Poly(deoxyribonucleotide):poly(deoxyribonucleotide)ligases. Enzymes that catalyze the joining of preformed deoxyribonucleotides in phosphodiester linkage during genetic processes during repair of a single-stranded break in duplex DNA. The class includes both EC 6.5.1.1 (ATP) and EC 6.5.1.2 (NAD).
Catalyze the joining of preformed ribonucleotides or deoxyribonucleotides in phosphodiester linkage during genetic processes. EC 6.5.1.
A diverse class of enzymes that interact with UBIQUITIN-CONJUGATING ENZYMES and ubiquitination-specific protein substrates. Each member of this enzyme group has its own distinct specificity for a substrate and ubiquitin-conjugating enzyme. Ubiquitin-protein ligases exist as both monomeric proteins multiprotein complexes.
Adenine nucleotide containing one phosphate group esterified to the sugar moiety in the 2'-, 3'-, or 5'-position.
An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.
A family of double-stranded DNA viruses containing one genus Asfivirus. It is the source of AFRICAN SWINE FEVER.
A subset of ubiquitin protein ligases that are formed by the association of a SKP DOMAIN PROTEIN, a CULLIN DOMAIN PROTEIN and a F-BOX DOMAIN PROTEIN.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
A family of structurally related proteins that were originally discovered for their role in cell-cycle regulation in CAENORHABDITIS ELEGANS. They play important roles in regulation of the CELL CYCLE and as components of UBIQUITIN-PROTEIN LIGASES.
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
Virulent bacteriophage and type species of the genus T4-like phages, in the family MYOVIRIDAE. It infects E. coli and is the best known of the T-even phages. Its virion contains linear double-stranded DNA, terminally redundant and circularly permuted.
Gram-negative aerobic rods found in warm water (40-79 degrees C) such as hot springs, hot water tanks, and thermally polluted rivers.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
The act of ligating UBIQUITINS to PROTEINS to form ubiquitin-protein ligase complexes to label proteins for transport to the PROTEASOME ENDOPEPTIDASE COMPLEX where proteolysis occurs.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
A coenzyme composed of ribosylnicotinamide 5'-diphosphate coupled to adenosine 5'-phosphate by pyrophosphate linkage. It is found widely in nature and is involved in numerous enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NAD+) and reduced (NADH). (Dorland, 27th ed)
A highly conserved 76-amino acid peptide universally found in eukaryotic cells that functions as a marker for intracellular PROTEIN TRANSPORT and degradation. Ubiquitin becomes activated through a series of complicated steps and forms an isopeptide bond to lysine residues of specific proteins within the cell. These "ubiquitinated" proteins can be recognized and degraded by proteosomes or be transported to specific compartments within the cell.
An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A zinc-binding domain defined by the sequence Cysteine-X2-Cysteine-X(9-39)-Cysteine-X(l-3)-His-X(2-3)-Cysteine-X2-Cysteine -X(4-48)-Cysteine-X2-Cysteine, where X is any amino acid. The RING finger motif binds two atoms of zinc, with each zinc atom ligated tetrahedrally by either four cysteines or three cysteines and a histidine. The motif also forms into a unitary structure with a central cross-brace region and is found in many proteins that are involved in protein-protein interactions. The acronym RING stands for Really Interesting New Gene.
Enzymes that catalyze the formation of acyl-CoA derivatives. EC 6.2.1.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
A class of enzymes that form a thioester bond to UBIQUITIN with the assistance of UBIQUITIN-ACTIVATING ENZYMES. They transfer ubiquitin to the LYSINE of a substrate protein with the assistance of UBIQUITIN-PROTEIN LIGASES.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.
A family of proteins that share the F-BOX MOTIF and are involved in protein-protein interactions. They play an important role in process of protein ubiquition by associating with a variety of substrates and then associating into SCF UBIQUITIN LIGASE complexes. They are held in the ubiquitin-ligase complex via binding to SKP DOMAIN PROTEINS.
The process by which a DNA molecule is duplicated.
A set of protein subcomplexes involved in PROTEIN SORTING of UBIQUITINATED PROTEINS into intraluminal vesicles of MULTIVESICULAR BODIES and in membrane scission during formation of intraluminal vesicles, during the final step of CYTOKINESIS, and during the budding of enveloped viruses. The ESCRT machinery is comprised of the protein products of Class E vacuolar protein sorting genes.
The rate dynamics in chemical or physical systems.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
A family of proteins that are structurally-related to Ubiquitin. Ubiquitins and ubiquitin-like proteins participate in diverse cellular functions, such as protein degradation and HEAT-SHOCK RESPONSE, by conjugation to other proteins.
A large multisubunit complex that plays an important role in the degradation of most of the cytosolic and nuclear proteins in eukaryotic cells. It contains a 700-kDa catalytic sub-complex and two 700-kDa regulatory sub-complexes. The complex digests ubiquitinated proteins and protein activated via ornithine decarboxylase antizyme.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.
Ligases that catalyze the joining of adjacent AMINO ACIDS by the formation of carbon-nitrogen bonds between their carboxylic acid groups and amine groups.
The state of weariness following a period of exertion, mental or physical, characterized by a decreased capacity for work and reduced efficiency to respond to stimuli.
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
The procedures involved in combining separately developed modules, components, or subsystems so that they work together as a complete system. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
The protein complement of an organism coded for by its genome.

A novel trinuclear platinum complex overcomes cisplatin resistance in an osteosarcoma cell system. (1/1149)

Multinuclear platinum compounds have been designed to circumvent the cellular resistance to conventional platinum-based drugs. In an attempt to examine the cellular basis of the preclinical antitumor efficacy of a novel multinuclear platinum compound (BBR 3464) in the treatment of cisplatin-resistant tumors, we have performed a comparative study of cisplatin and BBR 3464 in a human osteosarcoma cell line (U2-OS) and in an in vitro selected cisplatin-resistant subline (U2-OS/Pt). A marked increase of cytotoxic potency of BBR 3464 in comparison with cisplatin in U2-OS cells and a complete lack of cross-resistance in U2-OS/Pt cells were found. A detailed analysis of the cisplatin-resistant phenotype indicated that it was associated with reduced cisplatin accumulation, reduced interstrand cross-link (ICL) formation and DNA platination, microsatellite instability, and reduced expression of the DNA mismatch repair protein PMS2. Despite BBR 3464 charge and molecular size, in U2-OS and U2-OS/Pt cells, BBR 3464 accumulation and DNA-bound platinum were much higher than those observed for cisplatin. In contrast, the frequency of ICLs after exposure to BBR 3464 was very low. The time course of ICL formation after drug removal revealed a low persistence of these types of DNA lesions induced by BBR 3464, in contrast to an increase of DNA lesions induced by cisplatin, suggesting that components of the DNA repair pathway handle the two types of DNA lesions differently. The cellular response of HCT116 mismatch repair-deficient cells was consistent with a lack of influence of mismatch repair status on BBR 3464 cytotoxicity. Because BBR 3464 produces high levels of lesions different from ICLs, likely including intra-strand cross-links and monoadducts, the ability of the triplatinum complex to overcome cisplatin resistance appears to be related to a different mechanism of DNA interaction (formation of different types of drug-induced DNA lesions) as compared with conventional mononuclear complexes rather than the ability to overcome specific cellular alterations.  (+info)

Yeast and human genes that affect the Escherichia coli SOS response. (2/1149)

The sequencing of the human genome has led to the identification of many genes whose functions remain to be determined. Because of conservation of genetic function, microbial systems have often been used for identification and characterization of human genes. We have investigated the use of the Escherichia coli SOS induction assay as a screen for yeast and human genes that might play a role in DNA metabolism and/or in genome stability. The SOS system has previously been used to analyze bacterial and viral genes that directly modify DNA. An initial screen of meiotically expressed yeast genes revealed several genes associated with chromosome metabolism (e.g., RAD51 and HHT1 as well as others). The SOS induction assay was then extended to the isolation of human genes. Several known human genes involved in DNA metabolism, such as the Ku70 end-binding protein and DNA ligase IV, were identified, as well as a large number of previously unknown genes. Thus, the SOS assay can be used to identify and characterize human genes, many of which may participate in chromosome metabolism.  (+info)

Farnesol-induced growth inhibition in Saccharomyces cerevisiae by a cell cycle mechanism. (3/1149)

The growth of budding yeast, Saccharomyces cerevisiae, was inhibited in medium containing 25 microM farnesol (FOH). The FOH-treated cells were still viable, and were characterized by a transition from budded to unbudded phase as well as a significant loss of intracellular diacylglycerol (DAG). FOH-induced growth inhibition could be effectively prevented by the coaddition of a membrane-permeable DAG analogue which can activate yeast protein kinase C (PKC). However, yeast cell growth was not initiated upon addition of the PKC activator when the cells had been pretreated with FOH for 20 min. The failure in cell growth recovery was believed to be due to a signalling-mediated cell cycle arrest in FOH-pretreated cells. Differential display analysis demonstrated that the expression of cell cycle genes encoding DNA ligase (CDC9) and histone acetyltransferase (HAT2) was strongly repressed in FOH-treated cells. Repression of the expression of these genes was effectively cancelled when cells were grown in medium supplemented with DAG. The authors propose an interference with a phosphatidylinositol-type signalling which is involved in cell cycle progression as a cause of FOH-induced growth inhibition in yeast cells.  (+info)

Standard free energy for the hydrolysis of adenylylated T4 DNA ligase and the apparent pKa of lysine 159. (4/1149)

Equilibrium constants for the adenylylation of T4 DNA ligase have been measured at 10 pH values. The values, when plotted against pH, fit a titration curve corresponding to a pKa of 8.4 +/- 0.1. The simplest interpretation is that the apparent pKa is that of the 6-amino group of the AMP-accepting residue Lys159. Based on the pH dependence of the equilibrium constants, the value at pH 7.0 is 0. 0213 at 25 degrees C, corresponding to DeltaG'o = +2.3 kcal mol-1. From this value and the standard free energy change of -10.9 kcal mol-1 for the hydrolysis of ATP to AMP and PPi, we calculate that DeltaG'o for the hydrolysis of the adenylyl-DNA ligase is -13.2 kcal mol-1. The presence of conserved basic amino acid residues in the catalytic domain, which are proximal to the active site in the homologous catalytic domain of T7 DNA ligase, suggests that the pKa of Lys159 is perturbed downward by the electrostatic effects of nearby positively charged amino acid side chains. The lower than normal pKa 8.4 compared with 10.5 for the 6-amino group of lysine and the high energy of the alpha,beta-phosphoanhydride linkage in ATP significantly facilitate adenylylation of the enzyme.  (+info)

Differential behaviors toward ultraviolet A and B radiation of fibroblasts and keratinocytes from normal and DNA-repair-deficient patients. (5/1149)

Xeroderma pigmentosum (XP) and trichothiodystrophy (TTD) are rare genodermatoses transmitted as recessive and autosomal traits that result in reduced capacity to repair UV-induced DNA lesions. Although XP, but not TTD, patients are prone to basal and squamous cell carcinomas, to date no comparative studies of the XP and TTD phenotypes have included epidermal keratinocytes. We compared the DNA repair capacity (by unscheduled DNA synthesis) and cell survival (by clonal analysis) of epidermal keratinocytes and dermal fibroblasts grown from normal individuals and patients with xeroderma pigmentosum and trichothiodystrophy following UVA and UVB irradiation. The same dose of UVB (1000 J/m2) induced twice as many DNA lesions in normal fibroblasts as in normal keratinocytes. UV survival rates were always higher in keratinocytes than in fibroblasts. Normal and TTD keratinocytes survived better following UVA and UVB irradiation than XP-C and XP-D keratinocytes. XP-C keratinocytes exhibited exacerbated sensitivity toward UVA radiation. Unscheduled DNA synthesis at UV doses leading to 50% cell survival indicated that the ratio of DNA repair capacity to cell survival is higher in keratinocytes than in fibroblasts. In addition, UVA and UVB irradiation induced a transition from proliferative to abortive keratinocyte colonies. This transition varied between donors and was in part correlated with their cancer susceptibility. Altogether these data provide the first evidence of the differential behaviors of normal, XP, and TTD keratinocytes toward UV radiation.  (+info)

DNA binding of Xrcc4 protein is associated with V(D)J recombination but not with stimulation of DNA ligase IV activity. (6/1149)

Mammalian cells are protected from the effects of DNA double-strand breaks by end-joining repair. Cells lacking the Xrcc4 protein are hypersensitive to agents that induce DNA double-strand breaks, and are unable to complete V(D)J recombination. The residual repair of broken DNA ends in XRCC4-deficient cells requires short sequence homologies, thus possibly implicating Xrcc4 in end alignment. We show that Xrcc4 binds DNA, and prefers DNA with nicks or broken ends. Xrcc4 also binds to DNA ligase IV and enhances its joining activity. This stimulatory effect is shown to occur at the adenylation of the enzyme. DNA binding of Xrcc4 is correlated with its complementation of the V(D)J recombination defects in XRCC4-deficient cells, but is not required for stimulation of DNA ligase IV. Thus, the ability of Xrcc4 to bind to DNA suggests functions independent of DNA ligase IV.  (+info)

The human DNA ligase III gene encodes nuclear and mitochondrial proteins. (7/1149)

We provide evidence that the human DNA ligase III gene encodes a mitochondrial form of this enzyme. First, the DNA ligase III cDNA contains an in-frame ATG located upstream from the putative translation initiation start site. The DNA sequence between these two ATG sites encodes an amphipathic helix similar to previously identified mitochondrial targeting peptides. Second, recombinant green fluorescent protein harboring this sequence at its amino terminus was efficiently targeted to the mitochondria of Cos-1 monkey kidney cells. In contrast, native green fluorescent protein distributed to the cytosol. Third, a series of hemagglutinin-DNA ligase III minigene constructs were introduced into Cos-1 cells, and immunocytochemistry was used to determine subcellular localization of the epitope-tagged DNA ligase III protein. These experiments revealed that inactivation of the upstream ATG resulted in nuclear accumulation of the DNA ligase III protein, whereas inactivation of the downstream ATG abolished nuclear localization and led to accumulation within the mitochondrial compartment. Fourth, mitochondrial protein extracts prepared from human cells overexpressing antisense DNA ligase III mRNA possessed substantially less DNA ligase activity than did mitochondrial extracts prepared from control cells. DNA end-joining activity was also substantially reduced in extracts prepared from antisense mRNA-expressing cells. From these results, we conclude that the human DNA ligase III gene encodes both nuclear and mitochondrial enzymes. DNA ligase plays a central role in DNA replication, recombination, and DNA repair. Thus, identification of a mitochondrial form of this enzyme provides a tool with which to dissect mammalian mitochondrial genome dynamics.  (+info)

Developmental neurobiology: Alternative ends for a familiar story? (8/1149)

Somatic DNA recombination is essential for production of functional antigen receptor genes of T and B lymphocytes, but it is thought to be unique to the immune system. Recent studies have now shown that recombination-related genes are also necessary for normal neuronal development.  (+info)

