Nanotechnology in biology and medicine
Nanobiotechnology
Within the framework of a joint post-science project and Peter the Great St. Petersburg Polytechnic University, we publish a text by Mikhail Khodorkovsky, Candidate of Physical and Mathematical Sciences, dedicated to research in the field of life science in the framework of molecular biology laboratories.
What is nanobiotechnology
To define such a word as nanobiotechnology, it is necessary to refer to its constituent parts. There have been many attempts to define the field of science and technology with the prefix "nano", and none of them seems to be successful. We can try to give another one with a similar failure. A nanometer (and colloquially "nano") is one billionth of a meter. For example, the size of a nitrogen molecule is about a third of a nanometer, and such a large and important protein for humans as hemoglobin is a little more than six nanometers. In order to create an effective technology for any industry, knowledge is needed about the composition, structure and mechanisms of interaction of molecules and their complexes that determine the flow of technological processes.
So without understanding the processes that take place somewhere out there, in the nanowire, nothing worthwhile can be done. This may be the explanation of this strange name in relation to biotechnologies that cover all areas of human life. Those areas that relate to medicine, pharmaceuticals, agriculture and ecology are within the sphere of interests of our center, whose common task is to obtain fundamental knowledge about biological processes at the molecular level, followed by the implementation of research results in the "national economy" in cooperation with relevant organizations.
Revolutionary biotechnologies
In order to feel the complexity of the transition from basic research to practical use, let's consider a typical example. We were approached by colleagues from the St. Petersburg Clinical Scientific and Practical Center for Specialized Types of Medical Care with a proposal to develop a rapid diagnostic method to determine the boundary between healthy and pathological tissue cells. This method is necessary for our fellow surgeons to avoid mistakes during surgery and not to remove unnecessary or, conversely, not to leave the problem unresolved. The solution of this problem is impossible without the use of a large range of modern molecular biological methods, which will probably allow us to identify the specifics of "bad" cells and find a way to identify it online.
There are a lot of similar examples of appeals to us, and each time we understand that solving any of these tasks requires deep fundamental research in order to create a working nanobiotechnology. But there is also a reverse movement, when in the process of research, seemingly far enough from the applied goals in demand today, results are obtained, the introduction of which can lead to the creation of completely new, revolutionary technologies.
Research laboratories
The formation of the Nanobiotechnology Research Complex began in 2007-2008, when St. Petersburg Polytechnic University had no experience in creating such a multidisciplinary center yet. There was a department of biophysics, a faculty of medical physics and separate groups at engineering faculties, where students received good knowledge, but there was no modern center where students could use their knowledge to engage in research work in the field of "life science". The creation of such a center at the Polytechnic University made it possible to integrate in one place both the knowledge and experience of scientists of various specialties and the energy of young people.
To date, NanoBio has two research laboratories - the Laboratory of Molecular Microbiology (LMM) and the Laboratory of Molecular Biology of Nucleotide–Binding Proteins (LMB), two Collective Use Centers (CCPs) and a scientific and educational center.
Study of bacteria and CRISPR/Cas systems
The main goal of the LMM laboratory under the leadership of the brilliant leading scientist Konstantin Severinov is to study the interactions of bacteria with each other (through chemical signals, including antibiotics) and with mobile genetic elements. The results of the work only in the last period included, "from the side" of mobile genetic elements, the isolation of new bacteriophages and functional and structural studies of the products of their genes; from the "side" of bacteria, pioneering functional and structural studies of the mechanisms of regulation of restriction-modification systems and their actions at the level of individual cells and the molecular mechanism of action of CRISPR/Cas systems of various types to ensure the resistance of bacteria to mobile genetic elements (including unique experiments conducted at the level of individual cells).
From the point of view of the interaction of cells with each other, clusters of biosynthesis of new antibiotics were predicted, the genes of which spread due to horizontal transfer, the structure and mechanism of action of the obtained new bioactive substances were determined. Semi-synthetic substances with increased bioactivity were obtained, and certified toxicological preclinical tests were carried out for three substances, a team was created capable of developing regulations for the production of installation series of bioactive substances for their testing in the laboratory, and the appropriate infrastructure was organized. A surrogate strain was found for the conversion of syngas into a useful product, for example, into ethanol, the activity of genes necessary for conversion in laboratory cultivation was shown, and experiments were conducted showing the prospects of microbiological purification of biogas from syngas components.
