̽��ֱ�� of Cambridge - Ulrich Keyser

Gone fishing: highly accurate test for common respiratory viruses uses DNA as ‘bait’

sc604 — Mon, 16 Jan 2023 16:00:00 +0000

̽��ֱ��test uses DNA ‘nanobait’ to detect the most common respiratory viruses – including influenza, rhinovirus, RSV and COVID-19 – at the same time. In comparison, PCR (polymerase chain reaction) tests, while highly specific and highly accurate, can only test for a single virus at a time and take several hours to return a result.

While many common respiratory viruses have similar symptoms, they require different treatments. By testing for multiple viruses at once, the researchers say their test will ensure patients get the right treatment quickly and could also reduce the unwarranted use of antibiotics.

In addition, the tests can be used in any setting, and can be easily modified to detect different bacteria and viruses, including potential new variants of SARS-CoV-2, the virus which causes COVID-19. ̽��ֱ��results are reported in the journal Nature Nanotechnology.

̽��ֱ��winter cold, flu and RSV season has arrived in the northern hemisphere, and healthcare workers must make quick decisions about treatment when patients show up in their hospital or clinic.

“Many respiratory viruses have similar symptoms but require different treatments: we wanted to see if we could search for multiple viruses in parallel,” said Filip Bošković from Cambridge’s Cavendish Laboratory, the paper’s first author. “According to the World Health Organization, respiratory viruses are the cause of death for 20% of children who die under the age of five. If you could come up with a test that could detect multiple viruses quickly and accurately, it could make a huge difference.”

For Bošković, the research is also personal: as a young child, he was in hospital for almost a month with a high fever. Doctors could not figure out the cause of his illness until a PCR machine became available.

“Good diagnostics are the key to good treatments,” said Bošković, who is a PhD student at St John’s College, Cambridge. “People show up at hospital in need of treatment and they might be carrying multiple different viruses, but unless you can discriminate between different viruses, there is a risk patients could receive incorrect treatment.”

PCR tests are powerful, sensitive and accurate, but they require a piece of genome to be copied millions of times, which takes several hours.

̽��ֱ��Cambridge researchers wanted to develop a test that uses RNA to detect viruses directly, without the need to copy the genome, but with high enough sensitivity to be useful in a healthcare setting.

“For patients, we know that rapid diagnosis improves their outcome, so being able to detect the infectious agent quickly could save their life,” said co-author Professor Stephen Baker, from the Cambridge Institute of Therapeutic Immunology and Infectious Disease. “For healthcare workers, such a test could be used anywhere, in the UK or in any low- or middle-income setting, which helps ensure patients get the correct treatment quickly and reduce the use of unwarranted antibiotics.”

̽��ֱ��researchers based their test on structures built from double strands of DNA with overhanging single strands. These single strands are the ‘bait’: they are programmed to ‘fish’ for specific regions in the RNA of target viruses. ̽��ֱ��nanobaits are then passed through very tiny holes called nanopores. Nanopore sensing is like a ticker tape reader that transforms molecular structures into digital information in milliseconds. ̽��ֱ��structure of each nanobait reveals the target virus or its variant.

̽��ֱ��researchers showed that the test can easily be reprogrammed to discriminate between viral variants, including variants of the virus that causes COVID-19. ̽��ֱ��approach enables near 100% specificity due to the precision of the programmable nanobait structures.

“This work elegantly uses new technology to solve multiple current limitations in one go,” said Baker. “One of the things we struggle with most is the rapid and accurate identification of the organisms causing the infection. This technology is a potential game-changer; a rapid, low-cost diagnostic platform that is simple and can be used anywhere on any sample.”

A patent on the technology has been filed by Cambridge Enterprise, the ̽��ֱ��’s commercialisation arm, and co-author Professor Ulrich Keyser has co-founded a company, Cambridge Nucleomics, focused on RNA detection with single-molecule precision.

“Nanobait is based on DNA nanotechnology and will allow for many more exciting applications in the future,” said Keyser, who is based at the Cavendish Laboratory. “For commercial applications and roll-out to the public we will have to convert our nanopore platform into a hand-held device.”

“Bringing together researchers from medicine, physics, engineering and chemistry helped us come up with a truly meaningful solution to a difficult problem,” said Bošković, who received a 2022 PhD award from Cambridge Society for Applied Research for this work.