TY - JOUR. T1 - Identification of human autoantibodies to the DNA ligase IV/XRCC4 complex and mapping of an autoimmune epitope to a potential regulatory region. AU - Lee, Kyung Jong. AU - Dong, Xingwen. AU - Wang, Jingsong. AU - Takeda, Yoshihiko. AU - Dynan, William S.. PY - 2002/9/15. Y1 - 2002/9/15. N2 - The nonhomologous end-joining pathway is the principal mechanism for repair of ionizing radiation-induced, double-strand breaks in mammalian cells. Three polypeptides in this pathway, including the two subunits of Ku protein and the catalytic subunit of the DNA-dependent protein kinase, are known targets of autoantibodies in systemic rheumatic diseases. Here we show that two additional polypeptides in the pathway, DNA ligase IV and XRCC4, are also targets of autoantibodies. These Abs were present in 20% of patients with systemic lupus erythematosus and overlap syndrome. Previous work has shown that XRCC4 is subject to radiation-induced post-translational modification, including ...
DNA ligase 1 is an enzyme that in humans is encoded by the LIG1 gene. DNA ligases are important tools for DNA replication and repair in living organisms. There are two families of DNA ligases, ATP-dependent DNA ligases and NAD+ dependent DNA ligases. Dependence upon ATP or NAD+ is conferred in the ligase-adenylate formation and which substrate is to be used. ATP dependent ligases are found in eukaryotes, while NAD+ dependent ligases are found in prokaryotes. DNA ligase I is found in eukaryotes and therefore is in the family of ATP-dependent DNA ligases. Previously it had been known that DNA replication occurred through the breakage of the double DNA strand, but the mechanism of action and enzyme responsible for ligating the strands back together was unknown. In the 1960s Lehman laboratories investigated this mystery, discovering DNA ligase and its mechanism of action in 1967. The Gellert, Richardson, and Hurwitz laboratories are also credited for their help in the discovery of DNA ligases in the ...
DNA ligases are enzymes that seal breaks in the backbones of DNA, leading to them being essential for the survival of all organisms. DNA ligases have been studied from many different types of cells and organisms and shown to have diverse sizes and sequences, with well conserved specific sequences that are required for enzymatic activity. A significant number of DNA ligases have been isolated or prepared in recombinant forms and, here, we review their biochemical and structural characterization. All DNA ligases contain an essential lysine that transfers an adenylate group from a co-factor to the 5′-phosphate of the DNA end that will ultimately be joined to the 3′-hydroxyl of the neighbouring DNA strand. The essential DNA ligases in bacteria use β-nicotinamide adenine dinucleotide (β-NAD+) as their co-factor whereas those that are essential in other cells use adenosine-5′-triphosphate (ATP) as their co-factor. This observation suggests that the essential bacterial enzyme could be targeted ...
p, Non-homologous end joining (NHEJ) is the predominant mode of DNA double strand break (DSB) repair pathway in mammalian cells. At the heart of this repair pathway is Xrcc4-DNA ligase IV complex, which mediates ligation of the broken DNA strands. The C-terminal tandem BRCT repeats of human DNA ligase IV spanning residues 654-911 in complex with the functional fragment of Xrcc4 comprised of residues 1-203 were crystallized by the hanging drop vapour diffusion method at 20°C. Generation of single, well-packed, diffraction quality crystals suitable for structure determination involved usage of an Xrcc4 point mutant (A60E). Arriving at the crystallization condition included optimization of pH, variation of the precipitant concentration, investigation of the effects of small molecules, and alteration of the amount of crystal seed used as initial nuclei. A Crystal of selenomethionine-derived protein complex was grown using the above optimization steps and diffracted to 2.4 A resolution. Data ...
in Biophysical Journal (2004), 86(2), 1089-1104. In the last few years, an increased attention has been focused on NAD(+)-dependent DNA ligases. This is mostly due to their potential use as antibiotic targets, because effective inhibition of these ... [more ▼]. In the last few years, an increased attention has been focused on NAD(+)-dependent DNA ligases. This is mostly due to their potential use as antibiotic targets, because effective inhibition of these essential enzymes would result in the death of the bacterium. However, development of an efficient drug requires that the conformational modifications involved in the catalysis of NAD(+)-dependent DNA ligases are understood. From this perspective, we have investigated the conformational changes occurring in the thermophilic Thermus scotoductus NAD(+)-DNA ligase upon adenylation, as well as the effect of cofactor binding on protein resistance to thermal and chemical (guanidine hydrochloride) denaturation. Our results indicate that cofactor ...
ATP-dependent DNA ligase LigD phosphoesterase module / ATP-dependent DNA ligase LigD polymerase module; K01971 bifunctional non-homologous end joining protein LigD [EC:6.5.1.1] ...
DNA ligase IV functions in DNA non-homologous end-joining, in V(D)J recombination, and during brain development. We previously reported a homozygous mutation (R278H) in DNA ligase IV in a developmentally normal leukemia patient who overresponded to radiotherapy. The impact of this hypomorphic mutation has been evaluated using cellular, biochemical, and structural approaches. Structural modeling using T7 DNA ligase predicts that the activity and conformational stability of the protein is likely to be impaired. We show that wild type DNA ligase IV-Xrcc4 is an efficient double-stranded ligase with distinct optimal requirements for adenylate complex formation versus rejoining. The mutation impairs the formation of an adenylate complex as well as reducing the rejoining activity. Additionally, it imparts temperature-sensitive activity to the protein consistent with the predictions of the structural modeling. At the cellular level, the mutation confers a unique V(D)J recombination phenotype affecting ...
E. coli DNA Ligase catalyzes the formation of phosphodiester bonds between double-stranded DNA fragments containing juxtaposed 5-phosphate termini and 3-hydroxyl termini in the presence of the NAD cofactor. Both T4 DNA Ligase and E.coli DNA Ligase are used in various gene cloning experiments; however, unlike T4 DNA Ligase, E. coli DNA Ligase can only catalyze ligation of cohesive end-containing DNA fragments via standard reaction conditions. E. coli DNA Ligase is supplied in a buffer containing 10 mM potassium phosphate (pH 7.5), 50 mM KCl, 1 mM DTT, 1 mM EDTA and 50% glycerol.. ...
The SCOP classification for the Adenylation domain of NAD+-dependent DNA ligase family. Additional information, provided for both this family and the superfamily it belongs to, includes SUPERFAMILY links to genome assignments, alignments, domain combinations, taxonomic visualisation and hidden Markov model information.
Our findings provide a function for the carboxy-terminal region of ligase IV and suggest that BRCT domains of other proteins may mediate contacts between DNA repair components. In addition, our data implicate mammalian ligase IV in V(D)J recombination and the repair of radiation-induced DNA damage, …
tkm:TK90_1908 K07468 putative ATP-dependent DNA ligase [EC:6.5.1.1] , (GenBank) ATP dependent DNA ligase (A) MIERHVLQEAIDNRRAEALTFDELEYARLLEPVNHYPRGSVVLPDGSVVPGYPSIGRIQS LEAGLPRQFEQPFWAEEKIDGFNVRILRWQGRVYAFSRGGYVCAFSTDRVVDFMDPVIFN AEPNLILCAEIAGPDTPYLEGSTPRVAHDVGLFVFDLMRLGQPGFVSQPEKFALIERHAL PPAPLHGWFTPRDTRALGELIRRLDEEGAEGLVLKTADGQHRAKYVTGSSCVSDIRVCAE QLLDLPPEYFTNRLTRLAIFLSEHPDRHHADLDQALGQALLSGLHGAVAQHRRQGHVGHR YRCRFREHASALRFMNHMRATGGRHVSFAQDAPRQEDGYWLLEFERQFDRITGTLASALA GDRQYD ...
tal:Thal_0814 K07468 putative ATP-dependent DNA ligase [EC:6.5.1.1] , (GenBank) ATP dependent DNA ligase (A) MLSPELVKEALRKNKVKGENYRGLEYLRFTDDFKDIPRGTILFKESVIWGYPHIGRIFQL SSGLREQFNAPFFVEEKVDGYNVRIFYHEGQVLAVTRGGFVCPFTTDRVEEFIDADFFKE NPHLVLCAEVAGPENPYVDESPPYIREDIRFFVFDVMVKGEQRFLPYRQKLQLIEKYRLP SVERYGLYDVSKIGELKALLRRLNEEGREGVVFKEDSERDKRVKYITSYANLQDIRITSL NLMGLPADYYTNRLLRLALFMEEEGLQLEEDLLKELGSAFLEGIFEAIRQSKEEGRVYRT FRCRFRKKESALLFMEQIQHSSSQVQIIERGLKQEGSYWILEFDRVYLNMTGFLGHVLGG GSVFD ...
XRCC4 is a proteins connected with DNA Ligase IV, which is considered to sign up for two DNA ends at the ultimate stage of DNA double-strand break fix through nonhomologous end signing up for. cells, indicating that the phosphorylation was mediated by DNA-PK. These results recommended potential usefulness from the phosphorylation position of XRCC4 Ser320 as an signal of DNA-PK efficiency in living cells. nonhomologous end signing up for (NHEJ) and homologous recombination [1]. NHEJ can be involved in V(D)J recombination in the immune system to generate the diversity of immunoglobulin and T cell receptors. In NHEJ in vertebrate cells, seven molecules playing pivotal tasks have been recognized: Ku70, Ku86 VX-765 (also known as Ku80) [2, 3], DNA-dependent protein TRADD kinase catalytic subunit (DNA-PKcs) [4C7], XRCC4 [8], DNA ligase IV (LIG4) [9, 10], XRCC4-like element (XLF, also known as Cernunnos) [11, 12] and Paralog of XRCC4 and XLF (PAXX, also known as XLS for XRCC4-like small molecule), ...
Problems sequencing ligation product - posted in Molecular Cloning: Hi, as the title suggests im having some trouble getting a sequencing result from a shRNA dsDNA oligo that ive ligated into the pLKO-puro plasmid. I have previously sequenced this plasmid both with inserts (ligated by other group and resulting plasmid gifted to me) and with no insert (to check the plasmid was correct to begin with when I bought it in fresh). Sequencing is by sending away to Eurofins and prep is...
DNA ligation and trasformation - posted in Molecular Cloning: hello, i have performed ligation for my sample. the concentration of my vector is 8 ng/ul while insert is 15 ng/ul. i used 1:3 ratio of vector insert where insert + vector= 100ng..this sample done in 4,16,23 and 25oC. The ligation product then stored in -20oC and 4 ul of ligation product then used for transformation on dh5a. however i got no cloning culture. i used invitrogen t4 ligase..is there any problems in my methods?
ligD1; ATP-dependent DNA ligase clustered with Ku protein, LigD; K01971 bifunctional non-homologous end joining protein LigD [EC:6.5.1.1] ...
For the Rapid DNA Ligation Kit, we guarantee , 1 x 106 transformants per μg religated pUC18 vector (sticky end as well as blunt end), i.e., this means that only 2.96 pg of vector (1 molecule of pUC 18 = of 2,96 ag [attogram!]), have be to be religated to result in this yield in transformants. This rate of religation is easily achieved in 5 minutes with the Rapid DNA Ligation Kit.. Note: This also means that when ligation products are checked using an agarose gel, a substantial proportion of the vector DNA used will still show up „unligated“. Considering the above mentioned molecular weight of pUC 18 this is is easily visualized.. The rate and kinetics of concatemer ligation in cloning with λ-vectors are totally different from plasmid ligation. For ligation of concatemers ligase has to connect linear fragments in the presence of high amounts of DNA. For plasmid cloning an insert must first be ligated to one end of the linearized plasmid-vector, and then the other end of the same ...
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T4 DNA Ligase catalyzes the formation of phosphodiester bonds between juxtaposed 5 phosphate and 3 hydroxyl termini in double-stranded DNA using ATP as a coenzyme. Both blunt and cohesive end DNA ligation, as well as single-stranded nick repair of DNA, RNA and DNA/RNA, are possible via the T4 DNA ligase. This enzyme is supplied in a buffer of 10 mM Tris-HCl (pH 7.5), 50 mM KCl, 10 mM 2-mercaptoethanol, 0.1 mM EDTA and 50% glycerol. ...
This is a consensus protocol see the bottom of this article for specific protocols. DNA ligation is the process of joining together two DNA molecules or both ends of one DNA molecule. Specifically, it involves creating a phosphodiester bond bond between the 3 hydroxyl of one nucleotide and the 5 phosphate of another. This reaction is usually catalyzed by a DNA ligase enzyme. This enzyme will ligate DNA fragments having blunt or overhanging, complementary, sticky ends. Typically, it is easier to ligate molecules with complementary sticky ends than blunt ends. T4 DNA ligase is the most commonly used DNA ligase for molecular biology techniques and can ligate sticky or blunt ends. Most commonly, one needs to insert a DNA molecule of interest into a plasmid, ready for transformation into competent cells. Ideally, DNA and vector are individually cut with the same restriction enzyme, then both are added to a ligation reaction to be circularised by DNA ligase. The two components of the DNA in the ...
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.
A gapped BLAST reveals a number of significant hits to DNA Ligase proteins. For example, residues 6-667 are 42% similar to the DNA ligase of M.pneumoniae (DNLJ_MYCPN). Other significant hits included (but were not limited to) the DNA ligases of M.genitalium (DNLJ_MYCGE), H.influenzae (DNLJ_HAEIN), R.prowazekki (pid:e1342996) and E.coli(DNLJ_ECOLI). By similarity, all of the above mentioned DNA ligases belong to the NAD-dependent DNA Ligase family ...
6-azaindazole (compound 12) the researchers were able to make this hydrogen bond directly while also more effectively filling the pocket, providing a satisfying 70-fold boost in affinity. However, close inspection of the crystal structure and computational modeling suggested that this molecule was binding in an energetically unfavorable conformation. Simply adding a nitrogen to the pyridine ring alleviated this problem, providing another 15-fold boost in potency (compound 13). This molecule also showed antibacterial activity against a number of Gram-positive pathogens ...
We herein describe a new syndrome of immunodeficiency caused by hypomorphic mutations in the Artemis gene. The mutations resulted in truncations of the Artemis protein in the last exon, leaving intact the metallo-β-lactamase domain, in both studied kindreds. Hypomorphic mutations in NHEJ proteins encoding genes have also been described in DNA ligase IV (31). While complete DNA ligase IV KO is embryonic-lethal in mice (9, 10), development of both B and T lymphocytes can occur in DNA ligase IV-deficient patients with hypomorphic mutations. Similarly, hypomorphic mutations of the Artemis gene are compatible with low-level in vivo V(D)J recombination, as shown by the presence of both polyclonal B and T lymphocytes in these patients. The residual activity of Artemis translates into an absence of N diversity at the V(D)J junctions in these T cells, a situation reminiscent of that observed in Ku86 KO mice (29, 32). This suggests a possible requirement (and interaction?) for Artemis in the recruitment ...
DNA ligase I antibody [10H5] (ligase I, DNA, ATP-dependent) for IP, WB. Anti-DNA ligase I mAb (GTX70141) is tested in Human, Mouse samples. 100% Ab-Assurance.
T4 DNA Ligase,Modification Enzymes,Restriction Enzyme and Modification Enzyme,Products,Beijing TransGen Biotech Co.Ltd,OverviewContents& storageCitations & referencesRelated ImagesDownloadOverviewDescriptionT4 DNA Ligase catalyzes the formation
SCR7 and its Oxidized Form, SCR7-pyrazine Induce Cancer Cell Death by Inhibiting Nonhomologous DNA End joining in a Ligase IV Dependent Manner ...
Cited in 1 publications. View Mouse Monoclonal anti-DNA Ligase I Antibody (7A12) (NB100-2714). Validated Applications: WB, ELISA, IP. Validated Species: Human, Bovine.
