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Precision Biology
By Claire Tristram

Ever since James Watson and Francis Crick unveiled their helical model of DNA in 1953, it has been an iconographic symbol of science. But no matter how familiar the structure of DNA becomes, observing the molecular pieces from which it is built remains a tantalizing challenge–and one for which a number of competing technologies are being developed. A tool that consistently offers researchers a way to observe biological processes at the molecular level would be invaluable. In particular, the ability to closely observe the nucleotides that make up DNA, combined with the ongoing work on the human genome, could eventually yield more-powerful methods for diagnosing disease.

At Intel, technologists pursuing better biological imaging have adopted an analytical method widely used in semiconductor R&D. In May, Intel’s Precision Biology group published a paper describing its use of Raman spectroscopy to detect single molecules of two of the four nucleotides that make up DNA: deoxyguanosine monophosphate (dGMP) and deoxyadenosine monophosphate (dAMP). While single molecules of dAMP had previously been detected with Raman spectroscopy, dGMP molecules had not. And Intel”s approach greatly improved the consistency with which a Raman effect was detected. “We wanted to push the limits of sensitivity,” says Andrew Berlin, lead researcher for the five-year-old group.

Raman spectroscopy takes advantage of the fact that light beams passing through different substances will scatter in different ways, emerging with different sets of characteristic wavelengths. Such patterns can serve as fingerprints for identifying specific compounds. The Raman approach offers advantages over other technologies for single-molecule detection, in that it”s one of the most sensitive techniques available and can also be used to detect molecules in a very dilute solution of water–or potentially in the watery world of a cell. What”s more, the technique provides a way to directly observe molecules without labeling them with fluorescent tags.

One way to intensify the Raman effect is to induce it in close proximity to metal. Berlin”s team, adapting techniques already being used by Intel in its manufacturing processes, first created a layer of silicon that was pocked with nanoscale pores to increase the area of the surface to which molecules could bind. They next coated the silicon with molecules containing silver and deposited a biological sample on the coated surface. The group bombarded the sample with pulses from multiple lasers and, in recent experiments, caused a single nucleotide to emit a signal strong enough to be detected. “We’re right in the middle of one of the best labs in the world for optimizing nanoparts, so we could take advantage of all the experience that comes out of our processor research,” Berlin says.

The significance of Intel’s approach is that it can boost a molecule’s signal so dramatically–between 100 and 10,000 times, depending on the molecule being studied–that it will allow observation of single molecules without chemically altering them. “The Intel experiments are the first that demonstrate the great potential of this kind of Raman technique for detecting single molecules,” says Eric O. Potma, who is working on similar research at the University of California, Irvine. Also, while fluorescent labeling is used only for taggable molecules, Intel”s research will likely find broader applications. “With single-molecule Raman, we might be able to monitor the details of molecules that have remained invisible to us with fluorescence spectroscopy,” says Potma.

The ability to better see how molecules operate could help fulfill a dream cherished by many biologists. “Being able to study single molecules will transform our thinking,” says cell biologist Mark Roth of the Fred Hutchinson Cancer Research Center in Seattle, which is collaborating with Intel on this project.

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