Laboratory of Protein

Laboratory of Protein-DNA Interactions (Head scientist – Prof. V. Siksnys) studies the features of restriction enzymes (endonucleases), their structure and molecular mechanisms of catalytic activity. Type II restriction endonucleases are enzymes that specifically recognize nucleotide sequences of the particular length (usually, 4-6 base pairs in length) and in case of Mg²⁺ ions presence they cut phosphodiesteric joints. 3000 restriction elements that recognize more than 200 of different nucleotide sequences have been characterized so far (REBASE). Due to their unique specificity, type II restriction endonucleases gained application as indispensable “molecular tools” in experiments of gene cloning. However, there is much less of information about how they manage to distinguish one nucleotide sequence from another and to cut phosphodiesteric joint in a particular place. It is not clear so far whether these enzymes for DNA recognition and catalysis use the same or different mechanisms. The determination of such tendencies is important for both understanding the main principles of specific protein-DNA interaction and creating restriction endonucleases characterized by the new specificity.

The focus is on the following types of research:

• How restriction endonucleases distinguish one nucleotide sequence from the others?
• Whether the common principles of nucleotide sequence recognition and catalysis exist among restriction endonucleases that recognize related nucleotide sequences?
• How recognition of nucleotide sequence is related with catalysis?

The answers of these methods are solved by applying various methods:

• Dimensional structures of restriction endonucleases are determined by X-ray diffraction method (in association with Max Planck Institute of Biochemistry, Martinsried).
• The role of individual amino acids in specific recognition of nucleotide sequences and catalysis is studied by applying site-directed mutagenesis;
• Interact between restriction endonucleases and DNA mechanisms is researched by applying kinetic, spectroscopic, biochemical and thermodynamic methods.

The main projects of interaction between protein nucleic acids are conducted in the following directions: research of structure and functions of restriction enzymes that are independent of metals; research in determination of regulation principles of restriction enzymes activity, analysis of relations between structure, functions and specificity of restriction enzymes in subfamilies as well as studies of new structures of restriction enzymes.

If necessary, this laboratory could provide customers with information about the possibilities restriction enzymes’ application in plant biotechnology area as well as provide consultations in detection of plant protein structures.

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