Fast-Link™ DNA Ligation and Screening Kit-北京中北林格科技发展有限公司-ApplicationsRapidandefficientDNAligation.Rapidscreeningofclonesforinsertsize.TheFast-Link™DNALigationandScreeningKitcombinestherapidDNAligationsofthepopularFast-LinkDNALigationKitwiththerapidandsensitivescreeningofclonesaffordedbytheColonyFast-Screen™Kit(SizeScreen).TheFast-LinkDNALigationandScreeningKitreducesthetimerequiredforDNAligation,transformation,andscreeningofrecombinantplasmidsto24hoursorless.Thus,thekitisidealforbothroutineandhigh-throughputcloningandscreeningprojects.BenefitsCohesive-endligationsin5minutesatroomtemperature.Blunt-endligationsin15minutesatroomtemperature.LigationofPCRproductswithA-overhangsin1hourat16°C.Highligationefficiency.Desaltingofligationproductspriortoelectroporationisnotnecessary.Simpleandfast(1-hour)screeningofrecombinantplasmids,withouttheneedtogrowculturesorperformrestrictiondigests. Figure1.ResultsofrecombinantscreeningusingtheFast-Link™DNALigationandScreeningKit
Rabbit polyclonal DNA Ligase III antibody validated for WB, IHC and tested in Human. With 1 independent review. Immunogen corresponding to recombinant fragment
Essential protein. DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. Involved in repair of both single strand breaks (SSBs) and double strand breaks (DSBs). Required in the endosperm for embryogenesis, probably to repair DNA-breaks generated by DME.
DNA ligase activity is strongly accelerated in the presence of high concentrations of non-specific polymers, with an accompanying change in product distribution characteristics. The rate of blunt-end ligation of DNA substrate by T4 DNA ligase is particularly affected, with a product shift from closed circular species to linear oligomers. The method provides a way to increase the rate of enzymatic DNA ligation and the size of the linear products. It may be useful when preparing large amounts of polymers by ligation of oligomers or when ligating amounts of DNA or deoxyribooligomers so low in concentration that a reduced yield would otherwise result.
DNA ligases vary in their ability to join fragments, add adaptors, repair nicks or breaks, link vectors and inserts, and to circularize dsDNA. Ligases also vary in their type of activity. The specificity and accuracy of the ligation depends upon ligase selection and careful optimization of reaction conditions. With the right ligase, conditions and probes, even single-base variations in sequence can be reliably detected.
SWISS-MODEL Template Library (SMTL) entry for 3gde.1. The closed conformation of ATP-dependent DNA ligase from Archaeoglobus fulgidus
This is a consensus protocol. See the bottom of this article for specific protocols. DNA ligation is the process of joining together two DNA molecule ends (either from the same or different molecules). Specifically, it involves creating a phosphodiester bond bond between the 3 hydroxyl of one nucleotide and the 5 phosphate of another. This reaction is usually catalyzed by a DNA ligase enzyme. This enzyme will ligate DNA fragments having blunt or overhanging, complementary, sticky ends. Typically, it is easier to ligate molecules with complementary sticky ends than blunt ends. T4 DNA ligase is the most commonly used DNA ligase for molecular biology techniques and can ligate sticky or blunt ends. The two components of the DNA in the ligation reaction should be equimolar and around 100μg/ml. Most commonly, one wants to ligate an insert DNA molecule into a plasmid, ready for bacterial transformation. Typically, DNA and plasmid vector are individually cut to yield complementary ends, then both ...
Molecular Cloning, also known as Maniatis, has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential.
Dr. Tomas Lindahl is noted for his contributions to the comprehension of DNA repair at the molecular level in bacterial and mammalian cells. He was the first to isolate a mammalian DNA ligase and to describe a totally unanticipated novel group of DNA glycosylases as mediators of DNA excision repair. He has also discovered a unique class of enzymes in mammalian cells, namely the methyltransferases, which mediate the adaptive response to alkylation of DNA and has shown that the expression of these enzymes is regulated by the ada gene. More recently he has elucidated the molecular defect in Blooms syndrome [sic] to be the lack of DNA ligase I. Apart from providing profound insights into the nature of the DNA repair process his very important contributions promise to facilitate the design of more selective chemotherapeutic drugs for the treatment of cancer. Lindahl has also made a number of significant contributions to understanding at the DNA level the mechanism of transformation of B-lymphocytes ...
Physical contacts between DNA segments can be measured with the chromosome conformation capture (3C) technologies [11, 12]. The 3C approach (Figure 1b) uses formaldehyde to covalently link chromatin segments in vivo. Cross-linked chromatin is then digested with a restriction enzyme and ligated under conditions promoting intermolecular ligation of cross-linked segments. Cross-links are finally reversed by proteinase K digestion and DNA extraction to generate a 3C library. 3C libraries contain pair-wise ligation products, where the amount of each product is inversely proportional to the original three-dimensional distance separating these regions. These libraries are conventionally analyzed by semi-quantitative PCR amplification of individual head-to-head ligation junctions and agarose gel detection (for details, see [12]). 3C was first used to show that long-range interactions are essential for gene expression in several important mammalian genomic domains. For example, it was demonstrated ...
Adenyaltions has a particular application when it involves the adenylation of RNA. There is a known procedure that allows for RNA 5 adenylation using T4 DNA ligases. Basically this is an approach to adenylate RNA so that it becomes a 5,5-adenyl pyrophosphoryl cap structure. This new adenylated RNA structure is desirable in the sense that it can investigate certain natural biochemical pathways that require such intermediates. The 5 adenylated RNA is also useful for a certain amount of in vitro selection procedures to identify nucleic acid enzymes that specificially use the 5 adenlyated RNA as a reactive RNA substrate. This is particularly favorable given that the adenylated RNA is considered a transition state molecule which has evolved to become the most favorable of states when it comes to enzyme substrate complexes. in other words, the adenylation of the 5 RNA allows for a better enzyme substrate complex due to its nature of being a transitional state substrate for biochemical pathways ...
Cloning and Functional Characterization of an NAD+-Dependent DNA Ligase from Staphylococcus aureus: A Staphylococcus aureus mutant conditionally defective in DN
XRCC4-like factor (XLF) is the most recently discovered core member of the nonhomologous end joining (NHEJ) machinery. XLF enhances ligation of DNA ends by DNA ligase IV (LIG4) and functionally interacts with KU70. Previous results showed that some polymorphic changes in LIG4 impact on the efficiency of double strand breaks (DSBs) repair. A random Caucasian population sample was screened for XLF polymorphic mutations with similar functional impact. This analysis identified two novel noncoding single nucleotide polymorphisms (SNPs). To address the regulation of XLF and KU70, the acetylation status of both proteins were analysed. It has been found that XLF undergoes acetylation both in vitro and in vivo and the acetylation sites were mapped in vitro by mass spectrometry. Preliminary analysis has indicated that XLF deacetylation might be histone-deacetylase (HDAC3) dependent. For KU70, it has been found that lysine residues K317, K331 and K338 are critical for NHEJ. Cells overexpressing ...
example COMMENT The CAGE (cap analysis gene expression) is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20/21 nucleotides from 5 end mRNAs. Full-length cDNAs were at first selected with the Cap-Trapper method. Then, a specific linker (Linker1, some linker contain 5 bp sequences that have 15 variations for each rna sample) containing the ClassIIs restriction enzyme site MmeI was then ligated to the single-strand cDNA and then the second strand of cDNA synthesized. The resulting double-stranded cDNA was cleaved by the restriction enzyme MmeI and a second linker (Linker2) was ligated to the 2 bp overhang at the MmeI cleaved site, to produce a 5 20/21 tag having two linkers at both sides. The ligation products were separated from unmodified DNA with magnetic beads. The 5 end cDNA tags were released from the beads, and the DNA fragments were amplified in a PCR step by using the two linker-specific primers (Primer1 (uni-PCR), Primer2 (MmeI-PCR)). The ...
DNA microarrays have the potential to be useful in fast and efficient monitoring of complex microbic environment but the conventional array platforms may suffer from nonspecific background signals and low sensitivity. We have applied the ligation detection reaction (LDR) microarray method for municipal biowaste compost samples to develop a tool for monitoring the fungal species contributing to different phases of the decomposition process and to demonstrate the feasibility of LDR microarray for species-level detection from complex microbial communities. Previously, LDR has been successfully applied to detecting microbes from environmental samples [19-21]. These studies report 1-5 fmol sensitivity at 5% of total DNA using genus consensus sequences in probe design and group-selective PCR primers in template amplification. Better sensitivity has been achieved by PCR amplifying the ligation products [24, 47] but this approach requires long circulazing oligonucleotide probes, nuclease treatments and ...
Result: clones A, C, D, F seem to have the right construction. Digestion of 6 clones of GAFP1+K606013 = K1364002 (pSB1C3) by EcoR1 and Pst1 + electrophoresis. Date: 07/25/2014. 3. Cloning GAFP1+terminator(B0015) = K1364007 (pSB1C3). Digestion of GAFP1 on pEX-A2 and B0015 (terminator on pSB1C3) Date: 07/24/2014 Ligation of GAFP1 in B0015 (terminator on pSB1C3). Date: 07/24/2014. Transformation of ligation products in E.coli. Date: 07/24/2014. Culture of 6 clones: A, B, C, D, E, F transformed in E. coli. Date: 07/26/2014. QIAprep Spin Miniprep Kit Using a Microcentrifuge. Date: 07/28/2014. PCR of GAFP1+B0015 = K1364007 (pSB1C3) A, B, C, D, E, F + electrophoresis. Date: 07/28/2014 ...
Thursday, 23rd August: cloning of the iGEM linker into the shuttle vector (pBK25 and pBK26) and transformation in the NM522 strain; Kill: -Transformations results : All controls are okay Too much clones on Lyso+Dsp in shuttle vector transformation plate, so some clones are selected and spread and a new LB plate with the appropriate antibiotic 12 liquid culture in LB are launched for the clones Lyso+Dsp in PSB1C3 - Miniprep of 14 clones transformed with the ligation product [Constitutiv Promoter + RBS + Lysostaphin] in pBK25 and electrophoresis to analyse the extracted DNA : the transformation is succesful for 3 clones =) - The first plasmid [Constitutive Promoter + RBS + Lysostaphin] in pBK25 is put in storage under the reference pBK28 (1). - The second plasmid [Constitutive Promoter + RBS + Lysostaphin] in pBK25 is put in storage under the reference pBK28 (2). - The third plasmid [Constitutive Promoter + RBS + Lysostaphin] in pBK25 is put in storage under the reference pBK28 (3). Surfactant : - ...
A series of diethyltin(IV) complexes with carbohydrate ligands (aldoses, polyalcohols, sugar acids, sugar amines, and di- and trisaccharides] was prepared. The compositions of the complexes were...
Various approaches have been reported to inhibit or suppress NHEJ to increase rates of HDR including silencing genes encoding proteins involved in NHEJ like Ligase IV, Ku80 and Ku70 with dsRNA or by working in genetic backgrounds deficient in NHEJ (Ligase IV mutants).. Maruyama et al (2015) and Chu et al. (2015) both report their use of the Ligase IV inhibitor, Scr7, to increase rates of HDR in mammalian cells.. Maruyama et al (2015) work with human cells in culture and with mouse embryos. In both systems they show significant increases in HDR in the presence of Scr7, up to 19-fold improvement in one case. Maruyama et al. acknowledge the possible widespread applicability of this approach, depending on the degree of conservation of NHEJ machinery (Ligase IV) in your system of interest.. Particularly interesting is Maruyama et als inclusion of Scr7 in an injection mix they used to inject mouse zygotes, which is very much analogous to how insect scientists might apply this compound in a knock-in ...
If the ligation reaction is not mixed properly, low library yields may result. To ensure proper mixing, the reaction can be pipetted up and down 10 times, or vortexed for 3 seconds.
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ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.. About ASM , Contact Us , Press Room. ASM is a member of. ...
Other NAD-dependent enzymes include bacterial DNA ligases, which join two DNA ends by using NAD+ as a substrate to donate an ... This contrasts with eukaryotic DNA ligases, which use ATP to form the DNA-AMP intermediate. Li et al. have found that NAD+ ... "A newly identified DNA ligase of Saccharomyces cerevisiae involved in RAD52-independent repair of DNA double-strand breaks". ... Wilkinson A, Day J, Bowater R (2001). "Bacterial DNA ligases". Mol. Microbiol. 40 (6): 1241-8. doi:10.1046/j.1365-2958.2001. ...
... the RAD51-BRCA2 DNA recombination complex, and the DNA ligase shown at right. His group has written several broadly used ... "DNA ligase Molecule-of-the-Month". Pdb101.rcsb.org. Retrieved 3 July 2018. Lewis, T. E.; Sillitoe, I; Andreeva, A; Blundell, T ... Ochi T, Gu X, Blundell TL (2013). "Structure of the catalytic region of DNA ligase IV in complex with an artemis fragment sheds ... Pellegrini L, Yu DS, Anand S, Lee M, Blundell TL, Venkitaraman AR (2002). "Insights into DNA recombination from the structure ...
"LIGASE IV, DNA, ATP-DEPENDENT; LIG4". OMIM. Retrieved 2 January 2012. Altmann T, Gennery AR (October 2016). "DNA ligase IV ... LIG4 syndrome (also known as Ligase IV syndrome) is an extremely rare condition caused by mutations in the DNA Ligase IV (LIG4 ... Ligase IV is a critical component of the non-homologous end joining (NHEJ) mechanism that repairs DNA double-strand breaks. It ... Ben-Omran TI, Cerosaletti K, Concannon P, Weitzman S, Nezarati MM (2005). "A patient with mutations in DNA Ligase IV: clinical ...
Deoxycytidine monophosphate Nucleoside Oligonucleotide Pascal JM (February 2008). "DNA and RNA ligases: structural variations ...
Potts PR, Yu H (2005). "Human MMS21/NSE2 is a SUMO ligase required for DNA repair". Mol. Cell. Biol. 25 (16): 7021-32. doi: ... Nse1-Nse3-Nse4 subunits bridge the Smc5 head Smc6 and allow the binding of DNA. It is involved in the Alternative lengthening ... Palecek J, Vidot S, Feng M, Doherty AJ, Lehmann AR (December 2006). "The Smc5-Smc6 DNA repair complex: bridging of the Smc5- ... In the yeast Saccharomyces cerevisiae, SMC6 is necessary for resistance to DNA damage as well as for damage-induced ...
DNA ligase III-alpha mRNA encodes nuclear and mitochondrial versions of DNA ligase III-alpha. Nuclear DNA ligase III-alpha ... Compared with DNA ligases I and IV, DNA ligase III is the most active enzyme in the intermolecular joining of DNA duplexes. ... The essential role of DNA ligase III-alpha in mitochondrial DNA metabolism can be fulfilled by other DNA ligases, including the ... the DNA ligase III zinc finger is involved in binding to DNA strand breaks. Within the DNA ligase III polypeptide, the zinc ...
Upon germination, seeds of Vicia faba undergo DNA repair. A plant DNA ligase that is involved in repair of single- and double- ... Waterworth WM; Masnavi G; Bhardwaj RM; Jiang Q; Bray CM; West CE (September 2010). "A plant DNA ligase is an important ... Thus DNA damages that accumulate during dormancy appear to be a problem for seed survival, and the enzymatic repair of DNA ... Koppen G; Verschaeve L (2001). "The alkaline single-cell gel electrophoresis/comet assay: a way to study DNA repair in radicle ...
