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Graphene Crispr Chip Detects Small Genetic Differences

DNA chip graphic

(Gerd Altmann, Pixabay)

5 Apr. 2021. An academic-industry team designed a computer chip with graphene circuits using the gene-editing technique Crispr to detect fine genetic differences in samples. Researchers from Keck Graduate Institute in Claremont, California and biotechnology company Cardea Bio in San Diego describe their device in today’s issue of the journal Nature Biomedical Engineering.

The researchers, with associates from Vilnius University in Lithuania and other institutions, are seeking a technology to simplify genomic analysis from today’s systems that often require large-scale and expensive optical lab equipment and amplified DNA to conduct high-throughput sequencing. While results from these analytical engines are considered accurate and reliable, their scale and expense limit their use to sophisticated labs, when the need for genetic analysis can be at the point of care or at remote field locations.

The lab led by Keck biomedical engineering professor Kiana Aran studies bio-microelectromechanical systems for research and clinical use, including graphene-based devices, to help solve this problem. Among the lab’s work is a transistor built on graphene that applies the gene-editing technique Crispr to detect genomic sequences of target materials.

Graphene is a material with many desirable qualities for a range of industries. The material is very light, strong, chemically stable, and only one atom in thickness, arrayed in a hexagonal pattern. Graphene can conduct both heat and electricity, with many applications in electronics, energy, and health care.

SNP-Chip detects healthy from disease sequences

Aran is also co-founder and chief scientist of Cardea Bio that builds graphene semiconductors designed to detect biological signals for applications that combine molecular biology with advanced electronics, software, and artificial intelligence. As reported in Science & Enterprise last month, Cardea Bio is developing a graphene sensor for Department of Defense to quickly detect SARS-CoV-2 viruses in indoor air.

In their paper, Aran and colleagues demonstrate a graphene chip with Crispr circuits using Cas9 enzymes designed to detect genomic sequences with a high degree of precision, down to single nucleotides, basic building blocks in the genome. These granular differences, called single nucleotide polymorphisms, or SNPs (pronounced snips), occur throughout the human genome, about once in every 1,000 nucleotides. And because of their precision, SNPs can serve as important biomarkers for detecting or treating genetic diseases.

The researchers demonstrated their Crispr-Cas9 chip, called SNP-Chip, with DNA samples from individuals with and without specific diseases: sickle cell disease and amyotrophic lateral sclerosis or ALS. Donors of the samples have similar genetic characteristics, except for the key SNP mutations associated with these diseases. The team reports the SNP-Chip accurately detects the disease-associated sequences in the donated samples, and without a need for amplifying the DNA, further simplifying the process.

“The ability to detect SNPs on a chip does not just get to the core of human health genetics,” says Aran in a Cardea Bio statement released through BusinessWire, “it also gives us valuable and actionable insight into areas like agriculture, industrial bioprocesses, and even evolutionary change, such as mutations conferring resistance to antibiotics or mutating viruses.” Aran adds, “By eliminating the need for amplification and large optical instruments, SNP-Chip will make SNP genotyping for these purposes readily accessible.”

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