ITMO: DNA machine for pathogen detection

Main articles:

• Viruses
• DNA (Deoxyribonucleic acid)

2022: Announcement of a DNA machine for pathogen detection

On April 20, 2022, representatives ITMO University reported that scientists at ITMO University, together scientists with the University of Central Florida, developed DNA a machine for detecting pathogens - dangerous for, health viruses bacteria and other microorganisms. This method, unlike PCR tests, does not require the use of expensive equipment. The development allows testing even at room temperature. With the help of a color signal, the result can be seen with the naked eye. The article is published in the journal Chemical Communications.

As reported, PCR is one of the most accurate and sensitive methods of molecular diagnosis of infectious diseases as of April 2022. However, it also has its limitations: laboratory conditions, trained personnel and expensive equipment are needed to analyze samples for the presence of genetic material of the pathogen. For example, devices for increasing copies of nucleic acid fragments, RNA and DNA, are thermocyclers that change temperature at different stages. As an alternative, isothermal amplification methods are developed, in which the copying (amplification) of RNA and DNA occurs in the same temperature mode. They are close in accuracy to the PCR indicators.

ITMO biochemists were able to advance in this direction and create a convenient tool for verifying and visualizing the results of isothermal amplification.

RNA or DNA are usually in a folded state and unfold only at high temperatures, which complicates the detection of target fragments. We have developed DNA machines that are able, without special devices and heating, to detect the right sites, analytes, single-stranded RNAs belonging to certain pathogens. DNA machines "pick up to the target," embrace it and force the nucleic acid to turn around. explained by Daria Gorbenko, an employee of the International Scientific Center SCAMT University ITMO

The proposed DNA machine is a small platform of double-stranded nucleic acid. Special sections are connected to it, figuratively speaking, "hands" - there can be two, three or even four. For each pathogen, a different platform is created, it is enough to select it once. It should be arranged so that there is no probability of cross-complementarity, that is, undesirable crossing of the structural elements of the DNA machine with the RNA analyte.

If there is a pathogen in the sample, the machine will connect to the analyte and form a four-stranded DNA - G-quadruplex. The properties of this structure open up space for creating a simple and visual test system: when we add special reagents, we will receive a color signal. In our case, the sample is painted brown. explained by Daria Gorbenko

Daria Gorbenko, Fellow, SCAMT International Science Center, ITMO University

The whole process of testing using a DNA machine - from taking material and isolating a nucleic acid to forming a G-quadruplex and receiving a color signal - takes about two to three hours, but the authors of the project are sure that this time can be reduced. At this stage of the study, experiments were carried out on synthetic samples and on copies of RNA and DNA: the article describes the results of the detection of cytomegalovirus (a variety of herpes), a hemophilic stick that causes respiratory damage, and listeria monocytogenes (acute food poisoning).

An unexpected discovery was that the DNA machine in some cases coped with the detection of not only single-stranded RNAs, but also double-stranded DNA - and all this at room temperature.

The scientists plan to focus on detecting copies of DNA to explain this phenomenon, as well as increase the selectivity of the DNA machine to search for a specific nucleic acid in a solution from several others. According to the authors of the project, in the future the proposed method will be "packaged" in a compact device that can be used outside the laboratory.