So S, Adachi N, Lieber MR, Koyama H (2004). "Genetic interactions between BLM and DNA ligase IV in human cells". J. Biol. Chem ... DNA helicases function in DNA replication and DNA repair. BLM very likely functions in DNA replication, as cells from persons ... at nucleoli DNA helicases are enzymes that attach to DNA and temporarily unravel the double helix of the DNA molecule. ... Errors made during DNA replication can lead to mutations. The BLM protein is important in maintaining the stability of the DNA ...
"Nucleosome disruption by DNA ligase III-XRCC1 promotes efficient base excision repair". Mol. Cell. Biol. 31 (22): 4623-32. doi: ... "Distinct pattern of oxidative DNA damage and DNA repair in follicular thyroid tumours". J. Mol. Endocrinol. 48 (3): 193-202. ... Jiang Z, Hu J, Li X, Jiang Y, Zhou W, Lu D (2006). "Expression analyses of 27 DNA repair genes in astrocytoma by TaqMan low- ... 2005). "DNA glycosylase activities for thymine residues oxidized in the methyl group are functions of the hNEIL1 and hNTH1 ...
"ATM engages autodegradation of the E3 ubiquitin ligase COP1 after DNA damage". Science. 313 (5790): 1122-6. Bibcode:2006Sci... ... E3 ubiquitin-protein ligase RFWD2 is an enzyme that in humans is encoded by the RFWD2 gene. RFWD2 has been shown to interact ... Dornan D, Wertz I, Shimizu H, Arnott D, Frantz GD, Dowd P, O'Rourke K, Koeppen H, Dixit VM (2004). "The ubiquitin ligase COP1 ... "Human De-etiolated-1 regulates c-Jun by assembling a CUL4A ubiquitin ligase" (PDF). Science. 303 (5662): 1371-4. Bibcode: ...
DNA ligases, which join broken DNA together, were discovered earlier in 1967. By combining the two enzymes it became possible ... The transferred DNA is piloted to the plant cell nucleus and integrated into the host plants genomic DNA.The plasmid T-DNA is ... For known DNA sequences, restriction enzymes that cut the DNA on either side of the gene can be used. Gel electrophoresis then ... Traditionally DNA was isolated from the cells of organisms. Later, genes came to be cloned from a DNA segment after the ...
The insert and the destination vector are then mixed together with DNA ligase. A typical molar ratio of insert genes to ... for more information see DNA ligase), the insert should become successfully incorporated into the destination plasmid. The ... The mammalian DNA does not come with these restriction sites, so they are built in by overlap extension PCR. The primers are ... After a good number of bacterial colonies have grown, they can be miniprepped to harvest the plasmid DNA. In order to ensure ...
DNA ligase III along with its cofactor XRCC1 catalyzes the nick-sealing step in short-patch BER in humans. DNA ligase I ligates ... Cappelli, Enrico (1997). "Involvement of XRCC1 and DNA Ligase III Gene Products in DNA Base Excision Repair". Journal of ... This was the most frequent DNA repair abnormality found among the 8 DNA repair genes tested. NEIL1 was also one of six DNA ... "Long Patch Base Excision Repair with Purified Human Proteins DNA LIGASE I AS PATCH SIZE MEDIATOR FOR DNA POLYMERASES δ AND ε". ...
DNA ligase joins the strands together to form dsDNA. There are two subpathways for NER, which differ only in their mechanism ... WRNp is active in unwinding DNA, a step necessary in DNA repair and DNA replication. Since WRNp's function depends on DNA, it ... The DNA damage theory of aging proposes that aging is a consequence of the accumulation of naturally occurring DNA damages. The ... DNA helicases are enzymes that bind to double-stranded DNA and temporarily separate them. This unwinding is required in ...
... crystallization and preliminary crystallographic analysis of a multiple cofactor-dependent DNA ligase from". Acta ...
"NMR structure of the N-terminal domain of SUMO ligase PIAS1 and its interaction with tumor suppressor p53 and A/T-rich DNA ... Exposure to UV light, chemicals, and ionizing radiation can cause DNA damage, and the most detrimental type of DNA damage is a ... "Mammalian SUMO E3-ligases PIAS1 and PIAS4 promote responses to DNA double-strand breaks". Nature. 462 (7275): 935-9. Bibcode: ... Defects in the DNA repair system lead to a predisposition for developing cancer. At least some of the PIAS proteins are ...
... a DNA ligase is employed in repair of DNA single- and double-strand breaks during seed germination and this ligase is an ... Waterworth WM, Masnavi G, Bhardwaj RM, Jiang Q, Bray CM, West CE (2010). "A plant DNA ligase is an important determinant of ... In dry, aging rye seeds, DNA damages occur with loss of viability of embryos. Dry seeds of Vicia faba accumulate DNA damage ... In eukaryotes, the cellular repair response to DNA damage is orchestrated, in part, by the DNA damage checkpoint kinase ATM. ...
Waterworth WM, Masnavi G, Bhardwaj RM, Jiang Q, Bray CM, West CE (September 2010). "A plant DNA ligase is an important ... In particular, single- and double-strand breaks in DNA can be repaired. The DNA damage checkpoint kinase ATM has a major role ... Koppen G, Verschaeve L (2001). "The alkaline single-cell gel electrophoresis/comet assay: a way to study DNA repair in radicle ... Waterworth WM, Footitt S, Bray CM, Finch-Savage WE, West CE (August 2016). "DNA damage checkpoint kinase ATM regulates ...
Waterworth, W.M.; Masnavi, G.; Bhardwaj, R.M.; Jiang, Q.; Bray, C.M.; West, C.E. (2010). "A plant DNA ligase is an important ... The DNA checkpoint kinase ATM has a key role in integrating progression through germination with repair responses to the DNA ... Plants are capable of a DNA damage response that is a critical mechanism for maintaining genome stability. The DNA damage ... Waterworth, W.M.; Footitt, S.; Bray, C.M.; Finch-Savage, W.E.; West, C.E. (2016). "DNA damage checkpoint kinase ATM regulates ...
Johnston LH, Barker DG, Nurse P (1986). "Cloning and characterization of the Schizosaccharomyces pombe DNA ligase gene CDC17". ... Hartley JL, Temple GF, Brasch MA (2001). "DNA cloning using in vitro site-specific recombination". Genome Res. 10 (11): 1788-95 ...
Potts PR, Yu H (August 2005). "Human MMS21/NSE2 is a SUMO ligase required for DNA repair". Molecular and Cellular Biology. 25 ( ... RAD18 (SMC6), the DNA damage gene in fission yeast, also encodes an SMC-like protein and forms a heterodimeric complex with ... Nse1-Nse3-Nse4 subunits bridge the Smc5 head Smc6 and allow the binding of DNA. It is involved in the Alternative lengthening ... Palecek J, Vidot S, Feng M, Doherty AJ, Lehmann AR (December 2006). "The Smc5-Smc6 DNA repair complex: bridging of the Smc5- ...
... dependent E3 ubiquitin ligase that regulates DNA damage". Proceedings of the National Academy of Sciences of the United States ... They discovered parkin was an E3 ligase that is inactive in patients with genetic mutations in parkin, and that it is also ... protein ligase and promotes the degradation of the synaptic vesicle-associated protein, CDCrel-1". Proceedings of the National ... a first in class PAR-dependent E3 ligase. In the same screens, Botch was discovered which is an important inhibitor of Notch ...
... β also targets the ubiquitin ligase RNF8 to DNA double-strand breaks(Figure 2). In addition to localizing factors to ... One of these SNPs also associate with defective DNA repair and hematotoxicity in workers exposed to benzene. The WRAP53 gene ... December 2014). "The scaffold protein WRAP53β orchestrates the ubiquitin response critical for DNA double-strand break repair ... January 2009). "Large-scale evaluation of candidate genes identifies associations between DNA repair and genomic maintenance ...
... which also includes DNA ligases and RNA ligases. The enzymes of this superfamily share the following similarities: Conserved ... The NTase domain, conserved in capping enzymes, DNA and RNA ligases, is made up 5 motifs, I, III, IIIa, IV and V. Motif I or ... Shuman S, Schwer B (August 1995). "RNA capping enzyme and DNA ligase: a superfamily of covalent nucleotidyl transferases". ... an enzyme necessary for the transcription of DNA into pre-mRNA. When this complex of RNA polymerase II and the capping enzymes ...
... , acting as a ubiquitin ligase, mono-ubiquitinates γH2AX to tether DNA repair molecules at DNA lesions. In particular, RNF8 ... This protects the DNA ends and forms a platform for further DNA repair enzymes to operate. After the broken ends are rejoined, ... After the occurrence of a double-strand break in DNA, the chromatin needs to be relaxed to allow DNA repair, either by HRR or ... RNF8 promotes repair of DNA damage through three DNA repair pathways: homologous recombinational repair (HRR), non-homologous ...
Ymer, S. (1991). "Heat inactivation of DNA ligase prior to electroporation increases transformation efficiency". Nucleic Acids ... Damage to DNA - Exposure of DNA to UV radiation in standard preparative agarose gel electrophoresis procedure for as little as ... 10-100 pg of DNA may be used for transformation, more DNA may be necessary for low-efficiency transformation (generally ... and inactivation of ligase or chloroform extraction of DNA may be necessary for electroporation, alternatively only use a tenth ...
Cozzarelli was appointed a postdoctoral researcher with Arthur Kornberg and purified the T4-phage DNA ligase. From 1968 to 1982 ... It can thus unlink two linked DNA circles, and can even, at high enough concentrations of DNA, produce linked circles of DNA ... can cut both strands of a piece of DNA, pass another piece of DNA between the two ends, and then join the broken ends together ... From this he deduced that the DNA chains could not be intertwined, as we had suggested, but had to lie side by side. I ...
DLA probes are ligated at the 5' and 3' ends of the analyte by the joint action of T4 DNA ligase and T4 polynucleotide kinase. ... T4 DNA ligases are incompatible with ligation of RNA molecules as a donor (i.e. RNA at the 5' end of the ligation). Therefore, ... ligation by T4 DNA ligase being much less efficient over a bulge loop, which would happen for a 3' metabolite N-1 version of ... The kinase phosphorylates the 5'-end of the analyte and the ligase will join the capture probe to the analyte to the detection ...
Succinate-CoA ligase deficiency is responsible for encephalomyopathy with mitochondrial DNA depletion and mild methylmalonic ... "Deficiency of the alpha subunit of succinate-coenzyme A ligase causes fatal infantile lactic acidosis with mitochondrial DNA ... Succinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrial is an enzyme that in humans is encoded by the SUCLG1 gene. The ... As mitochondrial DNA depletion in muscle is not a constant finding in SUCLG1 patients, diagnosis should not be based on it; ...
Ho SR, Mahanic CS, Lee YJ, Lin WC (July 2014). "RNF144A, an E3 ubiquitin ligase for DNA-PKcs, promotes apoptosis during DNA ... RNF144A is an E3 ubiquitin ligase belonging to the RING-between RING (RBR) family of ubiquitin ligases, whose specific members ... The ubiquitin ligase activity of RNF144A catalyzes ubiquitin linkages at the K6-, K11- and K48- positions of ubiquitin in vitro ... Zhang Y, Liao XH, Xie HY, Shao ZM, Li DQ (November 2017). "RBR-type E3 ubiquitin ligase RNF144A targets PARP1 for ubiquitin- ...
DNA ligase is used in both DNA repair and DNA replication (see Mammalian ligases). In addition, DNA ligase has extensive use in ... It can also ligate blunt-ended DNA with much greater efficiency than E. coli DNA ligase. Unlike E. coli DNA ligase, T4 DNA ... Purified DNA ligase is used in gene cloning to join DNA molecules together to form recombinant DNA. The mechanism of DNA ligase ... it has been recognized as another DNA ligase and it is the reason for the unusual nomenclature of DNA ligases. DNA ligase from ...
DNA_LIGASE_A2 (PS00333). Accession PS00333 Integration. DNA ligase, ATP-dependent, conserved site (IPR016059) Member database. ...
View a chart of NEBs DNA and RNA ligases, their differences, and recommendations for optimal performance. ... Hi-T4 DNA Ligase displays increased thermotolerance compared to T4 DNA Ligase. Hi-T4 DNA Ligase can withstand temperatures as ... See also notes for T4 DNA Ligase.. T3 DNA Ligase. M0317S/L. 25°C. (4-37°C). N. ATP. A salt-tolerant enzyme for the ligation of ... Home Tools & Resources Selection Charts Properties of DNA and RNA Ligases Properties of DNA and RNA Ligases. NEB offers many ...
As with T4 DNA Ligase, blunt end ligation is enhanced by the addition of PEG 6000 to the reaction. T3 DNA Ligase exhibits a ... Cohesive ends, blunt ends, and nick sealing can all be efficiently catalyzed by T3 DNA Ligase. ... for NaCl in the reaction compared to T4 DNA Ligase, making the enzyme a versatile choice for in vitro molecular biology ... It will catalyze the formation of a phosphodiester bond between adjacent 5´ phosphate and 3´ hydroxyl groups of duplex DNA. ...
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PLN03113; DNA ligase 1; Provisional. pfam04675. Location:257 → 428. DNA_ligase_A_N; DNA ligase N terminus. ... PLN03113; DNA ligase 1; Provisional. pfam04675. Location:220 → 391. DNA_ligase_A_N; DNA ligase N terminus. ... PLN03113; DNA ligase 1; Provisional. pfam04675. Location:287 → 458. DNA_ligase_A_N; DNA ligase N terminus. ... PLN03113; DNA ligase 1; Provisional. pfam04675. Location:258 → 429. DNA_ligase_A_N; DNA ligase N terminus. ...
DNA ligase [Trypanosoma brucei brucei TREU927] DNA ligase [Trypanosoma brucei brucei TREU927]. gi,72390780,ref,XP_845684.1,,gnl ... Mismatch repairDNA mismatch repair (MMR) is a highly conserved biological pathway that plays a key role in maintaining genomic ... Base excision repairBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base ... Nucleotide excision repairNucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by ...
In this review, we will discuss the regulation of CRL ubiquitin ligases and their roles in control of DNA damage response. ... In this review, we will discuss the regulation of CRL ubiquitin ligases and their roles in control of DNA damage response. ... One of the main functions of CRLs is to regulate DNA damage response, a fundamental signaling cascade to maintain genome ... One of the main functions of CRLs is to regulate DNA damage response, a fundamental signaling cascade to maintain genome ...
T7 DNA Ligase[sunting , sunting sumber]. T7 DNA ligase merupakan DNA ligase dengan ukuran terkecil, yaitu sebesar 41 kDa.[2] ... DNA ligase ATP-dependent yang umum adalah T4 DNA ligase dan T7 DNA ligase.[2] ... T4 DNA Ligase[sunting , sunting sumber]. T4 DNA ligase berasal dari T4 bakteriofage.[5] Enzim ini akan meligasi fragmen DNA ... DNA ligase dapat digolongkan menjadi 2 jenis berdasarkan kofaktor yang diperlukan, yaitu NAD+ atau ATP.[1] DNA ligase NAD+- ...
DNA ligase that catalyzes the formation of phosphodiester linkages between 5-phosphoryl and 3-hydroxyl groups in double- ... It is essential for DNA replication and repair of damaged DNA. UniProt ... stranded DNA using NAD as a coenzyme and as the energy source for the reaction. ...
... those of the catalytic region of DNA ligase IV (LigIV), a specialized DNA ligase known to work in NHEJ, and of Artemis have ... those of the catalytic region of DNA ligase IV (LigIV), a specialized DNA ligase known to work in NHEJ, and of Artemis have ... DNA ligase 4. A, B. 610. Homo sapiens. Mutation(s): 0 Gene Names: LIG4. EC: 6.5.1.1. ... Structure of the catalytic region of DNA ligase IV in complex with an artemis fragment sheds light on double-strand break ...
The DNA ligase enzyme family catalyzes the formation of a phosphodiester bond between juxtaposed 5′‐phosphate and 3′‐hydroxyl ... Reaction conditions and applications for T4 DNA ligase, E. coli DNA ligase, and thermostable DNA ligases are described in this ... Keywords: T4 DNA ligase; Taq DNA ligase; DNA ligation; blunt‐end ligation; cloning ... Improvement of DNA adenylation using T4 DNA ligase with a template strand and a strategically mismatched acceptor strand. ...
DNA recombination and DNA repair in an ATP-dependent reaction. Binds specifically to DNA nicks containing a 3-OH and a 5- ... DNA ligase that seals nicks in double-stranded DNA during DNA replication, ... IPR012310. DNA_ligase_ATP-dep_cent. IPR016059. DNA_ligase_ATP-dep_CS. IPR016306. DNA_ligase_ATP-dep_T3. IPR012340. NA-bd_OB- ... IPR012310. DNA_ligase_ATP-dep_cent. IPR016059. DNA_ligase_ATP-dep_CS. IPR016306. DNA_ligase_ATP-dep_T3. IPR012340. NA-bd_OB- ...
