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The proposed technique combines and improves the efficiency of CRISPR–Cas and RCA-based sensing strategies and shows great potential in lab-based microRNA detection and cost-effective point-of-care testing.
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Unveiling a New, Robust miRNA Detection Method

Novel approach slashes down time required to detect microRNAs for the latter to be used as biomarkers for diseases such as cancer

Nanjing Agricultural University
Published:Apr 25, 2023
|3 min read
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In the early 1990s, scientists who were studying the development of a roundworm identified a small RNA molecule that regulated the expression of specific genes. This marked the discovery of microRNAs (miRNAs), which are now known to be present across all forms of life. As it turns out, these molecules play essential roles in many biological processes.

A few years later, researchers realized that diseases could dysregulate the expression of miRNAs, highlighting their potential as biomarkers. In fact, abnormal miRNA expression is a hallmark of all tumor-related diseases. Thus, miRNA detection techniques may be useful for the early detection of cancer.

However, miRNAs are small and degrade easily, which makes their rapid detection and quantification difficult. To detect miRNAs in a sample, it is usually necessary to replicate and amplify a target miRNA multiple times so that said miRNA is easier to detect through inexpensive methods. Unfortunately, most state-of-the-art techniques for miRNA amplification can take over five hours to complete, limiting their use in point-of-care testing.

Against this backdrop, a research team, including Chong Zhang, PhD, associate professor at Tsinghua University, China, recently pioneered a new methodology for fast miRNA amplification and detection. As explained in their latest paper, published recently in BioDesign Research, the team combined two well-studied biochemistry techniques into one in a way that greatly reduced the overall time required.

Two-step approach for quick miRNA detection

The first technique they used is called rolling circle amplification (RCA). In RCA, the idea is to design a circular DNA molecule (probe) to which the target RNA fragment binds. Then, once DNA polymerase enzymes and the necessary DNA building blocks are introduced, the RNA fragment is extended by adding nucleotides complementary to the circular probe. This process results in a long, single strand of genetic material that contains multiple copies of the circular probe.

This is where the second technique, CRISPR-Cas12a, comes into play. CRISPR-Cas12a is a widely used genetic tool in which a molecular complex is engineered to bind to a specific DNA sequence. In this case, the researchers designed the complex so that it would bind to a region in the complementary sequence to the circular probe. That is, the CRISPR-Cas12a complexes are bound multiple times along the single strand of DNA that was produced via RCA. Once these complexes were bound, the Cas12a portion activated, splitting a fluorescent probe from its quencher. In turn, this created an easily detectable fluorescent signal that got brighter with the number of initial target RNA copies.

Besides the combination of these techniques, the researchers improved the reaction time of the RCA step by using precircularized probes. That is, unlike most standard RCA procedures, the probes were given their circular shape prior to the reaction. As Zhang remarks, this made the detection process much quicker without compromising the system’s performance: “The detection of miRNA could be completed in only 70 minutes, rather than the usual five hours, with an excellent limit of detection of 8.1 pM and very high specificity.”

Overall, the proposed approach paints a bright future for miRNA detection and the use of miRNAs as biomarkers. Satisfied with the results, Zhang concludes, “Our design improves the efficiency of CRISPR–Cas and RCA-based sensing strategies and shows great potential in lab-based detection and point-of-care testing.” 

Since the techniques used in this methodology are not prohibitively expensive nor complex to perform, the widespread adoption of the proposed approach in clinical settings is feasible. These efforts will pave the way to design better diagnostic tools against cancer and other diseases that affect miRNA expression.

- This press release is supported by the Nanjing Agricultural University