Application to DNA-Protein Interactions

The first application of the MCF method (in its first version) to the interaction of two infinite chains, namely to the interaction of polyglycine (in different conformations) and different polynucleotide chains, was performed by Otto et This calculation represents the first step in the theoretiod treatment (at the ab initio level) for DNA-protein 

Despite the vast number of chemical and physical experiments, the available information is still insufficient to explain the detailed structiu e of the nucleohistones, with the exception of several DNA-repressor protein complexes. Some general tendencies, however, have been found the a-helix conformation of the polypeptides is predominant in histones, as has been shown by ORD experiments lysine-rich histones mainly occupy the major groove of B-DNA, while protamines are bound to DNA in the minor groove (for further details see Otto et alP ). 

The level of detailed knowledge is much higher for certain repressor proteins and their interactions with DNA. The structures of four polypeptides that specifically bind to DNA have been determined recently, namely the lac repressor protein, - the cro repressor protein from bacteriophage, the catabolite gene activator protein from Escheria coli, and the amino-terminal fragment of the Cl repressor protein from bacteriophage In addition to the primary structure of the polypeptide, the sequence of the base pairs in that DNA fragment to which the relatively short polypeptide is bound, is known. Furthermore, structural data about the conformation of the peptide backbone are available, e.g., strands of a-helices followed by antiparallel -pleated sheets. 

Already this short and by no means complete survey reveals the general problem inherent in the theoretical investigations of the interaction between DNA and proteins. One of the main difficulties in the treatment of complicated systems like DNA-peptide complexes consists 

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The ultimate goal of microarray-based expression analysis is to acquire a comprehension of the entire cellular process, in order to exploit and to standardize the multidi-menisional relations between genotype and phenotype. However, an increasingly important parameter, which has not yet been substantially taken into account, is the role of cellular translation. This means that mRNA expression data need to be correlated with the assortment of proteins actually present in the cell. One approach is based on the use of microarrays containing double-stranded DNA probes for the analysis of DNA-protein interaction and, thus, the detection and identification of DNA-binding proteins by means of fluorescence [130] or mass spectrometry analysis [131]. Moreover, substantial efforts are currently under way to develop protein, antibody, or even cell arrays, applicable to the cor-... 

The innate sensitivity of DNA-mediated CT to perturbations in the TT-stack has prompted us to employ this chemistry as a probe of stacking structure and dynamics. We have developed a new class of DNA-based diagnostic tools that diagnose DNA mutations such as single base-pair mismatches and lesions, analyze DNA-protein interactions, and probe the sequence-depen-dent dynamics and flexibility of DNA. These applications rely on electrochemical probing of CT in DNA films self-assembled on gold electrodes. 

Many of these methods are being tested on problems in biochemistry (e.g. protein-ligand, and DNA-protein interactions), and their applications to problems in supramolecular chemistry should be straightforward. 

Due to the simplicity of the technique and due to the quality of results obtained using it routinely, this technique has found many applications. The technique has been used to determine binding constants, co-operativity, and stoichiometry of DNA-protein interaction it has been used to define binding sites, binding requirements, protein domains involved in interaction and in genome scanning. 

A great deal of interest has been shown in the study of DNA-protein interactions [30]. As such, many reviews cite the application of AFM to these interactions [30,104,112,113]. AFM has been used to provide structmal information on DNA binding sites and the stoichiometry of proteins that bind to the DNA [62]. The regulation of bacterial transcription [104], and the mechanisms involved in its initialisation are of considerable interest [114,115], as is the application of AFM in order to elucidate mechanisms of DNA-protein interactions that are involved in the repair [62] and replication [90,116] of DNA. 

Theoretical methods for the investigation of interactions between polymer chains are described in Chapter 6. Besides the theoretically clear-cut but, in the case of polymers with larger unit cells, numerically unfeasible, superchain approach, theoretical perturbation methods and the mutually consistent field (MCF) procedure recently developed at Erlangen are reviewed. The first application of the MCF method, which takes into account both the electrostatic part and polarization forces, to polynucleotide-polypeptide interactions (modeling DNA-protein interactions) is presented. 

A number of applications have been described relying on fluorophores, and a strategy for high-throughput analysis of DNA-protein interactions has been reported/ Fluorescence has been used to monitor DNA base excision repair/ to monitor the activity of the endonuclease XPF-ERCCl/ as hybridisation probes/ for the detection of protein interactions/ in PCR and in fluorescence correlation spectroscopy... 

Biosensors normally offer highly specific molecular recognition reactions like enzyme/substrate-, antigen/antibody-, DNA/DNA-, or protein-interactions [67]. Due to their specific sensing principles and set-up they are limited to special applications and boundary conditions. The limited stability and reproducibility of these devices requires higher standards of maintenance and recalibration. 

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