Binding of Proteins to DNA

The BI for a system with three different binding sites is given in Eq. (5.3.4) in terms of the intrinsic binding constants k, /t, and and the various direct correlations. The more general form for the total BI, per binding system, is 

Clearly, with this BI one cannot resolve all the seven intrinsic binding constants kfl kj, k kgf, k, k, and k. These can be obtained, however, from the individual Bis which, for this case, are 

It should be stressed that the above individual Bis must be measured under the same conditions used for the total BI. This is not an easy experimental task, since one must follow the fractional saturation at a specific site, say a, while all other 

As shown in Section 5.3, under very special circumstances, W(a, b) and W a, b, c) reduce to the corresponding interaction energies U a, b) and U a, b, c), respectively. If this is the case, and when the sites a, b, and c are arranged linearly, then one can approximately assume that 

Sources of Long-Range and Nonadditivily of the Correlation Functions 

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Protein-DNA complexes are usually formed by adding small portions of the protein solution to the DNA. The formation of the complex is best monitored by observing the changes of the DNA imino proton signals in a ID spectrum after each step. A reversed approach, i.e. adding the DNA to a protein solution, is not recommended because of the formation of higher order complexes by nonselective binding of protein to DNA. 

Hard T, Lundback T. Thermodynanucs of sequence-specific protein-DNA interactions. Biophys. Chem. 1996 62 121-139. Spolar RS, Record MT Jr. Coupling of local folding to site-specific binding of proteins to DNA. Science 1994 263 777-784. 

Binding of protein to DNA can deform Its helical structure, causing local bending or unwinding of the DNA molecule. 

Spolar, R., and Record, M. (1994). Coupling of Local Folding to Site-specific Binding of Proteins to DNA, Science 263 777-783. 

Recent studies using osmotic pressure have allowed determination of the number of water molecules that are displaced in specific and nonspecific binding of protein to DNA. Such a method has been used to study the interaction of the gal repressor with DNA [15]. Depending upon the nature of the osmolyte, between 100 and 180 water molecules were displaced during the above protein-DNA complex formation. This appears to be an unusually large number and needs further confirmation. 

In spite of the enormous complexity, the study of the effect of various solutes on the solvation of biomolecules such as proteins, nucleic acids, glycoproteins, polysaccharides, etc., is important. The knowledge of such solute effects can give us a method of controlling biochemical processes such as enzymatic activity, binding of proteins to DNA, etc. No doubt, nature uses these same methods to control and regulate its own processes. 

The interaction of DNA with proteins is a good example of systems where hydrophobic interactions are of great importance. Essential genetic functions such as transcription, replication, cleavage and recombination rely on the ability of proteins to recognize and interact with specific sequences of DNA. Extensive studies have thus been performed to understand the underlying mechanism of the binding of proteins to DNA (e.g. for reviews see Refs. [66-68]). 

This reaction with tryptophan could have specific effects on mechanism of cellular control, since aromatic amino acids play a role in the specific binding of proteins to DNA. 

Regulation of transcription is a central mechanism by which cells respond to developmental and environmental cues. RNA polymerase Il-mediated transcription in eukaryotes is to a large extent regulated at the level of chromatin, which forms a physical barrier for the binding of proteins to the promoter region of a target gene. The basic unit of chromatin is the nucleosome, which consists of an octamer of histone proteins around which the DNA is wrapped (see Fig. la). 

An imderstanding of the mechanism by which the highly specific and selective recognition of a nucleotide sequence is achieved is only possible with knowledge of the structural details of specific protein-nucleic acid complexes. For the regulation of gene activity the binding of proteins to double-stranded DNA is of central importance. We... 

The Isoelectric Point of Histones Histones are proteins found in eukaryotic cell nuclei, tightly bound to DNA, which has many phosphate groups. The pi of histones is very high, about 10.8. What amino acid residues must be present in relatively large numbers in histones In what way do these residues contribute to the strong binding of histones to DNA ... 

PNAs bound to double-stranded DNA targets by triplex invasion inhibit the binding of proteins to these targets. This property has been exploited for development of genome analysis methods, and is also the basis for the potential development of PNAs as antigene therapeutic drugs. 

Gamer, M. M and Revzin, A. (1981) A gel-electrophoresis method for quantifying the binding of proteins to specific DNA regions—application to components of the Escherichia coll lactose operon regulatory system Nucleic Acids Res 9, 3047-3060. 

Footprinting. A technique that results in a DNA sequence ladder in which part of the ladder is missing due to the binding of protein to the DNA before processing. 

Another label-free optical detection method—FTIR-ATR—has been applied for detection of thrombin by means of DNA aptamers [73], The antithrombin DNA aptamer previously developed by Tasset et al. [17] was immobilized covalently onto Si surface using UV irradiation method. As a quantitative measure, the area of N-H and CH2 bands was used. This method allowed to detect thrombin with a sensitivity around 10 nmol/L. The specificity of binding of protein to aptamer was also investigated using DNA with no binding site for thrombin. It has been noted that for effective binding study by FTIR-ATR method, the concentration of protein should be kept lower than 100 nmol/L. 

Gamer, M.M., Revzin, A. (1981) A Gel Electrophoresis Method for Quantifying the Binding of Proteins to Specific DNA Regions Applications to Components of the Escherichia coli Lactose Operon Regulatory System, Nucleic Acids Res. 9, 3047-3060. 

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