1st ed. 427 s. : il.
- Keywords
- DNA,
- MeSH
- DNA-Binding Proteins MeSH
- DNA MeSH
- Genetic Techniques MeSH
- Publication type
- Handbook MeSH
DNA-protein interactions play an essential role in many regulatory mechanisms such as replication, transcription or translation and are responsible for the maintenance of the genome integrity. Isolation, identification and subsequent characterization of the biological function of DNA binding proteins propose insight into the pathological mechanisms that underlie various diseases. This review brings an overview of methods used for isolation and identification of DNA binding proteins (DNA-affinity chromatography coupled with quantitative proteomics and mass spectrometry) and subsequent methods for the characterization of their biological functions (fluorescence microscopy). Principles, advantages and disadvantages of individual methods are briefly discussed.
Local microirradiation with lasers represents a useful tool for studies of DNA-repair-related processes in live cells. Here, we describe a methodological approach to analyzing protein kinetics at DNA lesions over time or protein-protein interactions on locally microirradiated chromatin. We also show how to recognize individual phases of the cell cycle using the Fucci cellular system to study cell-cycle-dependent protein kinetics at DNA lesions. A methodological description of the use of two UV lasers (355 nm and 405 nm) to induce different types of DNA damage is also presented. Only the cells microirradiated by the 405-nm diode laser proceeded through mitosis normally and were devoid of cyclobutane pyrimidine dimers (CPDs). We also show how microirradiated cells can be fixed at a given time point to perform immunodetection of the endogenous proteins of interest. For the DNA repair studies, we additionally describe the use of biophysical methods including FRAP (Fluorescence Recovery After Photobleaching) and FLIM (Fluorescence Lifetime Imaging Microscopy) in cells with spontaneously occurring DNA damage foci. We also show an application of FLIM-FRET (Fluorescence Resonance Energy Transfer) in experimental studies of protein-protein interactions.
To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Prots. Struct. Funct. Genet., 41:271-287)] and dinucleotide conformers [Svozil, Kalina, Omelka and Schneider (2008) (DNA conformations and their sequence preferences. Nucleic Acids Res., 36:3690-3706)], respectively. Assembling the mutually interacting protein blocks and dinucleotide conformers into 'interaction matrices' revealed their correlations and conformer preferences at the interface relative to their occurrence outside the interface. The analyzed data demonstrated important differences between complexes of various types of proteins such as transcription factors and nucleases, distinct interaction patterns for the DNA minor groove relative to the major groove and phosphate and importance of water-mediated contacts. Water molecules mediate proportionally the largest number of contacts in the minor groove and form the largest proportion of contacts in complexes of transcription factors. The generally known induction of A-DNA forms by complexation was more accurately attributed to A-like and intermediate A/B conformers rare in naked DNA molecules.
- MeSH
- DNA-Binding Proteins chemistry MeSH
- DNA chemistry MeSH
- Phosphates MeSH
- Data Interpretation, Statistical MeSH
- Nucleic Acid Conformation MeSH
- Protein Conformation MeSH
- Models, Molecular MeSH
- Protein Binding MeSH
- Water chemistry MeSH
- Computational Biology MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The effects of the lesions induced by single, site-specific 1,2-GG or 1,3-GTG intrastrand adducts of cis-diamminedichloroplatinum(II) formed in oligodeoxyribonucleotide duplexes on energetics of DNA were examined by means of differential scanning calorimetry. These effects were correlated with affinity of these duplexes for damaged-DNA binding-proteins XPA and RPA; this affinity was examined by gel electrophoresis. The results confirm that rigid DNA bending is the specific determinant responsible for high-affinity interactions of XPA with damaged DNA, but that an additional important factor, which affects affinity of XPA to damaged DNA, is a change of thermodynamic stability of DNA induced by the damage. In addition, the results also confirm that RPA preferentially binds to DNA distorted so that hydrogen bonds between complementary bases are interrupted. RPA also binds to non-denaturational distortions in double-helical DNA, but affinity of RPA to these distortions is insensitive to alterations of thermodynamic stability of damaged DNA.
