The affinity of AP-DNA containing the abasic site is higher in comparison to unspecific DNA only by one order of magnitude (G 1

The affinity of AP-DNA containing the abasic site is higher in comparison to unspecific DNA only by one order of magnitude (G 1.1 kcal/mol to 1 1.5 kcal/mol). of structural elements of DNA fragments covered by globules of enzymes and proteins to the total affinity of DNA have been evaluated. Thermodynamic and catalytic factors providing discrimination of unspecific and specific Cilliobrevin D DNAs by these enzymes on the stages of primary complex formation following changes in enzymes and DNAs or RNAs conformations and direct processing of the catalysis of the reactions were found. General regularities of recognition of nucleic acid by DNA-dependent enzymes, proteins, and antibodies were established. Keywords:different enzymes and proteins, anti-DNA antibodies, general regularities of DNA recognition == 1. Introduction == DNA- and RNA-dependent enzymes, proteins, and antibodies play a vital role in many key cellular processestranscription, replication, recombination, repair, integration, chromosome dynamics, and protection from viruses and bacteria. Therefore, understanding the molecular mechanisms of DNA-dependent enzymes, proteins, and antibody action is critical from fundamental and applied points of view. It is evident that X-ray Rabbit Polyclonal to RyR2 analysis data on the structures of complexes between Cilliobrevin D enzymes (proteins) and DNA (or RNA), including conformational changes during their interactions, play an important role in the understanding of mechanisms of nucleic acid recognition Cilliobrevin D [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16]. However, X-ray analysis data cannot provide quantitative estimations of different molecular contacts relative importance, or the relative contributions of weak, moderate, or strong specific and unspecific contacts to the total affinity of proteins for nucleic acids (NAs). X-ray analysis of sequence-specific enzymes with DNAs or RNAs sometimes leads to a misunderstanding of the real role of some specific contacts. There is a point of view that the specific contacts between proteins and DNAs that are revealed by X-ray analysis can provide a high affinity for specific nucleotides or sequences of nucleic acids (reviewed in [11,12,13,14,15,16]). There are only a few literature data on the quantitative estimation of the relative individual contributions of individual-specific nucleotides and sequences to thermodynamic (formation of complexes) and kinetic (kcat, constant rates of reaction) steps to the affinity of enzymes and proteins for DNAs or to the specificity of enzymes actions [11,12,13,14,15,16]. However, only a detailed quantitative estimation of the relative contributions of all nucleotide units of NAs can provide a correct interpretation of data obtained using an X-ray structure analysis. Therefore, it has been have developed a special approachstepwise increase in ligand complexity (SILC)to estimate the relative contributions of all individual nucleotides or specific sequences and their various structural elements to an enzymes affinity for long DNAs [11,12,13,14,15,16]. The peculiarity of this approach is the gradual complication of the structure of Cilliobrevin D DNA ligands, starting with the possible minimum ligand (structural elements of DNA), which can form any bonds with proteins or enzymes according to the scheme: Using the SILC approach, we analyzed replication, restriction, integration, topoisomerization, six different repair enzymes (uracil DNA glycosylase, Fpg protein fromE. coli, human 8-oxoguanine-DNA glycosylase, human apurinic/apyrimidinic endonuclease, RecA protein, and DNA ligase), and NA-recognizing proteins (RNA helicase, lactoferrin, lactalbumin, human serum albumin (HSA), and IgGs against DNA). Analysis of various interactions of these enzymes, proteins, and antibodies with long nucleic acids by the SILC approach has shown that the formation of contacts between them and specific nucleotides or sequences of NAs cannot provide their observed high affinity for DNAs and RNAs. Actually, all nucleotide units covered by the DNA-binding clefts interact with enzymes and proteins. High affinity is mainly (58 orders of magnitude) provided by many weak, unspecific, additive interactions between the enzymes and proteins with different structural elements of many nucleotide units of DNAs and RNAs, mostly with internucleoside phosphate groups and only sometimes with hydrophobic bases [11,12,13,14,15,16]. The relative contribution of specific contacts to the total affinity of.

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