The technology provided by scientists from Perm Polytech University will allow to edit the genes more accurate

In recent decades, synthetic biology has got its development, within which unique biological systems with “programmed” functions and properties are created. The results of these studies can be used in the development of biosensors, drug delivery platforms, and biocomputers. Scientists from the Perm Polytech University have improved the accuracy of the repressilator, an artificial closed circuit that will allow predicting the behavior of genetic systems.

Perm National Research Polytechnic University

The scientists published the results of the work in the Computer Research and Modeling journal. The development was implemented with the support of the Ministry of Science and Higher Education of Russia and the world-class REC “Rational Subsoil Use”.

– Synthetic biology allows you to create artificial DNA chains and biological systems by “programming” the genetic code of living organisms. In particular, it is helpful in the development of biosensors, drug delivery platforms and biological computers. It is assumed that it is possible to predict the behavior of a genetic system before its implementation. The model of an artificial gene chain – a repressilator – allows to reproduce the dynamic processes that occur during gene expression, – says Maxim Buzmakov, the one of the developers, a postgraduate student of the Applied Physics Department of the Perm Polytech University.

The first repressor was created in 2000. It is a closed small-sized chain of three genes that suppress the ability to produce each other’s protein. The genes are of natural origin, but do not occur in such a combination in nature. According to scientists, due to such a chain structure, fluctuations in protein concentrations occur, which ensure the functioning of cells.

Schematic representation of the lag repressilator gene network

Scientists of the Perm Polytech University have described the dynamic processes in the artificial gene chain and improved the accuracy of its work. To do this, they proposed the use of a delayed repressor. According to them, the processes of gene expression consist of multi-stage reactions during which ensembles of complex organic compounds are formed. These processes are distributed over space, stretched out in time and come with a delay. Strong deviations of values ​​in the gene chain and a small number of molecules require the consideration of random and uncertain factors.

Diagram explaining the modified Gillespie algorithm

– The uniqueness of the technology is in the method of modeling the genetic system. We have replaced the processes of transcription and translation of genes with delayed expression. This made it possible to simplify the model significantly without losing the dynamic properties of the system. The model gives an idea of ​​how the protein concentration in the system changes over time. Our development will also allow us to track the movement of protein fields in space as a result of the interaction of cells with repressilators, – explains Dmitry Bratsun, leading researcher, Doctor of Physical and Mathematical Sciences, Associate Professor and the scientific supervisor of the research, the head of the of Applied Physics Department, Perm Polytech University.

Scientists have created a numerical algorithm and software package, and also carried out their test calculations. This made it possible to obtain more accurate information about the behavior of the system, which could not be done earlier using other methods.

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