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Methods for specific covalent binding of modified nucleic acids to proteins and enzymes with conservation of their native structures are discussed. Possible applications of synthetic nucleic acids containing reactive (nucleophilic and electrophilic) groups and groups that can be photoactivated for testing protein–nucleic acid contacts and studying protein functioning are considered. The structures of protein–nucleic acid conjugates formed in the enzymatic reactions are described. Methods for the isolation and analysis of covalently bound protein–nucleic acid complexes are generalised. The main attention is given to methods for determination of protein sites attached to nucleic acids. The bibliography includes 226 references.