CRISPR-Chip: Detecting Mutations from Raw DNA

Since its introduction to the world CRISPR technology has revolutionized every aspect of life and is creating a huge impact in every man’s life. The tech enables the editing of genes but with more focused research and technical advancements the tech is being used for creation of more sophisticated devices, in a recent efforts a team of researchers working at the UC Berkley, USA have recently developed a chip based device using CRISPR molecules for the detection of mutations from unamplified DNA samples. The team is headed by Dr. Kiana Aran who specialises in bio-medical engineering.

Need for the technology:

Genome sequencing and detection of anomalies inside the DNA are becoming prominent for accurate diagnosis and treatment of the disease. This technique of presice medicine has developed to a greater extent in past half century, but still requires some expensive machines, reagents, and trained workforce for proper functioning. Also it requires an additional imaging device for visualizing the results. All this is a set-back and consumes both money and time. So, new techniques regarding these kinds of diagnosis are required.  

Development of Chip:

In an effort to answer the problem Dr. Kiana Aran and her team at UC Berkeley developed a chip based diagnostic device. The device consists of two key components:

• The dRNP- CRISPR molecule
• Graphene based field effector transistor (gEFT)

The chip is formed by combining the two components, the CRISPR-CAS is a DNA cutting tool having the ability to detect specific DNA segment with extreme precision, for the detection chip module a slightly modified module of CRISPR is being used which is able to detect the specific DNA segment but its ability of cutting the DNA has been deactivated. These modified CRISPR molecules are stacked on top of the graphene transistor layer, the graphene layer was preferred over the silicon based layer due to its higher electric sensitivity than the silicon.
What is graphene? See: https://crisprpedia.blogspot.com/2019/09/graphene-magic-material.html

CRISPR-gEFT Chip module

Functioning of CRISPR-Chip:

The raw DNA sample without subjecting to any amplification process is loaded on to the chip set. The DNA is taken by the CRISPR molecules and unzipped, it analyzes the whole segment of the DNA until it reaches hat part of the DNA where a specific part of the DNA or gene is present that has complementary sequence to the guide RNA present inside the CRISPR molecules. When the specific part is identified it binds with it and this hybridization of target DNA with the CRISPR module influence the electrical characteristics of graphene surface. This produces a signal resulting detection of mutations and abnormalities in DNA in short period of time.

Initial Trial:

For initial validation of the device a trial was conducted to check the effectiveness of the tech for this Duchenne muscular dystrophy (DMD) disease was selected. This disease is caused by a exon deletion in the gene resulting in production of dysfunctional dystrophin resulting in to malformation of muscle fibres. Two of these exons the exon-3 and exon-51 are absent in all DMD patients. For the trial CRISPR chips specific for exon 3 and 51 were designed and DNA samples from the DMD patients and healthy donors were analysed using chip. Results exhibit that the healthy sample with exon 3 and 51 produces a strong signal in comparison to the DMD patient DNA sample.

Published Results-Courtesy Nature

Conclusion:

The device is an effective way for detecting certain mutation based disease on early stages, enabling on time detection and better diagnosis and treatment of the disease. The tech is a promising and effective one ensuring further enhancement in precision medicines.

Courtesy: Nature, UC Berkeley, Aran Lab.