authors tested oligonucleotide probes in this study, the microparticle probe region could be covalently attached to binding proteins and enzymes, allowing high-throughput proteomic detection. Therefore, the authors' design enables the mixed detection of multiple genes, proteins and metabolites in a single solution. Because particle generation and incubation required only several minutes each and detection used standard fluorescence microscopy, the authors believe that their approach will aid in patient diagnostics.