Nucleic acid - protein fingerprints. Novel protein classification based on nucleic acid - protein recognition

Protein chemistry uses protein description and classification based on molecular mass and isoelectric point as general features. Enzymes are also compared by enzymatic reaction constants, namely Km and kcat values. Proteins are also studied by binding to different oligonucleotides. Here we suggest a simple experimental method for such a comparison of DNA binding proteins, which we call "nucleic acid-protein fingerprints". The experimental design of the method is based on an use of short oligonucleotides immobilized inside microarray of hydrogel cells - biochip. As a first stage, we solved a simple experimental task: what is the shortest single strand oligonucleotide to be recognized by protein? We tested binding of oligonucleotides from 2 to 12 bases, and we have obtained unexpected result that tetranucleotide one is long enough for specific protein binding. This 4-mer can contain two universal bases - 5-nitroindole nucleoside analogue (Ni) and only two meaningful bases, like A, G, T and C. The result obtained opens a way for constructing the simplest protein binding microarray. This microarray consists of 16 meaningful dinucleotides, like AA, AG, CT, GG etc. Physical sequences of all the nucleotides were NiNiAA, etc, where Ni is bound to gel through the amino linker. We prepared such an array and tested it for specific binding of several DNA/RNA binding proteins, labeled with fluorescent dyes like Texas Red of Bodipy. We tested RNase A and Binase for binding on the simplest microarray. It contains only 16 units, and there is a significant difference in the binding patterns. The microarray based on 3-mers must contains 64 units and must have much more specificity. The new principle of protein classification based on nucleic acid-protein recognition has been proposed and experimentally proved. Such an experimental approach must lead to a universal classification of specific DNA/RNA binding proteins

ANSWERING THE ACUTE QUESTION: HOW TO USE AMINOXYL (NITROXIDE) FREE RADICALS APPROPRIATELY TO REGULATE OXIDATIVE/NITROSATIVE STRESS AND AS POTENTIAL MEDICINES // Ученые записки КФУ. Естественные науки 2010 N4

Представлен критический обзор современных способов фармакологического применения аминоксильных (нитроксильных) стабильных свободных радикалов с целью предотвращения цитотоксического воздействия оксидативного и нитрозативного стресса. Как и оксид азота (NO), свободные нитроксильные (аминоксильные) радикалы содержат фрагмент N-O. При помещении в органическую структуру оксид азота теряет свою сигнальную функцию, характеризуется триплетным спектром ЭПР, приобретает способность взаимодействовать с супероксидом и токсичными метаболитами оксида азота, сохраняя при этом некоторые виды биологической активности. Это может стать основой для будущего применения аминоксильных радикалов в фармакологии в качестве противораковых, противолучевых или гипотензивных препаратов. Аминоксильные радикалы рассматриваются как потенциальные лекарства для комплексного применения с индукторами оксида азота с целью избежать цитотоксических эффектов. Для использования аминоксильных свободных радикалов в качестве медицинских препаратов необходимо дополнительное изучение их нейротропных свойств

ANSWERING THE ACUTE QUESTION: HOW TO USE AMINOXYL (NITROXIDE) FREE RADICALS APPROPRIATELY TO REGULATE OXIDATIVE/NITROSATIVE STRESS AND AS POTENTIAL MEDICINES // Ученые записки КФУ. Естественные науки 2010 N4

Представлен критический обзор современных способов фармакологического применения аминоксильных (нитроксильных) стабильных свободных радикалов с целью предотвращения цитотоксического воздействия оксидативного и нитрозативного стресса. Как и оксид азота (NO), свободные нитроксильные (аминоксильные) радикалы содержат фрагмент N-O. При помещении в органическую структуру оксид азота теряет свою сигнальную функцию, характеризуется триплетным спектром ЭПР, приобретает способность взаимодействовать с супероксидом и токсичными метаболитами оксида азота, сохраняя при этом некоторые виды биологической активности. Это может стать основой для будущего применения аминоксильных радикалов в фармакологии в качестве противораковых, противолучевых или гипотензивных препаратов. Аминоксильные радикалы рассматриваются как потенциальные лекарства для комплексного применения с индукторами оксида азота с целью избежать цитотоксических эффектов. Для использования аминоксильных свободных радикалов в качестве медицинских препаратов необходимо дополнительное изучение их нейротропных свойств

Russian Institute for Advanced Study as a New Form of Training of Highly Trained Teaching Staff

Introduction: the aim of the paper is the analysis of role and capabilities of the Russian Institute for Advanced Study under Moscow State Pedagogical University in preparation of the top qualification scientific and teaching staff, possessing not only high potential in the narrow specialisation, but also inter- and transdisciplinary knowledge. The necessity for such staff is caused by rapid growth of scope and rates of new scientific knowledge accumulation, and, as a result, by development on their basis of new technologies in all sectors and by intensive introduction of such developments into all spheres of human activities. Materials and Methods: the processing of results of survey by the questionnaire method, as well as the synergistic and systemic approaches in their analysis and generalization, constituted the methodological basis for this study. Results: by analysis and generalisation of survey results it was shown that the Russian Institute for Advanced Study is unique form of training of top qualification scientific and teaching staff. The most important role of the Russian Institute for Advanced Study functioning format in implementation for Institute’s tasks is shown. During the work period at the Russian Institute for Advanced Study scientific and pedagogical employees are having unique possibility for finding non-standard approaches and methods for solving various problems, arising during projects implementation and which can’t be solved due to formal limitations of the traditional education system. Discussion and Conclusions: it is shown that the structure and principles of the Russian Institutes for Advanced Study functioning provide preparation of scientific and pedagogical staff of the highest qualification. The requirement for expanding Institutes for Advanced Study network in Russia is discussed. The results obtained represent practical importance for researchers engaged in the analysis of inter- and transdisciplinary knowledge role in the training of scientific and pedagogical staff. Further studies in this area can be devoted to analysis and generalization of inter- and transdisciplinary approach in the training of highly qualified scientific and pedagogical staff

Interfacial Interactions of Phosphatidylglycerol with Oligonucleotide DNA Revealed by Molecular Dynamics Method

An interaction of DNA with lipids is of great interest because of their functions. As fatty acids and lipids can specifically bind to nucleic acids forming a code sequence of the genomic DNA, it is important to study the interaction of the oligonucleotide DNA (dA)20.(dT)20 with phosphatidylglycerol by the molecular dynamics method. Molecular docking has shown that these components form a stable complex with 5.8 kcal/mole binding energy, wherein the lipid is located in the DNA minor groove. This configuration marks 354 atom groups separated by a distance less than 3.4 Ǻ. The van der Waals and hydrophobic interactions play the leading part in the DNA-phospholipid complex stabilization along with hydrogen bonds.3238-324