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  • vitro
  • Now that RFC from S. cerevisiae has been purified, all seven cellular factors previously shown to be required for SV40 DNA replication in vitro have been identified in S. cerevisiae. (cshl.edu)
  • zinc fingers
  • As zinc fingers are known to be involved in m-RNA regulation, reverse transcription, protection of synthesized viral DNA, transcription inhibition, and initial integration processes, prevention of zinc finger function can have drastic effects on the function of the cell or virus. (wikipedia.org)
  • The main drawback with this procedure is the specificities of individual zinc fingers can overlap and can depend on the context of the surrounding zinc fingers and DNA. (wikipedia.org)
  • This system combines pre-selected pools of individual zinc fingers that were each selected to bind a given triplet and then utilizes a second round of selection to obtain 3-finger arrays capable of binding a desired 9-bp sequence. (wikipedia.org)
  • repair
  • By taking advantage of endogenous DNA repair machinery, these reagents can be used to precisely alter the genomes of higher organisms. (wikipedia.org)
  • In some instances, however, the repair is imperfect, resulting in deletion or insertion of base-pairs, producing frame-shift and preventing the production of the harmful protein. (wikipedia.org)
  • site
  • Since the CCHC binding site is mutation resistant and involved in the replication of HIV-1, it makes a prime candidate for the prevention of HIV through zinc ejectors. (wikipedia.org)
  • This electrophilic interaction destabilizes the zinc binding site making it easier for the zinc ion to be withdrawn due to the new arrangement of bonds. (wikipedia.org)
  • If the zinc finger domains perfectly recognize a 3 basepair DNA sequence to generate a 3-finger array that can recognize a 9 basepair target site. (wikipedia.org)
  • affinity
  • The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets, including four-way junctions, but not distorted DNA minicircles, to which the proteins bind with very high affinity. (biochemsoctrans.org)
  • DNA-binding proteins are proteins composed of DNA-binding domains and thus have a specific or general affinity for either single or double stranded DNA. (wikipedia.org)
  • Following elution, the protein readily binds DNA, indicating the protein's high affinity for DNA. (wikipedia.org)
  • With an α-helical hydrophobic core and two positively charged β-ribbon arms, HU binds non-specifically to dsDNA with low affinity but binds to altered DNA-such as junctions, nicks, gaps, forks, and overhangs-with high affinity. (wikipedia.org)
  • An electrophoretic mobility shift assay (EMSA) or mobility shift electrophoresis, also referred as a gel shift assay, gel mobility shift assay, band shift assay, or gel retardation assay, is a common affinity electrophoresis technique used to study protein-DNA or protein-RNA interactions. (wikipedia.org)
  • If the starting concentrations of protein and probe are known, and if the stoichiometry of the complex is known, the apparent affinity of the protein for the nucleic acid sequence may be determined. (wikipedia.org)
  • While isotopic DNA labeling has little or no effect on protein binding affinity, use of non-isotopic labels including flurophores or biotin can alter the affinity and/or stoichiometry of the protein interaction of interest. (wikipedia.org)
  • coli
  • Dear all Presently I am trying to purifying a DNA binding protein from E.coli. (bio.net)
  • In E. coli, H-NS binds to a P1 promoter decreasing rRNA production during stationary and slow growth periods. (wikipedia.org)
  • In prokaryotic bacteria cells such as E. coli, facilitated diffusion is required in order for regulatory proteins to locate and bind to target sites on DNA base pairs. (wikipedia.org)
  • bacterial
  • Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. (nih.gov)
  • Since bacterial binding proteins have a diversity of functions, it has been difficult to develop a common function for all of them. (wikipedia.org)
  • Upon further investigation, it was discovered that the amino acid composition of HU resembles that of eukaryotic histones, thus prompting further research into the exact function of bacterial DNA binding proteins and discoveries of other related proteins in bacteria. (wikipedia.org)
  • HU is a small (10 kDa) bacterial histone-like protein that resembles the eukaryotic Histone H2B. (wikipedia.org)
  • DPS proteins are part of a complex bacterial defence system that protects DNA against oxidative damage and are distributed widely in the bacterial kingdom. (wikipedia.org)
  • posttranslational modifications
  • The Eastern blot is used for the detection of specific posttranslational modifications of proteins. (wikipedia.org)
  • Proteins are separated by gel electrophoresis before being transferred to a blotting matrix whereupon posttranslational modifications are detected by specific substrates (cholera toxin, concanavalin, phosphomolybdate, etc.) or antibodies. (wikipedia.org)
  • nucleus
  • Eukaryotic histones package DNA to help it to fit in the nucleus, and they are known to be the most conserved proteins in nature. (wikipedia.org)