Interaction of proteins with DNA, RNA and ATP
The LMB laboratory, established in cooperation with the St. Petersburg Institute of Nuclear Physics, studies the mechanisms and dynamics of the interaction of various proteins with DNA, RNA, ATP and other nucleotides using modern experimental biochemical and biophysical methods, as well as theoretical methods of molecular modeling and molecular dynamics. Obtaining new knowledge in this field allows us to deepen understanding of the mechanisms of carcinogenesis, hereditary diseases, aging, DNA repair, cell division, translation and many other biological processes and thereby contributes to the development of new approaches in the treatment of socially significant diseases (cancer, hereditary and infectious) based on knowledge of the individual characteristics of the patient, as well as in increasing the duration of human life.
These studies will help to create new antibiotics and agents that prevent the formation of resistance of microorganisms to antibiotics, and, in addition, accelerate the development of biotechnological strains of bacteria to neutralize radioactive waste and improve the human environment.
One of the latest impressive results of the laboratory's research is the discovery of small peptide molecules that inhibit the resistance of pathogenic bacteria to the action of antibacterial drugs. Obtaining this result would have been impossible without the combined efforts of the theoretical group of the laboratory, which provided full–atomic modeling of the molecular complex "protein - DNA", and highly professional experimenters who confirmed the effect using modern molecular biological methods, including single-molecular ones. At the moment, the obtained result is in the patenting stage.
Research methods
Fundamental research in the NIC is carried out using an integrated approach, including methods of genomic analysis, structural biology, mass spectrometry, bioinformatic analysis, molecular and classical genetics of bacteria, biochemical approaches, methods of mass and NMR spectrometry, CD spectroscopy, spectrophotometry and fluorometry, methods of vital fluorescence microscopy and automatic image analysis, subdifraction fluorescence microscopy, molecular modeling, as well as cutting-edge single cell and single molecule technologies.
In contrast to those listed above, single-molecular methods are practically unknown to a wide range of researchers in Russia, and, perhaps, a few words should be said about their capabilities using the example of the Laser Tweezers installation available in the NIC.
The methods allow us to study the properties of individual molecules, as well as to obtain data on the dynamics of their changes in real time, excluding averaging over an ensemble of thousands and millions of molecules, which is inevitable when studying in a "test tube". In this regard, single-molecular research methods, which have been actively developing abroad over the past 10-15 years, have become a necessary tool in the study of structural and mechanical aspects, for example, DNA-protein interactions and interactions of DNA with substances of a non-protein nature, as well as in the study of the dynamics of these processes.
One of these most promising research methods is the optical capture method implemented in the "Laser Tweezers" installation. Studies on it allow manipulating DNA molecules in an aqueous solution, as well as measuring the forces applied to them in a wide range (from hundreds of femtonewtons to tens and hundreds of piconewtons). This range includes forces developed by molecular motors representing individual biological molecules (for example, DNA polymerase), as well as forces whose application leads to a change in the structural properties of individual nucleic acid molecules (for example, the destruction of the secondary structure of DNA).
Unfortunately, despite the widespread use of these methods abroad, in Russia at the moment only we have a working installation, so we are forced to master and develop research methods by studying articles and exchanging experience with foreign colleagues.
Interdisciplinary complex
The staff of the research complex consists of researchers of different specialties. To master and develop methods using sophisticated physical equipment, highly professional physicists and engineers are needed, without whose efforts the research capabilities of biologists would be very limited. Almost all the work carried out in the NIC is an example of the interaction of groups with different professional specialization.
As an example, studies of the interaction of eukaryotic protein complexes can be cited Pontin and Reptin with DNA and ATP. These proteins are responsible for many processes of vital activity of cells of the human body: it is known that the level of synthesis of these proteins directly affects the development of liver cancer.
Several groups with different specializations are working on the study of this protein complex: theorists engaged in molecular modeling of the properties of the protein – DNA complex, biochemists synthesizing these proteins and their mutants, biophysicists investigating their activity by classical biophysical methods, and physicists investigating the dynamics of the formation of complexes of these proteins on individual DNA molecules using optical capture. Today, there are more than fifty employees in the NIC team, while more than 70% are graduate students and students of various specialties. It is behind them that we see the future successes and openings of our center.
About the author: Mikhail Khodorkovsky – Candidate of Physical and Mathematical Sciences, Director of the Research Complex "Nanobiotechnology" SPbPU, Head of the Laboratory of Molecular Biology of nucleotide-binding proteins.
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12.07.2016