Finalists of the ‘SPbU Start-up-2021’ contest — the ProteoSensity team — have created a prototype of a device that will allow faster and more accurate environmental analysis. As the result, environmental monitoring will become more cost-effective. People who are not specialists will be able to use it.

Eco monitoring in seven minutes

Currently, there are two popular methods to detect pollutants in water, air or soil. The first method involves taking samples and analysing them in a laboratory. The whole procedure takes a lot of time; because the researcher has to go to the location and then return to the laboratory. Moreover, laboratory analysis will usually require a few hours. Each of the laboratory devices is capable of detecting a narrow spectrum of analytes in a sample; therefore, the process will usually involve several major pieces of equipment. The laboratory equipment often costs over a million roubles and only qualified specialists can use it. All this makes the analysis expensive. Besides, there may be errors: some unstable substances can decompose during transportation.

The second method is to analyse samples on site in a mobile laboratory. While this saves time and increases the reliability of the results, the method has its own drawbacks.

‘We have come up with a device that will make environmental monitoring more convenient, cost-effective and faster,’ said Andrei Zolotarev, the team captain and a master’s student in bioinformatics. ‘Firstly, our device is versatile and capable of detecting a variety of substances in a sample; thus replacing several installations. Secondly, the device allows us to cut costs: it will cost between 150 and 300 thousand roubles. Thirdly, the device is automated and even non-professionals can operate it, which will help solving the personnel problems. Importantly, the sample analysis time will be substantially reduced: the technology enables the analysis procedures to be completed in five to seven minutes, while simultaneously measuring the content of different analytes in a sample.’

Get inside the nanopore

The device operates on the basis of interaction between DNA aptamers and protein nanopores. DNA aptamers are short DNA chains of approximately 80 nucleotides in length. The diameter of each of them is slightly less than the nominal pore size; therefore, only one such chain can pass through it. Nanopore technology is rapidly developing at the moment. A large number of projects have been launched in recent years, but there has been only one commercial implementation of them — related to DNA sequencing.

The device, developed by the ProteoSensity team, consists of modules, which determines how many substances can be analysed at the same time. Each module contains two chambers separated by a lipid membrane with a single opening — a protein nanopore. The entire process takes place within the chambers. The device is operated from a computer, and the analysis results are displayed on the monitor.

At the beginning of the analysis, a DNA aptamer and a sample are placed in one of the chambers. If the sample contains the targeted component, the DNA chain, due to the physical properties of its nucleotides, interacts with the analyte, binding itself to it. This cannot happen unless the targeted molecules are detected in the sample. Further, voltage is applied, and the DNA aptamer begins to move, trying to get into the adjacent chamber. In the first case, after locating and binding to the respective target sites, the aptamers cannot pass through the tiny aperture, but instead blocks it. The detector, which is connected to the nanopore, registers that the ionic current has stopped. This implies that the analyte has been found in the sample. In the second-case scenario, the DNA chain passes through the aperture unhindered, and the ionic current crosses the barrier. The changes associated with ionic currents are negligible, meaning that the targeted substance has not been found in the sample.

The members of the team admit that, despite the simplicity of the technology, implementation challenges remain. The fact is that in order to detect an analyte, it is first necessary to isolate a high-affinity target-specific aptamer. Its nucleotides must be located in such a way that the aptamer will bind the target analyte. The possible sequence variants are first simulated on a computer and then tested in a laboratory. A process of generating aptamer pairs with activity against a single target is time-consuming, with the active involvement of the researchers. Nonetheless, the developers expect to be able to accelerate this process by tailoring modern molecular modelling approaches for their tasks. This will allow them to test fewer DNA chains. To date, the team has isolated ten sequences required for the main types of environmental monitoring.

The inventors are certain that assessments using their device will not be costly. In addition to the device, it will be necessary to purchase solutions of DNA aptamers. The volume, required to check a sample for one target analyte, will cost around 100 roubles. A reagents kit for detecting pollutants in air or soil will be in the same price range. Using these reagents, it will be possible to prepare a test sample by converting the collected samples into a liquid state.

For eco-activists and retailers

‘Our potential customers are industrial and agricultural enterprises. They regularly conduct environmental monitoring, and they have to obtain the services of special laboratories,’ explained Andrei Zolotarev. ‘Our device will enable them to carry out the monitoring themselves. In addition, the device will be of interest to eco-activists living in environmentally hazardous industrial areas.’

The start-up entrepreneurs believe that their device can be successfully utilised in the food trade. Today, food chains cannot properly control the agricultural produce for compliance with food regulations. For this reason, it is not infrequent that inspectors from

Rospotrebnadzor (Russia’s consumer rights watchdog) and other authorities impose large fines for the violation of food safety regulations, while the consumers cannot be sure whether or not they buy safe food products.

According to the ProteoSensity team, their device will help to quickly track deviations from the established standards and prevent the consequences. If agricultural produce suppliers and food manufacturers join in for eco monitoring, it will be possible to ascertain at what stage the food safety standards become compromised and who is to blame for the violation. And then, because of the low cost of the device and its consumables, the monitoring initiative is unlikely to affect the final price of food products.

At present, the students are working on the membrane lipid composition and aptamer design and synthesis. The selected DNA chains, as well as a cursory prototype of the device, will be demonstrated at the finals of the competition. For the complete assembly, some of the materials have yet to be received from abroad — the delivery has been delayed due to the current restrictions.

The ProteoSensity team unites four people. Danil Moskvichev (programme ‘Chemistry’) is shaping the membrane composition. Lavrentii Danilov (programme ‘Cellular and Molecular

Biology’) is synthesising DNA aptamers. Ilia Melnikov (programme ‘Physics’) is responsible for the detector. The team captain Andrei Zolotarev (programme

‘Bioinformatics’) is engaged in molecular modelling and is developing the business plan. The research supervisor of the project is Anton Nizhnikov, Candidate of Biology, Associate Professor in the Department of Genetics and Biotechnology at St Petersburg University.

The ‘SPbU Start-up’ contest is being held at the University for the sixth time. Teams that have presented best knowledge-intensive and commercially viable business models will receive monetary prizes from the St Petersburg University Endowment Fund: 300,000 roubles for the first place; 200,000 for the second; and 100,000 for the third. Additionally, the two winning teams may be offered to establish a small innovative enterprise with the participation of St Petersburg University. Grants for their projects’ development will amount to 1,000,000 and 700,000 roubles for the first and second places respectively. For more detailed information about the ‘SPbU Start-up-2021’ student contest please visit the website of the Endowment Fund of St Petersburg University.