In brief

Using ExSELEX, researchers created novel six-letter DNA aptamers which identified dengue serotypes more precisely than conventional point-of-care tests.

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Rare six-letter DNA unlocks dengue diagnostic

10 Oct 2022

Synthetic DNA molecules could serve as an easy-to-manufacture alternative to traditional antibody-based rapid tests.

While ones and zeros make up the binary code that powers all things digital, in the living world, it’s the four-letter genetic code in DNA that has spelled out the language of life for millions of years. Now, scientists say expanding DNA’s genetic alphabet could unlock a whole new world of next-generation diagnostic technologies.

Working on this premise is Ichiro Hirao, a Principal Research Scientist at A*STAR’s Institute of Bioengineering and Bioimaging (IBB), who led a team in collaboration with the National Centre for Infectious Diseases, to see if this technique could help overcome the challenges of traditional antibody-based rapid tests.

“Antibodies have several shortcomings, such as quality control issues and difficult site-specific modifications,” explained Hirao, adding that antibodies are difficult to manufacture at scale because they are produced using living organisms. Small fragments of DNA called aptamers are a promising alternative: they are easy to make and can be modified to detect different viral variants.

However, while DNA could theoretically do the job of antibodies in point-of-care diagnostic tests, their four-letter code limits how sensitive, specific, and reliable they could be. In 2013, Hirao and his colleagues created a novel platform called ExSELEX (genetic alphabet Expansion for Systematic Evolution of Ligands by EXponential enrichment) that enables scientists to tack on additional letters to DNA aptamers with ease*.

The team put ExSELEX to the test using a notoriously difficult-to-diagnose infectious disease: dengue fever. There are four related members, or serotypes, in the dengue virus family, and consecutive infections from different serotypes can have serious life-threatening consequences for patients.

“Currently, there is no simple method to identify dengue serotypes in patients during the early and late phases of the disease,” said Hirao. Now, however, his team showed that their newly developed DNA aptamer dengue test could pick up the presence of distinct serotypes in patient blood samples.

According to Hirao, future iterations of the DNA-based dengue diagnostic test could potentially provide clinicians with even higher-resolution diagnostics by distinguishing between early- and late-stage infections**.

After successfully creating 5-letter aptamers with ExSELEX, Hirao’s team made a serendipitous discovery—the platform could be adapted to add on a sixth letter, significantly boosting the test’s sensitivity. This discovery is also the first report of 6-letter DNA aptamers being used for diagnostic applications, an innovation that Hirao says can be extended for diseases beyond dengue, and could even be used therapeutically.

Hirao and his colleague have since founded a local start-up, Xenolis, and are collaborating with other researchers to refine and commercialize the technology using a more advanced version of ExSELEX to bring 6-letter aptamer diagnostics to patients.

The A*STAR-affiliated researchers contributing to this research are from the Institute of Bioengineering and Bioimaging (IBB).

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1. Matsunaga, K., Kimoto, M., Lim, V.W., Tan H.P., Wong, Y.Q. et al. High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification. Nucleic Acids Research 49 (20), 11407-11424 (2021) | article
2. Kimoto, M., Yamashige, R., Matsunaga, K., Yokoyama, S, Hirao, I. Generation of high-affinity DNA aptamers using an expanded genetic alphabet. Nature Biotechnology 31, 453-457 (2013). | article
3. Matsunaga, K., Kimoto, M., Lim, V.W., Thein, T.-L., Vasoo, S. et al. Competitive ELISA for a serologic test to detect dengue serotype-specific anti-NS1 IgGs using high-affinity UB-DNA aptamers. Scientific Reports 11, 18000 (2021). | article

About the Researcher

Ichiro Hirao is a Senior Group Leader and Principal Research Scientist at the Institute of Bioengineering and Bioimaging (IBB), A*STAR, in Singapore. He received his PhD from Tokyo Institute of Technology in 1983. In 1992, he became an Associate Professor at Tokyo University of Pharmacy and Life Sciences. He joined the Japan Science and Technology Agency in 1997 as a Group Leader to begin work on unnatural base pairs. From 2006 to 2015, he led a synthetic biology team in RIKEN, Japan, which relocated to Institute of Bioengineering and Nanotechnology (IBN) in November 2015.

This article was made for A*STAR Research by Wildtype Media Group