̽��ֱ��research was supported in part by the European Research Council, the Winton Programme for the Physics of Sustainability, St John’s College, UK Research and Innovation (UKRI), Wellcome, and the National Institute for Health and Care Research (NIHR) Cambridge Biomedical Research Centre.

Reference:
Filip Bošković et al. ‘Simultaneous identification of viruses and viral variants with programmable DNA nanobait.’ Nature Nanotechnology (2022). DOI: 10.1038/s41565-022-01287-x

A new test that ‘fishes’ for multiple respiratory viruses at once using single strands of DNA as ‘bait’, and gives highly accurate results in under an hour, has been developed by Cambridge researchers.

Good diagnostics are the key to good treatments

Filip Bošković

Natalia Gdovskaia via Getty Images

Doctor examining a patient

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

Yes

DNA enzyme shuffles cell membranes a thousand times faster than its natural counterpart

sc604 — Thu, 21 Jun 2018 11:23:25 +0000

Researchers at the ̽��ֱ�� of Cambridge and the ̽��ֱ�� of Illinois at Urbana-Champaign say their lipid-scrambling DNA enzyme is the first to outperform naturally occurring enzymes – and does so by three orders of magnitude. Their findings are published in the journal Nature Communications.

“Cell membranes are lined with a different set of molecules on the inside and outside, and cells devote a lot of resources to maintaining this,” said study leader Aleksei Aksimentiev, a professor of physics at Illinois. “But at some points in a cell’s life, the asymmetry has to be dismantled. Then the markers that were inside become outside, which sends signals for certain processes, such as cell death. There are enzymes in nature that do that called scramblases. However, in some other diseases where scramblases are deficient, this doesn’t happen correctly. Our synthetic scramblase could be an avenue for therapeutics.”

Aksimentiev’s group came upon DNA’s scramblase activity when looking at DNA structures that form pores and channels in cell membranes. They used the Blue Waters supercomputer at the National Center for Supercomputing Applications at Illinois to model the systems at the atomic level. They saw that when certain DNA structures insert into the membrane – in this case, a bundle of eight strands of DNA with cholesterol at the ends of two of the strands – lipids in the membrane around the DNA begin to shuffle between the inner and outer membrane layers.

To verify the scramblase activity predicted by the computer models, Aksimentiev’s group at Illinois partnered with Professor Ulrich Keyser’s group at Cambridge. ̽��ֱ��Cambridge group synthesised the DNA enzyme and tested it in model membrane bubbles, called vesicles, and then in human breast cancer cells.

“ ̽��ֱ��results show very conclusively that our DNA nanostructure facilitates rapid lipid scrambling,” said co-first author Alexander Ohmann, a PhD student in Keyser’s group in Cambridge’s Cavendish Laboratory. “Most interestingly, the high flipping rate indicated by the molecular dynamics simulations seems to be of the same order of magnitude in experiments: up to a thousand-fold faster than what has previously been shown for natural scramblases.”

On its own, the DNA scramblase produces cell death indiscriminately, said Aksimentiev. ̽��ֱ��next step is to couple it with targeting systems that specifically seek out certain cell types, a number of which have already been developed for other DNA agents.

“We are also working to make these scramblase structures activated by light or some other stimulus, so they can be activated only on demand and can be turned off,” said Aksimentiev.

“Although we have still a long way to go, this work highlights the enormous potential of synthetic DNA nanostructures with possible applications for personalised drugs and therapeutics for a variety of health conditions in the future,” said Ohmann, who has also written a blog post on their new paper.

̽��ֱ��US National Science Foundation and the National Institutes of Health supported this work.

Reference:
Alexander Ohmann et al. ‘A synthetic enzyme built from DNA flips 10⁷ lipids per second in biological membranes.’ Nature Communications (2018). DOI: 10.1038/s41467-018-04821-5

Adapted from a ̽��ֱ�� of Illinois at Urbana-Champaign press release.

A new synthetic enzyme, crafted from DNA rather than protein, ‘flips’ lipid molecules within the cell membrane, triggering a signal pathway that could be harnessed to induce cell death in cancer cells.

This work highlights the enormous potential of synthetic DNA nanostructures for personalised drugs and therapeutics for a variety of health conditions.

Alexander Ohmann

Aleksei Aksimentiev

DNA scramblase

Yes