IPR012310. DNA_ligase_ATP-dep_cent. IPR016059. DNA_ligase_ATP-dep_CS. IPR012308. DNA_ligase_ATP-dep_N. IPR036599. DNA_ligase_N_ ... IPR012310. DNA_ligase_ATP-dep_cent. IPR016059. DNA_ligase_ATP-dep_CS. IPR012308. DNA_ligase_ATP-dep_N. IPR036599. DNA_ligase_N_ ... PF04679. DNA_ligase_A_C. 1 hit. PF01068. DNA_ligase_A_M. 1 hit. PF04675. DNA_ligase_A_N. 1 hit. ... PF04679. DNA_ligase_A_C. 1 hit. PF01068. DNA_ligase_A_M. 1 hit. PF04675. DNA_ligase_A_N. 1 hit. ...
Rabbit polyclonal DNA Ligase III antibody validated for WB, IHC, ICC/IF and tested in Human, Mouse and Rat. Referenced in 1 ... Anti-DNA Ligase III antibody. See all DNA Ligase III primary antibodies. ... Anti-DNA Ligase III antibody (ab185815) at 1/500 dilution + extracts of testis cell lines. Developed using the ECL technique. ... Belongs to the ATP-dependent DNA ligase family.. Contains 1 BRCT domain.. Contains 1 PARP-type zinc finger. ...
Ligases are vital for the production of recombinant DNA used to insert genes into plasmids, which are important tools in ... Ligases are, therefore, commercially-valuable proteins. Ligases have many other uses, such as being used to isotopically label ... Derivatives of the bacterial plasmid pET-16b containing genes from bacteriophage T4 that allow for the expression of one DNA ( ... Many biotechnological companies investigate ligases due to their importance in the regulation of gene expression. The optimised ...
Rabbit polyclonal DNA Ligase III antibody validated for WB, IHC and tested in Human. With 1 independent review. Immunogen ... Anti-DNA Ligase III antibody. See all DNA Ligase III primary antibodies. ... Anti-DNA Ligase III antibody (ab97404) at 1/1000 dilution + HepG2 whole cell lysate at 30 µg. Predicted band size: 113 kDa. 7.5 ... Recombinant fragment containing a sequence corresponding to a region within amino acids 116-403 of Human DNA Ligase III (NP_ ...
T4 DNA Ligase. T4 DNA Ligase catalyzes the formation of phosphodiester bonds between juxtaposed 5 phosphate and 3 hydroxyl ... Blunt and cohesive end DNA ligation*Blunt end linker addition*Single-strand DNA, RNA and DNA/RNA repair *DNA fragment insertion ... as well as single-stranded nick repair of DNA, RNA and DNA/RNA, are possible via the T4 DNA ligase. This enzyme is supplied in ... One ligation unit is defined as the amount of enzyme that ligates ,90% of 6 µg of Hind III-restricted lambda DNA in a 20 µL ...
Mouse monoclonal DNA Ligase I antibody [1A9] validated for WB, ELISA and tested in Human. Referenced in 1 publication and 1 ... DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. ... Aberrant DNA repair and DNA replication due to an inherited enzymatic defect in human DNA ligase I.. Mol Cell Biol 14:310-7 ( ... Anti-DNA Ligase I antibody [1A9]. See all DNA Ligase I primary antibodies. ...
DNA-PK) binds to the ends of the DSBs and brings them together. The DNA-PK catalytic subunit (DNA-PKcs) then recruits the ... through its interactions with DNA Ligase IV and DNA-PKcs. JEM, 209(5):955-963. ... Human DNA Ligase IV-Artemis Fragment Complex. Sean Smith 16 and Samantha White 16 ... DNA ligase IV (LigIV) is an enzyme that helps to repair double strand breaks (DSBs) through nonhomologous end joining (NHEJ). ...
Compare DNA Ligase 3 ELISA Kits from antibodies-online from leading suppliers on Biocompare. View specifications, prices, ... DNA Ligase 3 ELISA Kits from antibodies-online. The ELISA (enzyme-linked immunosorbent assay) is a widely used application for ... Your search returned 2 DNA Ligase 3 ELISA ELISA Kit across 1 supplier. ...
... there are only three known DNA ligases (DNA Lig1, DNA Lig3, and DNA Lig4) in mammalian cells to finish the last ligation step ( ... 2008) Human DNA ligases I and III, but not ligase IV, are required for microhomology-mediated end joining of DNA double-strand ... the only remaining nuclear DNA ligase is Lig3, whereas in Lig3−/−Lig4−/− cells, the only nuclear DNA ligase is Lig1. We also ... Ligase I and ligase III mediate the DNA double-strand break ligation in alternative end-joining. Guangqing Lu, Jinzhi Duan, ...
Ubiquitination of several DNA replication-repair proteins is a critical mechanism by which cellular DNA replication and DNA ... PCNA-mediated stabilization of E3 ligase RFWD3 at the replication fork is essential for DNA replication. Yo-Chuen Lin, Yating ... PCNA-mediated stabilization of E3 ligase RFWD3 at the replication fork is essential for DNA replication ... PCNA-mediated stabilization of E3 ligase RFWD3 at the replication fork is essential for DNA replication ...
In addition, our data implicate mammalian ligase IV in V(D)J recombination and the repair of radiation-induced DNA damage, … ... Our findings provide a function for the carboxy-terminal region of ligase IV and suggest that BRCT domains of other proteins ... Mammalian DNA double-strand break repair protein XRCC4 interacts with DNA ligase IV Curr Biol. 1997 Aug 1;7(8):588-98. doi: ... In addition, our data implicate mammalian ligase IV in V(D)J recombination and the repair of radiation-induced DNA damage, and ...
Invitrogen Anti-DNA Ligase III Polyclonal, Catalog # PA5-102510. Tested in Western Blot (WB), Immunofluorescence (IF), ... Protein Aliases: DNA ligase (ATP) 3; DNA ligase 3; DNA ligase III; ligase II, DNA, ATP-dependent; ligase III, DNA, ATP- ... DNA binding DNA ligase activity DNA ligase (ATP) activity protein binding ATP binding zinc ion binding nucleotide binding ... DNA replication DNA repair cellular response to DNA damage stimulus DNA ligation involved in DNA repair ...
It can be used to join DNA fragments with both sticky ends and blunt ends, and to repair nicks in double-stranded DNA with ... The Invitrogen Anza T4 DNA Ligase Master Mix facilitates the joining of abutted 5-phosphate and 3-hydroxyl termini in duplex ... DNA through the formation of a phosphodiester bond. ... Anza T4 DNA Ligase Master Mix is part of the Anza™ Restriction ... Anza T4 DNA Ligase is formulated as a 4X concentrated master mix. Ligation can be performed with DNA in water, TE, elution ...
View Mouse Monoclonal anti-DNA Ligase I Antibody (7A12) (NB100-2714). Validated Applications: WB, ELISA, IP. Validated Species ... Home » DNA Ligase I » DNA Ligase I Antibodies » DNA Ligase I Antibody (7A12) ... Four biochemically distinct DNA ligases, termed ligases I-IV, have been identified in mammalian cells. DNA ligase I is ... Reviews for DNA Ligase I Antibody (NB100-2714) (0) There are no reviews for DNA Ligase I Antibody (NB100-2714). By submitting a ...
Polynucleotide Ligase,T4 DNA Ligase; find Sigma-Aldrich-D2886 MSDS, related peer-reviewed papers, technical documents, similar ... DNA Ligase from T4-infected Escherichia coli buffered aqueous glycerol solution; CAS Number: 9015-85-4; EC Number: 232-770-0; ... T4 DNA Ligase. T4 DNA Ligase catalyzes the formation of a phosphodiester bond between the terminal 5′ phosphate and a 3′ ... T4 DNA Ligase forms an energy dependent phosphodiester linkage between the termini of adjacent polynucleotides of duplex DNA. ...
... dependent DNA ligase bound to AMP (adenosine monophosphate). DNA ligase is an enzyme that binds two strands of DNA ( ... NAD dependent DNA ligase. Molecular model of NAD(+)- ... DNA ligase is an enzyme that binds two strands of DNA ( ... Caption: NAD dependent DNA ligase. Molecular model of NAD(+)-dependent DNA ligase bound to AMP (adenosine monophosphate). ... dna, dna ligase, enzyme, healthcare, illustration, medical, medical illustration, medicine, model, molecular, molecular model, ...
DNA replication is strictly regulated to occur only once per cell cycle. In eukaryotes, the presence of licensing proteins at ... CUL-4 Ubiquitin Ligase Maintains Genome Stability by Restraining DNA-replication Licensing Nature. 2003 Jun 19;423(6942):885-9. ... Here we show that the CUL-4 ubiquitin ligase temporally restricts DNA-replication licensing in Caenorhabditis elegans. ... Inactivation of CUL-4 causes massive DNA re-replication, producing cells with up to 100C DNA content. The C. elegans orthologue ...
  • DNA ligase is a specific type of enzyme, a ligase, (EC 6.5.1.1) that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. (wikipedia.org)
  • Ligase will also work with blunt ends, although higher enzyme concentrations and different reaction conditions are required. (wikipedia.org)
  • Derived from a thermophilic bacterium, the enzyme is stable and active at much higher temperatures than conventional DNA ligases. (wikipedia.org)
  • 5X enzyme concentration over standard T4 DNA Ligase, good for increasing reaction rates or for bulk users. (neb.com)
  • T3 DNA Ligase exhibits a higher tolerance (2-fold) for NaCl in the reaction compared to T4 DNA Ligase, making the enzyme a versatile choice for in vitro molecular biology protocols requiring DNA ligase activity. (neb.com)
  • One unit is defined as the amount of enzyme required to give 50% ligation of 100 ng HindIII fragments of λ DNA in a total reaction volume of 20 μl in 1 minute at 25°C in 1X T3 DNA Ligase Reaction Buffer. (neb.com)
  • Enzymatic breakage and joining of deoxyribonucleic acid, I. Repair of single‐strand breaks in DNA by an enzyme system from Escherichia coli infected with T4 bacteriophage. (currentprotocols.com)
  • and this enzyme, along with other proteins, processes the ends of the DNA to be joined. (kenyon.edu)
  • Anza T4 DNA Ligase Master Mix is part of the Anza™ Restriction Enzyme Cloning System, unifying the traditional cloning processes. (thermofisher.com)
  • The enzyme efficiently joins blunt and cohesive ends and repairs single-stranded nicks in duplex DNA, RNA or DNA/RNA hybrids. (sigmaaldrich.com)
  • DNA ligase is an enzyme that binds two strands of DNA (deoxyribonucleic acid) together. (sciencephoto.com)
  • The 1.65 Å resolution crystal structure of the enzyme-adenylate complex reveals no unstructured loops or segments, and suggests that this enzyme binds the DNA without requiring full encirclement of the DNA duplex. (iucr.org)
  • enzyme is the first structure available for the minimal type of bacterial DNA ligases and is the smallest DNA ligase to be crystallized to date. (iucr.org)
  • This function is carried out by DNA ligases in a three-step reaction in which the enzyme first self-adenylates, followed by DNA binding and transfer of AMP to the 5′-phosphate terminus of the DNA nick, which is then activated for nucleophilic attack by the apposing 3′-OH group. (iucr.org)
  • DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. (embl.de)
  • Ampligase Enzyme & Buffer contain: Ampligase DNA Ligase and 10X Reaction Buffer (25 μl Buffer for each 50 U enzyme). (lucigen.com)
  • Here we provide genetic evidence supporting a role of this E3-enzyme in the maintenance of DNA replication integrity in Caenorhabditis elegans . (g3journal.org)
  • The crystal structure of the ATP-dependent S. solfataricus DNA ligase (ssLig) shows the three-domain enzyme in an extended conformation. (jbsdonline.com)
  • Heating a reaction containing T3 DNA Ligase at 65°C for 10 minutes will inactivate the enzyme. (neb.com)
  • Here, we report that the deubiquitylation enzyme ( DUB ) ataxin‐3 counteracts RNF 4 activity during the DNA double‐strand break ( DSB ) response. (embopress.org)
  • Here, removal of the checkpoint mediator MDC 1 by a SUMO ‐targeted ubiquitin ligase ( STU bL) is found to be delayed by SUMO ‐stimulated action of the deubiquitylation enzyme ( DUB ) ataxin‐3. (embopress.org)
  • In biochemistry , a ligase is an enzyme that can catalyze the joining of two large molecules by forming a new chemical bond , usually with accompanying hydrolysis of a small pendant chemical group on one of the larger molecules or the enzyme catalyzing the linking together of two compounds, e.g., enzymes that catalyze joining of C-O, C-S, C-N, etc. (wikipedia.org)
  • The common names of ligases often include the word "ligase", such as DNA ligase , an enzyme commonly used in molecular biology laboratories to join together DNA fragments. (wikipedia.org)
  • It is also said that a synthase is a lyase (a lyase is an enzyme that catalyzes the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond or a new ring structure) and does not require any energy, whereas a synthetase is a ligase (a ligase is an enzyme that binds two chemicals or compounds) and thus requires energy. (wikipedia.org)
  • Most experiments use T4 DNA Ligase (isolated from bacteriophage T4) which is most active at 25°C. However in order to perform successful ligations, the optimal enzyme temperature needs to be balanced with the melting temperature T m (also the annealing temperature) of the DNA fragments being ligated. (chemeurope.com)
  • An initial physical and biochemical characterization of the enzyme reveals that it exists as a monomer and can ligate nicked, cohesive, and blunt-ended DNA fragments. (semanticscholar.org)
  • One unit is defined as the amount of enzyme required to give 50% ligation of the 12-base pair cohesive ends of 1 µg of BstEII-digested λ DNA in a total reaction volume of 50 µl in 15 minutes at 45°C. (neb.sg)
  • Incubate DNA and enzyme in 1X Taq DNA Ligase Buffer at 45°C for 15 minutes or in a thermocycler with a program suited to the reaction described by Barany (1991) Genetic Disease Detection and DNA Amplification Using Cloned Thermostable Ligase. (neb.sg)
  • One unit is defined as the amount of enzyme required to give 50% ligation of HindIII fragments of λ DNA (5' DNA termini concentration of 0.12 μM, 300 μg/ml) in a total reaction volume of 20 μl in 30 minutes at 16°C in 1X E. coli DNA Ligase Reaction Buffer. (neb.sg)
  • This enzyme ligates only DNA fragments with cohesive termini. (neb.sg)
  • One unit is defined as the amount of enzyme required to give 50% ligation of 6 µg of Lambda-HindIII DNA in 30 minutes at 25°C in a total reaction volume of 20 µl. (nebiolabs.com.au)
  • It is better to vortex or spin the t4 dna ligase enzyme before pipetting to ensure that it is mixed well. (web.app)
  • T4 dna ligase recombinant form of the enzyme from t4. (web.app)
  • Another thermostable enzyme, dna ligase, is harnessed in the assay reported here that both amplifies dna and discriminates a singlebase substitution. (web.app)
  • This enzyme will join blunt end and cohesive end termini as well as repair single stranded nicks in duplex dna and some dna rna hybrids. (web.app)
  • T4 dna ligase is a ligation enzyme that can be used to join dna fragments by catalyzing the formation of phosphodiester bonds between juxtaposed 5 phosphate and 3 hydroxyl termini in doublestranded dna using atp as a coenzyme. (web.app)
  • An enzyme that joins the ends of two separate pieces of DNA. (washington.edu)
  • New covalent bonds between two molecules are created by the enzyme called ligase. (biospace.com)
  • DNA ligase is an enzyme that regulates irregularities. (biospace.com)
  • Research activities for sequencing applications, increase in the birth rate, rise in the incidence of infectious diseases, and increase in genetic disorders are key factors that are estimated to boost the global ligases enzyme market . (biospace.com)
  • However, high sensitivity of the enzyme to factors such as ligase concentration, DNA concentration, temperature, and buffer composition are expected to restrain the market. (biospace.com)
  • The global ligases enzyme market can be segmented based on source, application, end-user, and region. (biospace.com)
  • Based on source, the global ligases enzyme market can be classified into microorganisms, animal, and plant. (biospace.com)
  • In terms of application, the global ligases enzyme market can be divided into polymerase chain reaction, mutation detection, cloning, drug target, and next generation sequencing. (biospace.com)
  • Based on end-user, the global ligases enzyme market can be classified into diagnostic centers & hospitals and research institutes. (biospace.com)
  • In terms of region, the global ligases enzyme market can be divided into North America, Europe, Asia Pacific, Latin America, and Middle East & Africa. (biospace.com)
  • Other Anza DNA Modifying Enzymes include the Anza T4 PNK Kit , Anza DNA Blunt End Kit , and Anza DNA End Repair Kit . (thermofisher.com)
