Biochips Part 2

Breaker's invention opens the way for future RNA chips capable of revealing the molecular composition of complex mixtures― like blood serum and industrial waste―far more comprehensively than current biochips.
RNA Superchip
"Advanced versions of our RNA biochip could be used for many different targets like drugs, toxins and metabolites, as well as proteins and nucleic acids," Breaker says. "They should be able to detect almost anything that RNA can be made to bind to."
Furthermore, the preliminary success of Breaker's work "ushers in a new era of what might be termed 'active arrays'," declares Gerald Joyce, a molecular biologist at the Scripps Research Institute in La Jolla, CA. Indeed, it should be possible to engineer RNA switches to do "far more extraordinary things" than target identification, Breaker says. Regulating gene expression is one example.
Another benefit of RNA switches is their ability to withstand the sometimes unpredictable and harsh environment outside the lab. Breaker compares them with a protein biochip and says that the latter, if accidentally heated, fries like an egg. The proteins unfold and "you can never put the complex structures back together again," he says.
Breaker's RNA switches have been engineered to refold back to their original form after heating. "This snap-back character will give RNA biochips a considerable advantage for use in more exotic test environments," Breaker claims.
Protein Chips
When proteins misbehave, they can destroy our health in myriad ways, from amyloid proteins that gum up the brains of Alzheimer's patients, to proteins that cause runaway cancer-cell growth. Battling disease more effectively means getting a better grip on how proteins work and interact-and fail. The most important emerging tools in reading the vast protein library are micro-arrays―small chips containing thousands of protein samples that can be analyzed quickly and cheaply. "This is where people will get answers about how disease develops, how drugs work, and how to find new drugs," says Peter Wagner, chief technical officer of Zyomyx, a Hayward, CA-based protein-chip startup.
Zyomyx has nearly a dozen competitors, including Large-scale Proteomics, Ciphergen Biosystems, Packard BioScience, and Phylos. The industry's first products are expected on the market in a year, and while technologies vary, the new biochips are generally two-dimensional grids of proteins or protein fragments attached to a solid support.
When the protein micro array is exposed to bio chemicals or solutions of other proteins, some of those molecules will stick and some will wash off; various markers, such as fluorescent tags, can identify the ones that stick. Molecules that adhere strongly to specific proteins are valuable leads in the search for new drugs, because that binding ability is what makes pharmaceuticals effective. And for diagnostics, measuring abnormally high amounts of telltale proteins in a blood sample using these biochips could be a fast method for early detection of heart attacks and cancer.
But making a protein chip is far more vexing. While DNA is pretty sturdy, proteins are shrinking violets. Proteins are exquisitely folded strings of subunits called amino acids, and a lot of what proteins do depends on the precise three-dimensional pattern that the string folds into. Outside a narrow range of environmental conditions, proteins will "denature"―the amino-acid chain will lose its three-dimensional structure, collapsing like a pile of overcooked spaghetti. In making micro arrays, researchers have to keep the proteins in a watery solution at just the right temperature the whole time.
Protein micro arrays could make it possible to quickly and cheaply test thousands of protein samples. To demonstrate that they could pick a protein of interest out of a vast array, researchers at Harvard University's Center for Genomic Research prepared a 2.5 cm by 7.5 cm slide that held 10,799 samples of one protein and a single dot of another protein. They then exposed the array to two compounds (one fluorescently tagged blue, the other red); the blue-labeled compound selectively attached to the first protein and the red-labeled compound to the second protein.
The U.S. Department of Energy said its Sandia National Laboratories unit, with operations in Livermore, has signed a cooperative research and development agreement with Celera Genomicsi and Compaq Computer Corp. The goal of the project is to develop next-generation software and computer hardware solutions that will be specifically designed for the demands of computational biology as well as a full range of life sciences applications. The three entities will work together to increase computing capability with the goal of achieving 100 trillion operations per second.
Testing Goes Whole Cell
DNA chips―fingernail-sized micro arrays that can analyze thousands of genes at once―have had been around for the last five years. But the new cell micro array takes the idea of massive parallel analysis in a new direction.
David Sabatini and his research team began by printing an array of about 200 DNA samples―each corresponding to a particular gene―onto a glass slide. The slide was then placed in a culture of mammalian cells, which adhered to and covered it. (With conventional DNA chips, genes, rather than living cells, are applied to the DNA on the chip surface.)
The cells that came into contact with DNA absorbed it. By dividing, they formed distinct cell clusters, each manufacturing the particular protein encoded in the absorbed DNA. (Genes are recipes for proteins.) The remaining cells surrounded these clusters, acting as controls. The result is a living array of gene expression, giving researchers a unique test bed in which to experiment with gene and protein behavior.
The Zyomyx Approach
Zyomyx is developing technologies, which close the gap between protein biochemistry and micro-fabricated devices, resulting in a broad variety of miniaturized, protein biochip architectures and BioMEMS devices containing fully functional proteins. Zyomyx biochips are the result of the integration of proprietary advancements in the areas of advanced materials, protein immobilization, and high-resolution protein dispensing and ultra-sensitive detection technologies. A transition from 'solution-based' to 'surface-based' assays is imperative to future developments in highly parallel, high-throughput protein analysis.
Zyomyx believes that their core technology platform can be used to develop protein biochips to innovate many facets of protein characterization. These include protein discovery, protein profiling, structure determination, activity measurements, as well as the assessment of protein-protein and protein-small molecule interactions. These biochips will be differentiated by architecture, the types of proteins immobilized on the surface, and the detection system.
Zyomyx biochips will have a profound impact on the biological sciences. For the pharmaceutical industry, for example, this development will expedite the process of target discovery and validation. Zyomyx protein biochips will also play a pivotal role in changing the way that medicines are used through the development of more precise methods for clinical diagnosis, leading the way for the evolution of patient-specific medicines. Highly parallel, miniaturized devices will enable a fundamental change in the way that protein analysis are conducted and maximize the utility of the sequencing of the human genome.