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New CRISPR-Chip Can Finds DNA Mutations without Amplification

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March 25, 2019

New CRISPR-Chip Can Finds DNA Mutations without AmplificationEach individual chip can be coated with Cas9 proteins equipped with different RNA guides to detect different sequences of DNA. (Keck Graduate Institute photo)

A team of engineers at the UC Berkeley and the Keck Graduate Institute (KGI) of The Claremont colleges combined CRISPR with electronic transistors made from graphene to create a new hand-held device that can detect specific genetic mutations in a matter of minutes, and can be used to quickly diagnose genetic disorders and diseases or determine the accuracy of gene-editing techniques.

The device, dubbed CRISPR-Chip, as reported on in the journal Nature Biomedical Engineering, uses nano-electronics to detect genetic mutations in DNA without first “amplifying” or replicating the segment of interest millions of times over through polymerase chain reaction (PCR). This means it could be used to perform genetic testing in a doctor’s office or field work setting without having to send a sample off to a lab.

“You just put your purified DNA sample on the chip, allow CRISPR to do the search and the graphene transistor reports the result of this search in minutes.” said Kiana Aran, an assistant professor at KGI who conceived of the technology while a postdoctoral scholar in UC Berkeley bioengineering professor Irina Conboy’s lab.

The new technology works by taking a deactivated Cas9 protein — a variant of Cas9 that can find a specific location on DNA, but doesn’t cut it — and tethered it to transistors made of graphene. After finding the targeted spot, the CRISPR binds to it and begins changing the graphene’s electrical conductance, thus changing the transistor’s electrical characteristics. The hand-held device developed by the researchers can then detect these changes in turn.

“Graphene’s super-sensitivity enabled us to detect the DNA searching activities of CRISPR,” Aran said. “CRISPR brought the selectivity, graphene transistors brought the sensitivity and, together, we were able to do this PCR-free or amplification-free detection.”

Aran and her research colleagues demonstrated the system’s effectiveness by testing for the digital detection of DNA mutations in Duchenne Muscular Dystrophy, a genetic disorder that results in progressive muscle degeneration and shortened life expectancy.

Aran notes that the system, which enables users to run a test in less than an hour, has potential applications beyond diagnostics. She explains that these include multiplexing capabilities to run hundreds or thousands of tests at the same time. Another potential application is for quality control purposes within companies that use CRISPR for therapeutics; the system could enable them to better evaluate the efficiency of the CRISPR technology.

In the future, the researchers want to integrate fast-growing electronics technologies with modern biology not only to develop better diagnostic tools, but also to gain a better understanding of biological events using nanoscale electronics devices.

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