MICROSPHERES READ DNA ARRAYS GENE ANALYSIS: Electrostatic repulsion detects DNA pairing
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NA MICROARRAYS—devices that measure
gene expression—could become easier to use, thanks to a new readout method based on electrostatic repulsion. Such devices are used in biological research and clinical diagnostics. University of California, Berkeley, chemistry professor Jay T. Groves, postdoc Khalid Salaita, and graduate student Nathan G. Clack have devised a way to use negatively charged silica microspheres to detect spots on DNA microarrays where single-stranded DNA hybridizes to form double-stranded DNA (Nat. Biotechnol., DOI: 10.1038/nbt1416). “We’re throwing millions of particles on the sample and letting the particles scan the surface randomly by Brownian motion,” Groves says. “By doing a statistical analysis of their motion, we’re able to determine with high precision what the charge on the surface is.” The setup consists of a glass surface modified with aminosilanes so that it has a positive charge. The researchers tune the charge such that single-stranded DNA printed on the surface makes the net charge approximately neutral or only slightly positive. Any DNA added to the surface as a result of hybridization drives the overall charge toward negative at that spot. When a solution of the negatively charged microspheres flows over the surface, the beads move away from the surface at the negatively charged spots where double-stranded DNA is present. The researchers monitor the position of the spheres
with optical methods such as reflection interference contrast microscopy or darkfield or brightfield microscopy. Such detection methods may not always be necessary, however, because the microspheres scatter light so strongly that the pattern of spots with hybridized DNA can be seen with the unaided eye, Groves says. “The way to think of it is like a dust for fingerprints, except you can dust for DNA hybridization,” Groves says. “You could imagine LEVITATION Electrostatic having a glass chip out in the field repulsion causes silica microspheres in a developing country, doing a to rise to different heights above the tuberculosis DNA screen to see background (white) and spots coated which strain you have, and just with single-stranded (light orange) or holding it up to the light to see.” double-stranded (dark orange) DNA. Using a “charge ladder,” in which a series of neighboring spots with the same DNA sequence have slightly different charges, the visual method becomes quantitative. “As you go up this ladder, it takes progressively more hybridization to get the spot to switch from positive to negative,” Groves says. The last spot in the ladder to switch reveals how much DNA has hybridized. The Berkeley team also used the method to detect RNA taken from cells without amplification or labeling. “We imagine this taking what right now is a difficult outsourced problem of doing gene expression profiling and turning it into something that you can do quickly in the lab,” Groves says. Groves hopes that the technology will be commercialized. “We hope to see a company help develop the technology for real-world applications,” he says.— CELIA ARNAUD
ALTERNATIVE ENERGY First municipal waste-based ethanol plant is set for Canada Two Canadian companies have won government backing for what they say will be the world’s first facility to convert municipal solid waste into ethanol on an industrial scale. The $70 million plant will be built in Edmonton, Alberta, by GreenField Ethanol, Canada’s largest ethanol producer, and Enerkem, a Quebec-based biofuels technology company. The city of Edmonton and the Alberta Energy Research Institute (AERI) will contribute $20 million and the two companies the rest. The city will also put $50 million into separate waste processing and research facilities. The technology comes from Enerkem,
which has research ties to Quebec’s University of Sherbrooke. Enerkem’s ethanol process sorts and gasifies municipal waste and purifies the gases into the mixture of carbon monoxide and hydrogen known as syngas. It then catalytically converts syngas into ethanol and methanol. The company claims a cost advantage over competing second-generation ethanol production techniques that use enzymes to break down cellulose into sugars for fermentation into ethanol. Edmonton Mayor Stephen Mandel says the plant, set to open in late 2010, will help reduce greenhouse gases and make the city the first in North America
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to divert 90% of its residential waste from landfills. John J. Murphy, president of Catalyst Group Resources, a consulting firm that monitors catalytic biofuel processes, says AERI’s backing is a sign that Enerkem’s process is technologically sound. He notes, however, that government monetary backing is a sign that the plant may not be financially sound. “Support from an ExxonMobil or a ConocoPhillips would give it more economic credibility,” he says. “Return on investment is not measured the same when taxpayers are paying as it is when shareholders are paying.”—MICHAEL MCCOY
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