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Showing 1 to 20 of 50 for “"Protein-DNA interactions"”.
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Protein/DNA interactions during site-specific recombination
… of the tyrosine recombinase family. Previous DNase I footprinting experiments demonstrated that IntDOT interacts with five arm-type sites, but exactly how the arm-type sites participate in the integration and excision of CTnDOT was not known. I constructed site-directed mutations in each of …
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Computational Methods for the Measurement of Protein-DNA Interactions
It is of interest to know where in the genome DNA binding proteins act in order to effect their gene regulatory function. For many sequence specific DNA binding proteins we plan to predict the location of their action by having a model of their affinity to short DNA sequences. Existing and new …
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Dynamics of protein-DNA interactions in a Mu transpososome
… allows movement of a defined stretch of DNA, a transposon, from one DNA location to another. This process is required for the life-cycles of many viruses, from bacteriophage Mu to HIV; it is spreading antibiotic resistances between bacterial populations; and it is responsible for …
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Dithioated Phosphates in DNA Duplex Thermodynamics and Protein-DNA Interactions
Phosphorodithioated DNA contains sulfur atoms at both non-bridging phosphoryl oxygen positions. As an achiral chemical modification of the internucleotide linkage it imparts altered biophysical properties to the phosphate moiety, but still retains normal DNA characteristics such as the ability to …
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On mass spectrometry analysis of gene regulatory protein-DNA interactions
Contains fulltext : 194868.pdf (Publisher’s version ) (Open Access)
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The Role of Water-Adenine Complexes in Protein-Dna Interactions
… investigate the role of specific water-mediated interactions in protein-DNA complexes. The analogues create a ""bound"" water molecule that will be distinct from the water molecules of bulk solvent."
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Recognition, stability, and assembly in protein folding and protein-DNA interactions
… structure and function is crucial to utilizing proteins and nucleic acids as therapeutic agents, as research tools, and in industrial and environmental applications. To elucidate the principles of macromolecular assembly and recognition, two systems were studied using genetic engineering, …
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Application of the Theory of Elasticity to Modeling of Protein -Dna Interactions
… to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending anisotropy, and electrostatic properties. All the model parameters are considered to be …
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Computational Inference of Genome-Wide Protein-DNA Interactions Using High-Throughput Genomic Data
… regulation is the interaction between regulatory proteins, such as transcription factors (TF) and nucleosomes, and the genome. Different high-throughput techniques have been invented to map these interactions genome-wide, including ChIP-based methods (ChIP-chip, ChIP-seq, etc.), nuclease digestion …
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Protein -Dna Interactions Required for Regulation of the Proline Utilization Operon in Salmonella
… approach was used to enrich for put control DNA molecules defective in PutA binding in vitro. These experiments identified nucleotide residues that may be important for the specificity of the PutA-put control region interaction. Using the lambda Red system, the wild-type put control region in …
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A study of protein-DNA interactions using atomic force microscopy and DNA origami
… of the top concerns. Much of the detail of how proteins find their target sites and how they cleave at the sites remains unclear. Despite much progress in lab environments, where the tolerance for imprecise cutting is relatively high, in vivo treatment remains difficult. Most genome editing …
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Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing
DNA replication is a fundamental process that ensures the faithful duplication of genetic material in all living organisms. In eukaryotic cells, DNA replication proceeds bidirectionally from origins of replication. At the heart of this process is the eukaryotic replicative helicase, Mcm2-7, which …
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Predicting protein-DNA interactions using statistical modeling and biophysical representations of high-throughput sequencing data
Proteins are the cell’s most abundant component, excluding water, and participate in almost every biological process. Their functions include gene regulation, metabolic catalysis, molecular transportation, immune defense, and other critical roles. Such diverse capabilities arise from their …
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High-Throughput Detection of Protein---Protein and Protein---Dna Interactions via Photonic Crystal Biosensors: Applications to Apoptosis Inducing Factor
… high-throughput techniques. Macromolecular interactions including protein---small molecule, protein---nucleic acid, protein---protein, and whole cell interactions can be measured using PC biosensors. Presented herein is the first application of PC biosensors to a protein---nucleic acid …
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High-throughput detection of protein—protein and protein—DNA interactions via photonic crystal biosensors: applications to apoptosis inducing factor
… high-throughput techniques. Macromolecular interactions including protein—small molecule, protein—nucleic acid, protein—protein, and whole cell interactions can be measured using PC biosensors. Presented herein is the first application of PC biosensors to a protein—nucleic acid interaction …
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High-Throughput Screening Development Using Photonic-Crystal Optical Biosensor
Protein-DNA interactions are essential for fundamental cellular processes such as transcription, DNA damage repair, and apoptosis. As such, small molecule disruptors of these interactions could be powerful tools for investigation of these biological processes, and such compounds would have great …
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Biophysical Analyses of Intermolecular Ion-Pairs in Protein-DNA Complexes
… processes, one of the most fundamental interactions is the formation of the ion pair. In protein-DNA complexes, ion pairs form between basic side chains, such as lysine and arginine, and the phosphate backbone of DNA. Moreover, ion pairs are found in dynamic equilibrium between two major …
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Studies of a DNA modification methyltransferase from Rhodobacter sphaeroides
The DNA methyltransferases represent an interesting class of enzymes for the study of protein-DNA interactions due to their high specificity, structural simplicity, and biological importance. RsrI methyltransferase (M$\cdot$RsrI) from Rhodobacter sphaeroides recognizes duplex d(GAATTC) and deposits …
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A genetic analysis of bacteriophage lambda integrase-core site interactions
… recombination system to integrate its DNA into the E. coli chromosome during lysogeny. The viral protein, Integrase (Int), catalyzes strand exchange between the phage attachment site, attP, and the host target sequence, attB to generate the prophage sites, attL and attR. attP contains …
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