Digital DNA Detection

A CRISPR-based electronic sensor flags target DNA sequences at high speed.

Searching a sample of DNA for a particular sequence—be it a mutation, a researcher-inserted transgene, or evidence of an infecting organism—is a common practice in many molecular biologies and diagnostic laboratories around the world. Often, such searches take the form of target amplification, which involves using sequence-specific oligonucleotide primers and the action of a DNA polymerase to pull out the sequence of interest. But amplification not only adds a step to the search process—requiring optimization, reagents, and time—it can also introduce errors such as amplification bias.

To move away from amplification, Kiana Aran of the Keck Graduate Institute in California and her colleagues turned to the CRISPR-Cas family of nucleases, which, when paired with a specific guide RNA, can scour the whole genome to find and cut a precise sequence. Aran, whose background is in electrical engineering, incorporated this search capacity into an electrical biosensor called CRISPR-Chip.

Target variant detected

Target variant not detected

The chip uses a Cas9 enzyme that has been deactivated to prevent DNA cutting, paired with a guide RNA that detects a particular sequence. Together, the enzyme and RNA covalently adhere to a graphene transistor. A sample of purified DNA is then pipetted onto the transistor, and if the RNA-Cas9 complex binds its target, the transistor’s electrical current changes, providing a readout in minutes. At present, the proof-of-concept device detects one sequence per non-reusable chip, but the researchers plan to expand its capacity to detect many different sequences simultaneously.

“The simplicity of the chip and no need for amplification make the system readily deployable, but more engineering is needed to boost the sensitivity beyond the low femtomolar range, as many clinical applications require sensitivities that are 1,000 [times] better,” genetic and biological engineer Omar Abudayyeh of the McGovern Institute for Brain Research at MIT who was not involved with developing the device.

While it’s true that for certain clinical applications, such as infection detection, higher sensitivity would be needed, says Aran, the system has already been used to detect a transgene in a human cell line and two Duchenne muscular dystrophy–associated deletions in patient DNA samples.

The handheld chip “is very creative” and “elegantly simple,” says Anthony Shuber of Genetics Research LLC, a company that develops CRISPR-based technologies but was not involved with the project. He adds that the transistor’s speed and scale mean “it has real potential at the point of care.”