  • Eukaryotic DNA ligases are ATP-dependent enzymes that catalyse the joining of single and double-strand DNA breaks, which is an essential final step in DNA replication, recombination and repair. (novusbio.com)
  • DNA ligases are a structurally diverse class of enzymes which share a common catalytic core and seal breaks in the phosphodiester backbone of double-stranded DNA via an adenylated intermediate. (iucr.org)
  • Also, the ligase, like most enzymes, is in some percentage of glycerol which tends to stick to the sides of your tip. (openwetware.org)
  • At least three classes of activities, known as E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 (ubiquitin-protein ligase) enzymes, cooperate in catalyzing protein ubiquitination ( 34 ). (asm.org)
  • DNA ligase enzymes catalyse the joining of adjacent polynucleotides and as such play important roles in DNA replication and repair pathways. (biomedcentral.com)
  • These enzymes seal gaps in the sugar-phosphate backbone of DNA that arise during DNA replication, DNA damage and repair. (biomedcentral.com)
  • Proliferating cell nuclear antigen (PCNA) is a trimeric, ring-shaped protein that encircles duplex DNA and serves as a docking site at the replication fork for several nucleic acid enzymes, including polymerase, endonuclease, and ligase. (jbsdonline.com)
  • Ligases are classified as EC 6 in the EC number classification of enzymes. (wikipedia.org)
  • For example, DNA ligases are used with restriction enzymes to insert DNA fragments, often genes, into plasmids. (chemeurope.com)
  • Activity of dna modifying enzymes in cutsmart buffer neb. (web.app)
  • Mammalian cells contain three different dna ligase enzymes, each with different properties but all involved in dna replication and repair. (web.app)
  • No- it must have to do with the simple fact that T4 DNA ligase, one of the most easily produced and common workhorse enzymes in molecular biology, costs an outrageous $64.00 for 20,000 units! (wordpress.com)
  • If you're familiar with recombinant fusion enzymes possessing enhanced activity- recently innovated high-fidelity polymerases such as Phusion come to mind- then you may find it initially puzzling that the holy grail of non-sequence specific DNA binding proteins sso7d was not utilized over p50. (wordpress.com)
  • Lindahl showed that DNA is inherently unstable and requires active repair, and established the role of DNA glycosylase enzymes in base excision repair. (nature.com)
  • Modrich was instrumental in understanding a process called mismatch repair that is involved in repairing errors caused by the DNA replication machinery, while Sancar demonstrated biochemically how enzymes repair damage to DNA from ultraviolet rays, by a process called nucleotide excision repair. (nature.com)
  • The growing list of enzymes that correct or prevent these reactions, akin to those that combat DNA and protein damage, have important roles in maintaining homeostasis and preventing disease. (nature.com)
  • Same as all enzymes, ligases are embedded with proteins that have a target molecule identification site. (biospace.com)
  • Ligases are one of the 50 enzymes present in the human body. (biospace.com)
  • North America is expected to be the leading revenue contributor to the global ligases enzymes market. (biospace.com)
  • DNA ligases are enzymes that seal breaks in the backbones of DNA, leading to them being essential for the survival of all organisms. (uea.ac.uk)
  • The recent development of modified derivatives of nucleotides highlights that the continued combination of structural, biochemical and biophysical techniques will be useful in targeting these essential cellular enzymes.Several recent studies have synthesised novel derivatives and their biological activity against a range of DNA ligases has been evaluated as inhibitors for drug discovery and/or nonnatural substrates for biochemical applications. (uea.ac.uk)
  • In addition, DNA ligase has extensive use in molecular biology laboratories for recombinant DNA experiments (see Research applications). (wikipedia.org)
  • Purified DNA ligase is used in gene cloning to join DNA molecules together to form recombinant DNA. (wikipedia.org)
  • DNA ligase III: complexes with DNA repair protein XRCC1 to aid in sealing DNA during the process of nucleotide excision repair and recombinant fragments. (wikipedia.org)
  • An E. coli strain containing a recombinant gene encoding T3 DNA Ligase. (neb.com)
  • In Enzymology Primer for Recombinant DNA Technology, pp. 109‐133. (currentprotocols.com)
  • Recombinant fragment corresponding to Human DNA Ligase III (C terminal). (abcam.com)
  • Ligases are vital for the production of recombinant DNA used to insert genes into plasmids, which are important tools in genetic engineering where they are used to express, clone or amplify certain genes. (uea.ac.uk)
  • Recombinant fragment containing a sequence corresponding to a region within amino acids 116-403 of Human DNA Ligase III (NP_039269). (abcam.com)
  • Antigen: Full-length recombinant human DNA Ligase III-b. (qedbio.com)
  • DNA ligase I: ligates Okazaki fragments during lagging strand DNA replication and some recombinant fragments. (chemeurope.com)
  • DNA ligases have become an indispensable tool in modern molecular biology research for generating recombinant DNA sequences. (chemeurope.com)
  • Single Strand DNA Ligase, thermostable, recombinant, Solution recombinant proteins Most stable storage is at - 81 C or lower but some lyophilised proteins can be stored at +4C. (antibody-antibodies.com)
  • Please read carefully the data sheet of the Single Strand DNA Ligase, thermostable, recombinant, Solution. (antibody-antibodies.com)
  • Dnase i, recombinant, rnasefree, is a dna specific endonuclease that hydrolyzes the phosphodiester linkages of double and singlestranded dna to a mixture of mono and oligonucleotides. (web.app)
  • the authors who conceived of this recombinant ligase originally, fusion of p50 to T4 ligase resulted in approximately 7-fold and 1.6-fold improvements in cohesive-end and blunt-end ligation, respectively [1]. (wordpress.com)
  • T4 DNA ligase is isolated from a recombinant E. coli strain and is suitable for ligation of sticky- and blunt ended DNA fragments. (genecraft.de)
  • A significant number of DNA ligases have been isolated or prepared in recombinant forms and, here, we review their biochemical and structural characterization. (uea.ac.uk)
  • one successful approach, for example, tested T4 DNA ligase fused to several alternative DNA binding proteins and found that the constructs with either p50 or NF-kB as fusion partners were over 160% more active in blunt-end ligations for cloning purposes than wild type T4 DNA ligase. (wikipedia.org)
  • Ligases are, therefore, commercially-valuable proteins. (uea.ac.uk)
  • Our findings provide a function for the carboxy-terminal region of ligase IV and suggest that BRCT domains of other proteins may mediate contacts between DNA repair components. (nih.gov)
  • There are four distinct ligase proteins found in mammalian cells. (thermofisher.com)
  • These proteins repair double strand breaks in DNA molecules. (sciencephoto.com)
  • In addition, DNA ligase IV has a long C-terminal extension comprising of two BRCT domains (after the C-terminal domain of a breast cancer susceptibility protein, BRCA1), which are phosphopeptide-binding modules found in many proteins that regulate DNA damage responses (such as BRCA1, MDC1 and BARD1). (axonmedchem.com)
  • Rsp5 is an E3 ubiquitin-protein ligase of Saccharomyces cerevisiae that belongs to the hect domain family of E3 proteins. (asm.org)
  • Cullin-RING E3-Ligases (CRLs), the largest family of E3 ubiquitin-Ligases, regulate diverse cellular processes by promoting ubiquitination of target proteins. (g3journal.org)
  • Using a protein-DNA cross-linking assay during repair in human whole cell extracts, we monitored proteins involved in the initial steps of repair of a substrate containing a site-specific abasic site to address the molecular events following incision of the abasic site by AP endonuclease. (lancs.ac.uk)
  • We have studied the mechanism of the DNA ligase-PCNA interaction with a structural and biochemical approach using proteins from Sulfolobus solfataricus . (jbsdonline.com)
  • A large number of ubiquitin ligases mediates the ubiquitin‐dependent recruitment of DNA damage response proteins to DSBs. (embopress.org)
  • Some ligases associate with biological membranes as peripheral membrane proteins or anchored through a single transmembrane helix , [2] for example certain ubiquitin ligase related proteins. (wikipedia.org)
  • RNA strands are created using DNA strands as a template in a process called transcription , where DNA bases are exchanged for their corresponding bases except in the case of thymine (T), which RNA substitutes for uracil (U). [4] Under the genetic code , these RNA strands specify the sequence of amino acids within proteins in a process called translation . (wikipedia.org)
  • Within eukaryotic chromosomes, chromatin proteins, such as histones , compact and organize DNA. (wikipedia.org)
  • These compacting structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed. (wikipedia.org)
  • The group is particularly interested in addressing how these site-specific proteins initially locate target sequences that are buried amongst large stretches of non-target DNA. (port.ac.uk)
  • This gene encodes a member of the ATP-dependent DNA ligase protein family. (nih.gov)
  • The encoded protein functions in DNA replication, recombination, and the base excision repair process. (nih.gov)
  • Interacts with DNA-repair protein XRCC1 and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. (abcam.com)
  • This is accomplished when DNA protein kinase (DNA-PK) binds to the ends of the DSBs and brings them together. (kenyon.edu)
  • By using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, we generated mouse CH12F3 cell lines in which, in addition to Lig4, either Lig1 or nuclear Lig3, representing the cells containing a single DNA ligase (Lig3 or Lig1, respectively) in their nucleus, was completely ablated. (pnas.org)
  • Mammalian cells deficient in the XRCC4 DNA repair protein are impaired in DNA double-strand break repair and are consequently hypersensitive to ionising radiation. (nih.gov)
  • These features are shared by cells lacking components of the DNA-dependent protein kinase (DNA-PK). (nih.gov)
  • Protein mapping studies revealed that XRCC4 interacted with ligase IV via the unique carboxy-terminal ligase IV extension that comprises two tandem BRCT (BRCA1 carboxyl terminus) homology motifs, which are also found in other DNA repair-associated factors and in the breast cancer susceptibility protein BRCA1. (nih.gov)
  • DNA Ligase III gene product migrates as a 100 kDa (a-form) protein in somatic tissues, is ubiquitously expressed and complexes with XRCC-1 and a 97 kDa (beta form) protein that is found in testis. (thermofisher.com)
  • The core components include the Ku70/Ku86 heterodimer, DNA-dependent protein kinase, X-ray cross complementation factor 4 (XRCC4), and DNA ligase IV (Lig4) ( 1 , 2 ). (pnas.org)
  • The joining of Okazaki fragments during lagging strand DNA replication in mammalian cells is due to DNA ligase I. A combination of DNA polymerase epsilon, PCNA, replication factor C, replication protein A, and DNA ligase I is well-suited to the task of creating nucleotide excision repair patches. (novusbio.com)
  • DNA-binding regions (PATCHDOCK) and interactome (STRINGS) of the protein were also predicted. (springer.com)
  • Molecular model of the DNA (deoxyribonucleic acid) repair protein XRCC4 complexed with DNA ligase IV. (sciencephoto.com)
  • Detection of human Ligase I protein in Raji whole cell lysate using GeneTex DNA Ligase I 10H5 monoclonal antibody GTX70141. (genetex.com)
  • Single-stranded DNA oligomers stimulate error-prone alternative repair of DNA double-strand breaks through hijacking Ku protein. (genetex.com)
  • These findings indicate altered DNA-protein interactions due to S6G incorporation. (aspetjournals.org)
  • The evolutionarily conserved Leucine Rich Repeat protein 1 ( LRR-1 ) is a substrate-recognition subunit of a CRL2 LRR-1 E3-ligase. (g3journal.org)
  • DNA replication is a tightly regulated multistep process that requires the sequential action of several protein complexes that select DNA replication origins, recruit on these origins the DNA replication fork helicase that once activated, unwinds and duplicates the DNA. (g3journal.org)
  • We also find that the cross-linking efficacy of the DNA ligase III-XRCC1 heterodimer was decreased about 2-fold in the Pol -deficient cell extract but was rescued by addition of purified wild type but not a mutant Pol protein that does not interact with the DNA ligase III-XRCC1 heterodimer. (lancs.ac.uk)
  • Below are the list of possible SPBc2 prophage-derived DNA ligase-like protein products. (mybiosource.com)
  • Future studies will focus on the dynamics of the protein interface to understand the mechanisms that allow the ligase-PCNA complex to efficiently process breaks in DNA. (jbsdonline.com)
  • A large part of DNA (more than 98% for humans) is non-coding , meaning that these sections do not serve as patterns for protein sequences . (wikipedia.org)
  • The first step of DNA replication occurs when a protein triggers the unwinding of the DNA helix. (reference.com)
  • A protein known as helicase is responsible for breaking down the hydrogen bonds between strands of DNA during replication. (reference.com)
  • DNA translation is the process by which a protein is made using an RNA template. (reference.com)
  • A recent PhD student (Dr Claire Fraser) has completed a series of studies looking at the importance of AMP-containing cofactors, substrate order-of-addition studies, and length-dependency and processivity studies (unpublished) to look for evidence of facilitated diffusion and 1D vs. 3D protein motion on nicked DNA. (port.ac.uk)
  • The overall goal of this ongoing work is to discover how the ligase protein behaves on multiple-nicked substrates and investigate whether further protein partners (like the β-sliding clamp) are involved in vivo. (port.ac.uk)
  • Use of ligases in protein engineering are expected to offer growth opportunities to the market in developing regions such as Latin America, Middle East & Africa, and Asia Pacific. (biospace.com)
  • DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair in an ATP-dependent reaction. (uniprot.org)
  • Artemis C-terminal region facilitates V(D)J recombination through its interactions with DNA Ligase IV and DNA-PKcs. (kenyon.edu)
  • In addition, our data implicate mammalian ligase IV in V(D)J recombination and the repair of radiation-induced DNA damage, and provide a model for the potentiation of these processes by XRCC4. (nih.gov)
  • The activity of these DNA ligases is required for the joining of DNA strand breaks that occur during DNA replication, repair and recombination. (thermofisher.com)
  • Nonhomologous end-joining (NHEJ) is the major DNA double-strand break (DSB) repair pathway in mammals and resolves the DSBs generated during both V(D)J recombination in developing lymphocytes and class switch recombination (CSR) in antigen-stimulated B cells. (pnas.org)
  • It is active during DNA replication, DNA repair and DNA recombination. (embl.de)
  • DNA ligase IV (EC 6.5.1.1), which is conserved in all eukaryotes, is part of a family of ATP-dependent DNA ligases that are involved in DNA replication, recombination and repair. (axonmedchem.com)
  • One vital, and often tricky, aspect to performing successful recombination experiments involving ligase is controlling the optimal temperature. (chemeurope.com)
  • It is responsible for three general functions: sealing repairs in the DNA, connecting Okazaki fragments that are formed during the replication of double-stranded DNA in the cell, and sealing recombination fragments. (biospace.com)
  • Interaction with methylated LIG1 promotes the recruitment of UHRF1 to DNA replication sites and is required for DNA methylation maintenance. (nih.gov)
