[An important role for weak interactions during the recognition of long DNA and RNA molecules by enzymes]

Recognition of small ligands by the enzymes occurs usually due to the strong specific contacts, such as hydrogen bonds, electrostatic and stacking interactions. A complex formed by long DNA or RNA molecules and site-specific enzymes includes, as a rule, not all mononucleotide units of an enzyme binding cleft. Recognition is based preferentially on the strong interaction of the enzymes with certain structural elements or specific nucleotides of the sequences. The weak hydrophobic of van-der-Waals (electrostatic) interactions usually are not very important in enzyme interaction with small ligands or definite units of long nucleic acid molecules and do not exceed the Kd estimation limits. However, some enzymes catalyzing reactions of nucleic acid conversion independently of their structures, most likely, interact with all mononucleotide units within the protein molecules. In this case, due to the additivity of the free energies, when the length of the recognized substrate is about 10-30 nucleotides, the contribution of the weak interactions to the substrate affinity may be about 4-7 orders of magnitude. These interactions become stronger than any other. New approaches for studying the weak interactions were analyzed. An attempt is made to prove the extremely important role of DNA/RNA weak interactions with the enzymes in their recognition and conversion with reference to some important enzymes participating in replication and repair processes.