  • When cells are exposed to UV radiation, DDB1 moves from the cytosol to the nucleus and binds to DDB2, thus forming the UV-DDB complex. (wikipedia.org)
  • biological
  • p>This section provides any useful information about the protein, mostly biological knowledge. (uniprot.org)
  • Motifs do not allow us to predict the biological functions: they are found in proteins and enzymes with dissimilar functions. (wikipedia.org)
  • double-stranded
  • The histones form a disk-shaped complex called a nucleosome, which contains two complete turns of double-stranded DNA wrapped around its surface. (wikipedia.org)
  • targets
  • Thus, these proteins are often the targets of the signal transduction processes that control responses to environmental changes or cellular differentiation and development. (wikipedia.org)
  • ID proteins could be potential targets for systemic cancer therapies without inhibiting the functioning of most normal cells because they are highly expressed in embryonic stem cells, but not in differentiated adult cells. (wikipedia.org)
  • Also, on the DNA contour, the motion is slower and target sites are easy to localize while in the cytoplasm, the motion is faster but the TF's are not sensitive to their targets and so binding is restricted. (wikipedia.org)
  • identical
  • DPS are highly symmetrical dodecameric proteins of 200 kDa characterized from a shell-like structure of 2:3 tetrahedral symmetry assembled from identical subunits with an external diameter of ~ 9 nm and a central cavity of ~ 4.5 nm in diameter. (wikipedia.org)
  • structural
  • The individual A and B boxes (which, although broadly similar, show both structural and functional differences) exhibit many of the structure-specific properties of the whole protein. (biochemsoctrans.org)
  • Within chromosomes, DNA is held in complexes with structural proteins. (wikipedia.org)
  • When H-NS is bound with RNA Polymerase to the promoter region, there are structural differences in the DNA that are accessible. (wikipedia.org)
  • In proteins, a structural motif describes the connectivity between secondary structural elements. (wikipedia.org)
  • In addition to secondary structural elements, protein structural motifs often include loops of variable length and unspecified structure. (wikipedia.org)
  • Sequence motif Short linear motif PROSITE Database of protein families and domains SCOP Structural classification of Proteins CATH Class Architecture Topology Homology FSSP FSSP PASS2 PASS2 - Protein Alignments as Structural Superfamilies SMoS SMoS - Database of Structural Motifs of Superfamily S4 S4: Server for Super-Secondary Structure Motif Mining Chiang YS, Gelfand TI, Kister AE, Gelfand IM (2007). (wikipedia.org)
  • Fragment
  • The control lane (DNA probe without protein present) will contain a single band corresponding to the unbound DNA or RNA fragment. (wikipedia.org)
  • However, assuming that the protein is capable of binding to the fragment, the lane with protein present will contain another band that represents the larger, less mobile complex of nucleic acid probe bound to protein which is 'shifted' up on the gel (since it has moved more slowly). (wikipedia.org)
  • When using a biotin label, streptavidin conjugated to an enzyme such as horseradish peroxidase is used to detect the DNA fragment. (wikipedia.org)
  • Southern blotting combines transfer of electrophoresis-separated DNA fragments to a filter membrane and subsequent fragment detection by probe hybridization. (wikipedia.org)
  • UniProt
  • p>When browsing through different UniProt proteins, you can use the 'basket' to save them, so that you can back to find or analyse them later. (uniprot.org)
  • mRNA
  • It has also been found that H-NS can affect translation as well by binding to mRNA and causing its degradation. (wikipedia.org)
  • locates
  • There are 2 main steps involved: the protein binds to a non-specific site on the DNA and then it diffuses along the DNA chain until it locates a target site, a process referred to as sliding. (wikipedia.org)
  • aggregation
  • The lysine-rich N-terminus is required for self-aggregation as well as for Dps-driven DNA condensation. (wikipedia.org)
  • Protein shells served as a template to restrain particle growth and as a coating to prevent coagulation/aggregation between NPs. (wikipedia.org)
  • junctions
  • the protein was found to be required to regulate the subcellular wrapping of motoneuron axons, promote synaptic growth and the formation of glutamate receptor clusters at the neuromuscular junctions . (sdbonline.org)
  • histones
  • These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription. (wikipedia.org)
  • Histone-like proteins were unknown to be present in bacteria until similarities between eukaryotic histones and the HU-protein were noted, particularly because of the abundancy, basicity, and small size of both of the proteins. (wikipedia.org)
  • cytoplasmic
  • Acts as a cytoplasmic DNA sensor which, when activated, induces the recruitment of TBK1 and IRF3 to its C-terminal region and activates the downstream interferon regulatory factor (IRF) and NF-kappa B transcription factors, leading to type-I interferon production. (uniprot.org)