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posted by Fnord666 on Sunday April 16 2017, @06:41AM   Printer-friendly
from the combine-with-IBM's-Watson-and-watch-out dept.

A new CRISPR-related tool cuts RNA in a way that can be used to diagnose the presence of viruses or diseases:

Far to the right side of the decimal point—beyond milli, micro, nano, pico, and femto—lives the atto, the metric prefix representing 10-18. Slap it in front of a unit of concentration, such as molar, and it means that something exists in an extraordinarily small amount—think one part per quintillion. That's the realm of SHERLOCK, a new diagnostic system that can detect attomolar levels of viruses in a sample and also distinguish Zika from its close relative, dengue. This exquisitely sensitive and specific tool promises to help detect diseases that other diagnostics miss, and it's simple and cheap to use. Sexier still, it exploits a variation of CRISPR, the genome-editing method that has become the rage in biology. "It's very nice work and very well done," says Erik Sontheimer, an RNA specialist who did early CRISPR work and is at the University of Massachusetts Medical School in Worcester. Harvard University's George Church, who co-founded a CRISPR therapeutics company with one of SHERLOCK's inventors but is not involved with this work, sums up his reaction in one word: "Wow."

Scientists recognized as early as 2010 that they might be able to transform CRISPR into a virus detection device [open, DOI: 10.1128/AEM.01109-10] [DX]. But earlier efforts at making a viral detector became overshadowed by CRISPR's wild success at editing genomes. [...] SHERLOCK differs from the CRISPR-Cas9 system in fundamental ways. It uses an RNA guide that gloms onto RNA, not DNA, and an enzyme called Cas13a cuts the genetic material. Once Cas13a snips the target, it starts indiscriminately cutting any RNA it encounters. A team lead by bioengineer James Collins and CRISPR genome-editing pioneer Feng Zhang, both from the Broad Institute in Cambridge, Massachusetts, has now shown that these "collateral" cuts can form the basis for the SHERLOCK diagnostic. "Nature has a lot of very amazing tools," Zhang says. The researchers demonstrate that SHERLOCK can detect viral and bacterial infections, cancer mutations found at low frequencies, and subtle DNA sequence variations known as single nucleotide polymorphisms that are linked to other diseases. (SHERLOCK, a somewhat strained acronym coined by the team, stands for specific high sensitivity enzymatic reporter unlocking.)

Nucleic acid detection with CRISPR-Cas13a/C2c2 (DOI: 10.1126/science.aam9321) (DX)


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  • (Score: 0) by Anonymous Coward on Sunday April 16 2017, @11:11AM (2 children)

    by Anonymous Coward on Sunday April 16 2017, @11:11AM (#494771)

    how does this mechanism actually work for detection?

  • (Score: 3, Informative) by takyon on Sunday April 16 2017, @05:39PM

    by takyon (881) <reversethis-{gro ... s} {ta} {noykat}> on Sunday April 16 2017, @05:39PM (#494875) Journal

    To exploit SHERLOCK for detecting small amounts of virus, the researchers spiked samples containing Zika or dengue virus with so-called fluorescent reporter RNA. When this RNA is cut, it effectively shoots off fluorescent flares. The team then unleashed Cas13a connected to a bit of RNA that targeted genetic sequences from either Zika or dengue. Once Cas13a found and sliced even a few viral sequences, it subsequently snipped the fluorescent reporters and created a detectable signal indicating the presence of the virus, the team reports today in Science.

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  • (Score: 0) by Anonymous Coward on Sunday April 16 2017, @06:10PM

    by Anonymous Coward on Sunday April 16 2017, @06:10PM (#494883)

    Their idea is that they can set up an enzyme (cas13a) to only cut RNA when it binds to a specific RNA sequence (target). In the presence of the RNA target it will begin indiscriminately chopping up all the RNA molecules around, while it should do nothing if the target is not present. Then there are various schemes you can use to check for widespread, nonspecific RNA degradation (which purportedly indicates presence of the RNA target sequence).