- MeSH
- Calorimetry, Differential Scanning MeSH
- DNA-Binding Proteins chemistry metabolism MeSH
- DNA chemistry metabolism MeSH
- Financing, Organized MeSH
- Nucleic Acid Conformation MeSH
- DNA Damage MeSH
- Replication Protein A chemistry metabolism MeSH
- Base Sequence MeSH
- Thermodynamics MeSH
- Binding Sites MeSH
- Hydrogen Bonding MeSH
- Xeroderma Pigmentosum Group A Protein chemistry metabolism MeSH
One of the most important functions of the tumor suppressor p53 protein is its sequence-specific binding to DNA. Using a competition assay on agarose gels we found that the p53 consensus sequences in longer DNA fragments are better targets than the same sequences in shorter DNAs. Semi-quantitative evaluation of the competition experiments showed a correlation between the relative p53-DNA binding and the DNA lengths. Our results are consistent with a model of the p53-DNA interactions involving one-dimensional migration of the p53 protein along the DNA for distances of about 1000 bp while searching for its target sites. Positioning of the p53 target in the DNA fragment did not substantially affect the apparent p53-DNA binding, suggesting that p53 can slide along the DNA in a bi-directional manner. In contrast to full-length p53, the isolated core domain did not show any significant correlation between sequence-specific DNA binding and fragment length.
- MeSH
- Time Factors MeSH
- DNA genetics chemistry MeSH
- Electrophoresis, Agar Gel MeSH
- Financing, Organized MeSH
- Genes, p53 MeSH
- Binding, Competitive MeSH
- Humans MeSH
- Tumor Suppressor Protein p53 genetics MeSH
- Plasmids metabolism MeSH
- Recombinant Proteins chemistry MeSH
- DNA Restriction Enzymes metabolism MeSH
- Models, Statistical MeSH
- Protein Structure, Tertiary MeSH
- Binding Sites MeSH
- Check Tag
- Humans MeSH
A simple approach to DNA tail-labelling using terminal deoxynucleotidyl transferase and modified deoxynucleoside triphosphates is presented. Amino- and nitrophenyl-modified dNTPs were found to be good substrates for this enzyme giving 3'-end stretches of different lengths depending on the nucleotide and concentration. 3-Nitrophenyl-7-deazaG was selected as the most useful label because its dNTP was efficiently incorporated by the transferase to form long tail-labels at any oligonucleotide. Accumulation of many nitrophenyl tags per oligonucleotide resulted in a considerable enhancement of voltammetric signals due to the nitro group reduction, thus improving the sensitivity of electrochemical detection of the tail-labelled probes. We demonstrate a perfect discrimination between complementary and non-complementary target DNAs sequences by tail-labelled hybridization probes as well as the ability of tumour suppressor p53 protein to recognize a specific binding site within tail-labelled DNA substrates, making the methodology useful in electrochemical DNA hybridization and DNA-protein interaction assays.
- MeSH
- DNA Probes analysis chemistry MeSH
- DNA-Binding Proteins chemistry MeSH
- DNA Nucleotidylexotransferase chemistry MeSH
- Electrochemical Techniques methods MeSH
- Nucleic Acid Hybridization methods MeSH
- Molecular Structure MeSH
- Purine Nucleotides chemistry MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
HU protein is a member of nucleoid-associated proteins (NAPs) and is an important regulator of bacterial virulence, pathogenesis and survival. NAPs are mainly DNA structuring proteins that influence several molecular processes by binding the DNA. HU ́s indispensable role in DNA-related processes in bacteria was described. HU protein is a necessary bacterial transcription factor and is considered to be a virulence determinant as well. Less is known about its direct role in host-pathogen interactions. The latest studies suggest that HU protein may be secreted outside bacteria and be a part of the extracellular matrix. Moreover, HU protein can be internalized in a host cell after bacterial infection. Its role in the host cell is not well described and further studies are extremely needed. Existing results suggest the involvement of HU protein in host cell immune response modulation in bacterial favor, which can help pathogens resist host defense mechanisms. A better understanding of the HU protein's role in the host cell will help to effective treatment development.