  • The rs156641 polymorphism of DNA ligase 1 (LIG1) was significantly associated with lung cancer risk, whereas no association was found between rs3730931/rs439132/rs20579 polymorphisms and lung cancer. (nih.gov)
  • Cells having only one ligase (Lig1 or nuclear Lig3) are capable of DNA replication and DNA repair after exposure to a wide range of genotoxins. (pnas.org)
  • Here, we report that CSR levels are not further reduced by deletion of either of the two remaining DNA ligases (Lig1 and nuclear Lig3) in Lig4 −/− cells. (pnas.org)
  • DNA ligase 1 (LIG1) is present in all eukaryotes where it is required for joining DNA fragments produced during DNA replication. (biomedcentral.com)
  • The activity of E. coli DNA ligase can be enhanced by DNA polymerase at the right concentrations. (wikipedia.org)
  • Enhancement only works when the concentrations of the DNA polymerase 1 are much lower than the DNA fragments to be ligated. (wikipedia.org)
  • Interaction between DNA Polymerase β and BRCA1. (genetex.com)
  • Human DNA polymerase beta polymorphism, Arg137Gln, impairs its polymerase activity and interaction with PCNA and the cellular base excision repair capacity. (genetex.com)
  • Consequences of 6-thioguanine incorporation into DNA on polymerase, ligase, and endonuclease reactions. (aspetjournals.org)
  • After annealing of the synthetic oligonucleotides to form a duplex DNA containing a one-nucleotide gap (opposite cytosine in the 40-mer), the 19-mer was extended with 2'-deoxythioguanosine 5'-triphosphate using DNA polymerase, forming a nicked duplex DNA. (aspetjournals.org)
  • DNA polymerase Beta promotes recruitment of XRCC1-Ligase III alpha to sites of base excision repair. (lancs.ac.uk)
  • We find that after dissociation of AP endonuclease from the incised abasic site, both DNA polymerase (Pol ) and the DNA ligase III-XRCC1 heterodimer efficiently bind/cross-link to the substrate DNA. (lancs.ac.uk)
  • The alternative, a single-strand break, is easily fixed by DNA polymerase using the complementary strand as a template but still requires DNA ligase to create the final phosphodiester bond to fully repair the DNA. (chemeurope.com)
  • The bacteriophage T7 DNA ligase gene was amplified using polymerase chain reaction-based methods and cloned into a T7 promoter-based expression vector. (semanticscholar.org)
  • T3 DNA Ligase is also active in buffers without PEG 6000, such as our T4 DNA Ligase Buffer and NEBuffers 1-4, for applications in which PEG 6000 is detrimental. (neb.com)
  • Ligation can be performed with DNA in water, TE, elution buffer, or 1X Anza™ buffers. (thermofisher.com)
  • Continue to use 1 ul, and check the ligase buffer. (protocol-online.org)
  • Also referring to Sambrook's Molecular Cloning, I prefer to "relax" the dna (vector and insert) in 45c for 5 mins and then chill on ice before i put in buffer and then ligase. (protocol-online.org)
  • One unit of Ampligase DNA Ligase catalyzes the ligation of 50% of the cos sites in 1 µg of lambda DNA in 1 minute at 45°C in 1X Ampligase Reaction Buffer. (lucigen.com)
  • Ampligase DNA Ligase Kit contains: Ampligase DNA Ligase, 10X Reaction Buffer, and Control DNA. (lucigen.com)
  • 1X Taq DNA Ligase Reaction Buffer and DNA (20 µg/ml). (neb.sg)
  • 1X Taq DNA Ligase Reaction Buffer requires NAD + as a cofactor. (neb.sg)
  • 400 units of T4 DNA Ligase (NEB #M0202) or Hi-T4 DNA Ligase (NEB #M2622) were pre-incubated at 45°C in 1X T4 DNA Ligase Buffer in the absence of DNA substrate for the indicated time. (nebiolabs.com.au)
  • 1,000 units of T4 DNA Ligase (NEB #M0202) or Hi-T4 DNA Ligase (NEB #M2622) in (1X) T4 DNA Ligase Buffer were cycled in the presence of DNA at 42°C (A) or 50°C (B) for 5 minutes followed by 16°C for 5 minutes in the presence of 1 μg pBR322. (nebiolabs.com.au)
  • B6030 10x t4 dna ligase buffer 10x t4 dna ligase buffer b6030 500mm trishci 100 mm mgcl 2 50 mm dtt 10 mm atp ph 7. (web.app)
  • T4 dna ligase is provided with 10x reaction buffer. (web.app)
  • T4 dna ligase buffer contains atp, so repeated freeze thaw cycles can degrade atp, thereby decreasing the efficiency of ligation. (web.app)
  • 1 unit is defined as the amount of T4 DNA Ligase required to join 50% of 100 ng of DNA fragments with cohesive termini in 50 µl 1X T4 DNA Ligase Buffer following a 30 minute incubation at 23°C. (focusbio.com.au)
  • The E. coli DNA ligase is encoded by the lig gene. (wikipedia.org)
  • Mutations in this gene that lead to DNA ligase I deficiency result in immunodeficiency and increased sensitivity to DNA-damaging agents. (nih.gov)
  • Human DNA ligase i (ligi) gene and risk of cervical cancer in North Indian women. (nih.gov)
  • Cloning, overexpression and nucleotide sequence of a thermostable DNA ligase‐encoding gene. (currentprotocols.com)
  • Many biotechnological companies investigate ligases due to their importance in the regulation of gene expression. (uea.ac.uk)
  • Although the XRCC4 gene has been cloned, the function(s) of XRCC4 in DNA end-joining has remained elusive. (nih.gov)
  • DNA ligase I is functionally homologous to the DNA ligase encoded by the Saccharomyces cerevisiae Cdc9 gene. (novusbio.com)
  • Purified from an E. coli strain containing the cloned ligase gene from Thermus thermophilus HB8 (1-3). (neb.sg)
  • Allele-specific gene detection using Ligase Detection Reaction and Ligase Chain Reaction (4). (neb.sg)
  • Purified from E. coli strain containing a cloned E. coli DNA Ligase gene. (neb.sg)
  • AMP is required for the ligase reaction, which proceeds in four steps: Reorganization of activity site such as nicks in DNA segments or Okazaki fragments etc. (wikipedia.org)
  • DNA ligase I: ligates the nascent DNA of the lagging strand after the Ribonuclease H has removed the RNA primer from the Okazaki fragments. (wikipedia.org)
  • Ligases have many other uses, such as being used to isotopically label RNA fragments by ligating labelled and unlabelled fragments together for use in NMR experiments to study the secondary structures present. (uea.ac.uk)
  • It can be used to join DNA fragments with both sticky ends and blunt ends, and to repair nicks in double-stranded DNA with 3'-hydroxyl and 5'-phosphate ends. (thermofisher.com)
  • Rapid and efficient method for cloning of blunt-ended DNA fragments. (sigmaaldrich.com)
  • Sample preparation converts input sample DNA (e.g., cell-free DNA) into sequencing-capable library fragments by the appropriate attachment of adapter molecules to both ends of the input molecules. (codexis.com)
  • In this multi-step process, adapter ligation via the use of T4 DNA ligase is the limiting step in complete conversion of sample to ligated library fragments. (codexis.com)
  • DNA ligase I migrates as a 125kDa phosphoprotein and is implicated in joining Okazaki fragments during DNA synthesis. (genetex.com)
  • This finding suggests that incorporation of S6G at the 3' terminus of Okazaki fragments would inhibit lagging strand DNA synthesis. (aspetjournals.org)
  • Ligase can join two complementary fragments of nucleic acid and repair single stranded breaks that arise in double stranded DNA during replication. (wikipedia.org)
  • The shorter the DNA fragments, the lower the T m . (chemeurope.com)
  • For ligation of blunt-ended fragments use T4 DNA Ligase. (neb.sg)
  • Residual ligase activity was tested by adding 0.12 μM HindIII (cohesive end) fluorescently-labeled fragments and incubating at 37°C for 15 minutes. (nebiolabs.com.au)
  • T4 dna ligase can be used to join dna fragments with staggered or blunt ends. (web.app)
  • It also joins dna fragments with either cohesive or blunt term. (web.app)
  • Functionally tested for the capacity to join cohesive- and blunt-end DNA fragments. (focusbio.com.au)
  • The following antibody was used in this experiment: DNA Ligase III Polyclonal Antibody from Thermo Fisher Scientific, catalog # PA5-102510, RRID AB_2851912. (thermofisher.com)
  • By Western blot, this antibody detects a band of 125 kDa, which corresponds to the predicted molecular weight of DNA ligase I. (novusbio.com)
  • Immunohistochemistry (IHC) analyzes of DNA Ligase I antibody (Cat. (acris-antibodies.com)
  • Western blot (WB) analysis of DNA Ligase I antibody (Cat. (acris-antibodies.com)
  • Western blot analysis of DNA liage 1 Antibody (N-term) (Cat. (acris-antibodies.com)
  • Specificity: This antibody recognizes human, mouse, and chicken DNA Ligase III. (qedbio.com)
  • abstract = "Ligases conduct the final stage of repair of DNA damage by sealing a single-stranded nick after excision of damaged nucleotides and reinsertion of correct nucleotides. (elsevier.com)
  • Cullin/RING ubiquitin ligases (CRL) comprise the largest subfamily of ubiquitin ligases. (frontiersin.org)
  • In this review, we will discuss the regulation of CRL ubiquitin ligases and their roles in control of the DDR. (frontiersin.org)
  • Thus far, more than 600 ubiquitin ligases have been identified in the human genome, although many of them have not been linked to any substrates or biological activities. (frontiersin.org)
  • Based on their domain characteristics, ubiquitin ligases can be separated into two sub-groups, HECT domain E3 ligases and RING finger domain E3 ligases ( Pickart, 2004 ). (frontiersin.org)
  • Loss of ataxin‐3 results in reduced DNA damage‐induced ubiquitylation due to impaired MDC 1‐dependent recruitment of the ubiquitin ligases RNF 8 and RNF 168, and reduced recruitment of 53 BP 1 and BRCA 1. (embopress.org)
  • Nonhomologous end joining (NHEJ) is central to the repair of double-stranded DNA breaks throughout the cell cycle and plays roles in the development of the immune system. (rcsb.org)
  • The NHEJ ligase complex is then recruited, and LigIV, XRCC4 and XLF-Cernunnos work to connect the two DNA strands. (kenyon.edu)
  • DNA double-strand breaks (DSBs), one of the most harmful types of DNA damage, are repaired mainly by homologous repair (HR) and nonhomologous end-joining (NHEJ). (pnas.org)
  • Surprisingly, in cells deficient for core classic NHEJ factors such as DNA ligase IV (Lig4), substantial end-joining activities have been observed in various situations, suggesting the existence of alternative end-joining (A-EJ) activities. (pnas.org)
  • DNA ligase IV (Lig4) is essential for nonhomologous end-joining (NHEJ), the major pathway for repairing DNA double-strand breaks in mammalian cells. (pnas.org)
  • Deletion of DNA ligase IV (Lig4), a core component of the NHEJ pathway, reduces CSR efficiency in a mouse B-cell line capable of robust cytokine-stimulated CSR in cell culture. (pnas.org)
  • Low levels of DNA ligases III and IV sufficient for effective NHEJ. (genetex.com)
  • The finding that DNA ligase 1 plays an important role in DSB repair in addition to its known function in SSB repair, demonstrates the existence of a previously uncharacterised novel pathway, independent of the conserved NHEJ. (biomedcentral.com)
  • Non-homologous end joining (NHEJ) is the predominant mode of DNA double strand break (DSB) repair pathway in mammalian cells. (mcmaster.ca)
  • Its half-life is 48 hours at 65 °C and greater than 1 hour at 95 °C. Ampligase DNA Ligase has been shown to be active for at least 500 thermal cycles (94 °C/80 °C) or 16 hours of cycling.10 This exceptional thermostability permits extremely high hybridization stringency and ligation specificity. (wikipedia.org)
  • Its half-life is 48 hours at 65°C and greater than 1 hour at 95°C. Ampligase DNA Ligase has been shown to be active for at least 500 thermal cycles (94°C/80°C) or 16 hours of cycling. (lucigen.com)
  • Ampligase DNA Ligase has no detectable activity in ligating blunt-ended DNA and has no activity on RNA or RNA:DNA hybrids. (lucigen.com)
  • One unit of Ampligase DNA Ligase is equivalent to at least 15 of the "cohesive end units" or "nick ligation units" defined elsewhere. (lucigen.com)
  • Ampligase DNA Ligase is free of detectable exo- and endonuclease and RNase activities. (lucigen.com)
  • It can ligate either cohesive or blunt ends of DNA, oligonucleotides, as well as RNA and RNA-DNA hybrids, but not single-stranded nucleic acids. (wikipedia.org)
  • Salt-T4 DNA Ligase will join cohesive end termini at salt concentrations as high as 300 mM without any loss in activity. (neb.com)
  • Cohesive ends, blunt ends, and nick sealing can all be efficiently catalyzed by T3 DNA Ligase (1). (neb.com)
  • Polymer‐stimulated ligation: Enhanced blunt‐ or cohesive‐end ligation of DNA or deoxyribooligonucleotides by T4 DNA ligase in polymer solutions. (currentprotocols.com)
  • Both blunt and cohesive end DNA ligation, as well as single-stranded nick repair of DNA, RNA and DNA/RNA, are possible via the T4 DNA ligase. (clontech.com)
  • This minimal-type ligase, like its close homologues, is able to ligate singly nicked double-stranded DNA with high efficiency and to join cohesive-ended and blunt-ended substrates to a more limited extent. (iucr.org)
  • E. coli DNA Ligase catalyzes the formation of a phosphodiester bond between the 5´-phosphate and the 3´-hydroxyl of two adjacent DNA strands in duplex DNA with cohesive ends. (neb.sg)
  • Hi-T4 DNA Ligase will join blunt end and cohesive end termini as well as repair single-stranded nicks in duplex DNA, RNA or DNA/RNA hybrids at temperatures as high as 50ºC. (nebiolabs.com.au)
  • T4 DNA Ligase steadily loses activity at 45°C, whereas Hi-T4 DNA Ligase retains full activity on a cohesive end substrate, even after 72 hours at 45°C. (nebiolabs.com.au)
  • Following the indicated number of cycles (0, 15, 30, 45 or 60), ligase activity was tested on a fluorescently-labeled, cohesive-end substrate (HindIII overhang, 25°C for 10 minutes). (nebiolabs.com.au)
  • It can ligate cohesive ends of dna or oligonucleotides, as well as rna and rna dna hybrids and is particularly efficient at sealing nicks in duplex dna. (web.app)
  • T4 dna ligase catalyzes the joining of two cohesive or bluntended strands of dna between the 5. (web.app)
  • Cohesive ligation with T4 DNA Ligase can be completed in less than 10 min. (focusbio.com.au)
  • The T4 DNA Ligase catalyzes the formation of a phosphodiester bond between the adjacent 5'-phosphate and 3'-hydroxyl on the blunt or cohesive end of dsDNA. (ushelf.com)
  • 1. Pheiffer, B.H., Zimmermann, S.B., Polymer-stimulated ligation: enhanced blunt- or cohesive-end ligation of DNA or deoxyribo-oligonucleotides by T4 DNA Ligase in polymer solutions, Nucleic Acids Res. (genecraft.de)
  • It does not ligate blunt-ended DNA except under conditions of molecular crowding with polyethylene glycol, and cannot join RNA to DNA efficiently. (wikipedia.org)
  • It can also ligate blunt-ended DNA with much greater efficiency than E. coli DNA ligase. (wikipedia.org)
  • Does not ligate RNA to DNA (4). (neb.sg)
  • When the concentrations of Pol I DNA polymerases are higher, it has an adverse effect on E. coli DNA ligase The DNA ligase from bacteriophage T4 (a bacteriophage that infects Escherichia coli bacteria). (wikipedia.org)
  • Further purification and properties of polynucleotide ligase from Escherichia coli infected with bacteriophage T4. (currentprotocols.com)
  • Characterization of a temperature-sensitive DNA ligase from Escherichia coli. (semanticscholar.org)
  • [1] Secara biologis, DNA ligase diperlukan untuk menggabungkan fragmen Okazaki saat proses replikasi, menyambung potongan-potongan DNA yang baru disintesis, serta berperan dalam proses reparasi DNA. (wikipedia.org)
  • DNA ligase II: A purification artifact resulting from proteolytic degradation of DNA ligase III. (wikipedia.org)
  • A simple, three‐step procedure for the large scale purification of DNA ligase from a hybrid lambda lysogen constructed in vitro. (currentprotocols.com)
  • Kits are available for total RNA purification, plasmid miniprep, gel extraction, and DNA & RNA cleanup. (neb.com)
  • 2004. Staphylococcus aureus DNA ligase: characterization of its kinetics of catalysis and development of a high-throughput screening compatible chemiluminescent hybridization protection assay. (wikipedia.org)
  • We found that XRCC4 is a nuclear phosphoprotein and was an effective substrate in vitro for DNA-PK. (nih.gov)
  • To evaluate S6G-containing DNA as a substrate for DNA ligases, two oligodeoxynucleotides (19- and 20-mers) antisense to a 40-mer were synthesized so that the 40-mer coded for guanine at the 3' terminus of the 19-mer. (aspetjournals.org)
  • We further demonstrate that Pol and the DNA ligase III-XRCC1 heterodimer are present at equimolar concentrations in whole cell extracts and that Pol has a 7-fold higher affinity to the incised abasic site containing substrate than DNA ligase III. (lancs.ac.uk)
  • Taken together, these data suggest that following incision by AP endonuclease, DNA Pol recognizes and binds to the incised abasic site and promotes recruitment of the DNA ligase III-XRCC1 heterodimer through its interaction with XRCC1. (lancs.ac.uk)
  • You've even generously used half of your lab's supply of uncommon restriction endonuclease in an effort to get your beautifully designed DNA construct, "faster", for your PI. (wordpress.com)
  • It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such as DNA ligase IV) may specifically repair double-strand breaks (i.e. a break in both complementary strands of DNA). (wikipedia.org)
  • It will catalyze the formation of a phosphodiester bond between adjacent 5´ phosphate and 3´ hydroxyl groups of duplex DNA. (neb.com)
  • The Invitrogen Anza™ T4 DNA Ligase Master Mix facilitates the joining of abutted 5'-phosphate and 3'-hydroxyl termini in duplex DNA through the formation of a phosphodiester bond. (thermofisher.com)
  • T4 DNA Ligase forms an energy dependent phosphodiester linkage between the termini of adjacent polynucleotides of duplex DNA. (sigmaaldrich.com)
  • T4 DNA Ligase catalyzes the formation of a phosphodiester bond between the terminal 5′ phosphate and a 3′ hydroxyl groups of duplex DNA or RNA. (sigmaaldrich.com)
  • Ampligase® Thermostable DNA Ligase catalyzes NAD-dependent ligation of adjacent 3´-hydroxylated and 5´-phosphorylated termini in duplex DNA structures that are stable at high temperatures. (lucigen.com)
  • A thermotolerant variant of T4 DNA Ligase, Hi-T4™ DNA Ligase catalyzes the formation of a phosphodiester bond between juxtaposed 5´ phosphate and 3´ hydroxyl termini in duplex DNA or RNA and is designed to function at higher temperatures than wild type T4 DNA Ligase. (nebiolabs.com.au)
  • It plays a role in repairing singlestrand breaks in duplex dna in living organisms, but some forms such as dna ligase iv may specifically repair doublestrand breaks i. (web.app)
  • Thermo scientific t4 dna ligase catalyzes the formation of a phosphodiester bond between juxtaposed 5phosphate and 3hydroxyl termini in duplex dna or rna. (web.app)
  • Das Enzym verbindet die 'blunt'-Enden und die kohäsiven Enden, repariert Einzelstrangbrüche in der duplex DNA, RNA, oder DNA/RNA-Hybriden. (geneon.net)
  • We provide structural insights into features of LigIV among human DNA ligases. (rcsb.org)
  • DNA and RNA ligases: Structural variations and shared mechanisms. (currentprotocols.com)
  • Eukaryotic DNA ligases: structural and functional insights. (axonmedchem.com)
  • Bre1, a conserved E3 ubiquitin ligase in Saccharomyces cerevisiae , together with its interacting partner Lge1, are responsible for histone H2B monoubiquitination, which regulates transcription, DNA replication, DNA damage response and repair, ensuring the structural integrity of the genome. (elifesciences.org)
  • Here the authors present a structural analysis of a CMG Pol ɛ on a DNA fork, providing insight on the steps leading productive helicase engagement to the DNA junction. (nature.com)
  • An additional active conformation of ssLig is inferred from crystal packing interactions and a complex with ATP cofactor, further highlighting the flexibility and remarkable mobility of the ligase domains during the course of the ligation reaction. (jbsdonline.com)
  • Few things bring the gentle molecular biologist to anger, but the experience of setting up your perfect ligation reaction only to find the DNA ligase tube as dry as the agarose gel that's been on the bench for 3 weeks is one of them. (wordpress.com)
  • Identification and validation of human DNA ligase inhibitors using computer-aided drug design. (medchemexpress.com)
  • Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair. (medchemexpress.com)
  • A series of small molecule inhibitors of human DNA ligases were previously identified using a rational structure-based approach. (unm.edu)
  • Three of these inhibitors, L82, a DNA ligase I selective inhibitor, and L67, an inhibitor of DNA ligases I and III, and L189, an inhibitor of all three human DNA ligases, have related structures. (unm.edu)
  • Several recent studies have synthesized novel derivatives and their biological activity against a range of DNA ligases has been evaluated as inhibitors for drug discovery and/or non-natural substrates for biochemical applications. (uea.ac.uk)
  • It catalyzes the final step in the non-homologous end joining DNA double-strand break repair pathway. (wikipedia.org)
  • Structure of the catalytic region of DNA Ligase IV in complex with an artemis fragment sheds light on double-strand break repair. (kenyon.edu)
  • DNA double-strand breaks (DSBs) are one of the most severe forms of DNA damage that can result from pathological conditions such as replication stress, exposure to ionizing radiation (IR), free radicals, or other DNA-damaging drugs or because of failed single-strand break repair (SSBR) ( 1 , 2 ). (pnas.org)
  • Here, we demonstrate that EDD is necessary for G(1)/S and intra S phase DNA damage checkpoint activation and for the maintenance of G(2)/M arrest after double strand DNA breaks. (garvan.org.au)
  • Ubiquitylation and SUMO ylation are key elements in DNA damage response signaling at DNA double‐strand breaks ( DSB s). (embopress.org)
  • In molecular biology, DNA ligase is a particular type of ligase ( EC 6.5.1.1) that can link together DNA strands that have double-strand breaks (a break in both complementary strands of DNA). (chemeurope.com)
  • Nonhomologous end joining of complex DNA double-strand breaks with proximal thymine glycol and interplay with base excision repair. (semanticscholar.org)
  • DNA double-strand breaks (DSB) were shown to occur at the replication fork barrier in the ribosomal DNA of Saccharomyces cerevisiae using 2D-gel electrophoresis. (unibas.ch)
  • There are two forms of DNA ligase, one requires ATP ( EC 6.5.1.1 ), the other NAD ( EC 6.5.1.2 ), the latter being restricted to eubacteria. (embl.de)
  • These results indicate that DNA ligase 1 functions in both DNA replication and in repair of both ss and dsDNA strand breaks in higher plants. (biomedcentral.com)
  • Ligation experiments using bacteriophage T4 DNA ligase were carried out with purine lesions in four positions surrounding the nick site in a total of 96 different duplexes. (elsevier.com)
  • Oct 07, 20 bacteriophage t4 dna ligase atp the most widely used dna ligase is derived from the t4 bacteriophage. (web.app)
  • DNA ligase from eukaryotes and some microbes uses adenosine triphosphate (ATP) rather than NAD. (wikipedia.org)
  • A conserved physical and functional interaction between the cell cycle checkpoint clamp loader and DNA ligase I of eukaryotes. (genetex.com)
  • Eukaryotes possess multiple DNA ligases with distinct roles in DNA metabolism, with clear differences in the functions of DNA ligase orthologues between animals, yeast and plants. (biomedcentral.com)
  • DNA ligase 1, present in all eukaryotes, plays critical roles in both DNA repair and replication and is indispensable for cell viability. (biomedcentral.com)
  • Eukaryotes have evolved multiple DNA ligase isoforms, with both specific and overlapping roles in the replication and repair of the nuclear and organellar genomes. (biomedcentral.com)
  • Taq DNA Ligase is a thermostable ligase that catalyzes the formation of a phosphodiester bond between the 5´-phosphate and the 3´-hydroxyl of two adjacent DNA strands. (neb.sg)
  • At the heart of this repair pathway is Xrcc4-DNA ligase IV complex, which mediates ligation of the broken DNA strands. (mcmaster.ca)
  • The two DNA strands are also known as polynucleotides as they are composed of simpler monomeric units called nucleotides . (wikipedia.org)
  • The nitrogenous bases of the two separate polynucleotide strands are bound together, according to base pairing rules (A with T and C with G), with hydrogen bonds to make double-stranded DNA. (wikipedia.org)
  • Both strands of double-stranded DNA store the same biological information . (wikipedia.org)
  • The two strands of DNA run in opposite directions to each other and are thus antiparallel . (wikipedia.org)
  • This is followed by a separation of the DNA strands prior to the transfer of genetic data to the newly assembled DNA strands. (reference.com)
  • Single-strand breaks are repaired by DNA ligase using the complementary strand of the double helix as a template, with DNA ligase creating the final phosphodiester bond to fully repair the DNA. (wikipedia.org)
  • DNA ligase in E. coli, as well as most prokaryotes, uses energy gained by cleaving nicotinamide adenine dinucleotide (NAD) to create the phosphodiester bond. (wikipedia.org)
  • DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. (rcsb.org)
  • T4 DNA Ligase catalyzes the formation of phosphodiester bonds between juxtaposed 5' phosphate and 3' hydroxyl termini in double-stranded DNA using ATP as a coenzyme. (clontech.com)
  • The sealing of breaks in the phosphodiester backbone of double-stranded DNA is essential for the replication and survival of all organisms. (iucr.org)
  • The phosphodiester backbone of DNA is maintained by DNA ligases. (unm.edu)
  • T4 dna ligase catalyzes the formation of phosphodiester bonds in the presence of atp between doublestranded dnas with 3 hydroxyl and 5 phosphate termini. (web.app)
  • T4 dna ligase catalyzes the formation of phosphodiester bonds between neighbouring 3hydroxyl and 5phosphate ends in doublestranded dna. (web.app)
  • Enzymatic assembly of DNA molecules up to several hundred kilobases. (currentprotocols.com)
  • Other common names for ligases include the word "synthetase", because they are used to synthesize new molecules. (wikipedia.org)
  • We quantified these DSBs and show that a surprising 14% of replicating ribosomal DNA molecules are broken at the replication fork barrier in replicating wild-type cells. (unibas.ch)
  • We use these to study several nucleic-acid binding molecules, including DNA helicases, DNA ligases and DNA triple helices. (port.ac.uk)
  • Ligases catalyze the addition of two molecules, deriving the needed energy from the cleavage of an energy-rich phosphate bond. (biospace.com)
  • It generates a break in the strong backbone of double-stranded DNA molecules in the process. (biospace.com)
  • The excessive probes would be masked by the ligase reaction that closes the nick and forms a long DNA strand fully complementary to the hairpin domain. (rsc.org)
  • Unlike E. coli DNA ligase, T4 DNA ligase cannot utilize NAD and it has an absolute requirement for ATP as a cofactor. (wikipedia.org)
  • This contrasts with E. coli DNA Ligase which requires NAD. (neb.com)
  • Stimulation of intermolecular ligation with E. coli DNA ligase by high concentrations of monovalent cations in polyethylene glycol solutions. (currentprotocols.com)
  • E. coli DNA Ligase is active at a range of temperatures (4° C - 37° C). (neb.sg)
  • Belongs to the ATP-dependent DNA ligase family. (abcam.com)
  • Molecular model of NAD(+)-dependent DNA ligase bound to AMP (adenosine monophosphate). (sciencephoto.com)
  • Here, the structure and activity of a recombinantly produced ATP-dependent DNA ligase from the bacterium Psychromonas sp. (iucr.org)
  • Of the all known mammalian DNA ligases, only Lig III has been found to be present in mitochondria. (wikipedia.org)
  • Highly thermostable DNA ligase for applications where ligation at high temperature is beneficial High thermostability allows ligation using high-stringency hybridization conditions High specificity and stringency permits sensitive detection of SNPs11 Applications. (astralscientific.com.au)
  • Consistent with this, XRCC4 and DNA ligase IV copurified exclusively and virtually quantitatively over a variety of chromatographic steps. (nih.gov)
  • Direct comparison of nick‐joining activity of the nucleic acid ligases from bacteriophage T4. (currentprotocols.com)
  • Immunohistochemistry (Formalin/PFA-fixed paraffin-embedded sections) analysis of rat brain tissue labelling DNA Ligase III with ab185815 at 1/200. (abcam.com)
  • Immunohistochemical detection of DNA Ligase I on paraffin embedded section of a human breast cancer with AM26565AF-N. (acris-antibodies.com)
  • It is essential for DNA replication and repair of damaged DNA. (rcsb.org)
  • Reduced levels of Arabidopsis DNA ligase 1 in the silenced lines are sufficient to support plant development but result in retarded growth and reduced cell size, which may reflect roles for AtLIG1 in both replication and repair. (biomedcentral.com)
  • Additional sequence analysis of chromosome translocation junction microhomology revealed the specificity of different ligase-containing complexes. (pnas.org)
  • Inefficiency at this step, particularly with low-concentration DNA samples, currently limits the sensitivity of NGS-based molecular diagnostics. (codexis.com)
  • The FA pathway senses and repairs DNA crosslinks that occur after exposure to chemicals including chemotherapeutic agents and alcohol, but also as a result of normal cellular metabolism. (lightsources.org)
  • Preventing oxidation of cellular XRCC1 affects PARP-mediated DNA damage responses. (genetex.com)
  • The cellular response to DNA damage is critical for maintenance of genomic integrity and inhibition of tumorigenesis. (garvan.org.au)
  • The process in which DNA makes an exact copy of itself is known as DNA replication and occurs through many steps during cellular replication. (reference.com)
  • The C-terminal tandem BRCT repeats of human DNA ligase IV spanning residues 654-911 in complex with the functional fragment of Xrcc4 comprised of residues 1-203 were crystallized by the hanging drop vapour diffusion method at 20°C. Generation of single, well-packed, diffraction quality crystals suitable for structure determination involved usage of an Xrcc4 point mutant (A60E). (mcmaster.ca)
  • DNA ligase is used in both DNA repair and DNA replication (see Mammalian ligases). (wikipedia.org)
  • Aberrant DNA repair and DNA replication due to an inherited enzymatic defect in human DNA ligase I. (abcam.com)
  • It plays an important role in the process of DNA repair and DNA replication. (biospace.com)
  • The optimal incubation temperature for T4 DNA ligase is 16 °C. Bacteriophage T4 ligase mutants have increased sensitivity to both UV irradiation and the alkylating agent methyl methanesulfonate indicating that DNA ligase is employed in the repair of the DNA damages caused by these agents. (wikipedia.org)
  • T4 dna ligase inactivation t4 dna ligase can be completely inactivated by a 10 min incubation at 65c. (web.app)
  • Now, to be completely transparent we should note that diluting and using lower concentrations of ligase with overnight incubation times is a viable alternative, however overnight incubations have been noted to decrease subsequent transformation efficiency by promoting long, linear DNA strand formation. (wordpress.com)
  • Klonierung von Restriktionsverdau-Fragmenten, verbinden der Linker und Adapter zu 'blunt-ended' DNA, Gen- (Genfragment) Synthese. (geneon.net)
  • PEG (Polyehtylenglycol) greatly increases the rate of ligation of blunt-ended DNA (1). (genecraft.de)
  • Binds specifically to DNA nicks containing a 3'-OH and a 5'-phosphate group. (uniprot.org)
  • PCNA binds DNA ligase and strongly stimulates DNA joining activity in this hyperthermophilic organism. (jbsdonline.com)
  • SAXS analysis of the ligase-PCNA complex demonstrates that ssLig binds to one location on the outside edge of the ssPCNA ring in an extended conformation. (jbsdonline.com)

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