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.
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).
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.
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 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.
Catalyze the joining of preformed ribonucleotides or deoxyribonucleotides in phosphodiester linkage during genetic processes. EC 6.5.1.
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.
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.
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.
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 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.
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.
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.
Ligases that catalyze the joining of adjacent AMINO ACIDS by the formation of carbon-nitrogen bonds between their carboxylic acid groups and amine groups.
Complexes of enzymes that catalyze the covalent attachment of UBIQUITIN to other proteins by forming a peptide bond between the C-terminal GLYCINE of UBIQUITIN and the alpha-amino groups of LYSINE residues in the protein. The complexes play an important role in mediating the selective-degradation of short-lived and abnormal proteins. The complex of enzymes can be broken down into three components that involve activation of ubiquitin (UBIQUITIN-ACTIVATING ENZYMES), conjugation of ubiquitin to the ligase complex (UBIQUITIN-CONJUGATING ENZYMES), and ligation of ubiquitin to the substrate protein (UBIQUITIN-PROTEIN LIGASES).
An oligomer formed from the repetitive linking of the C-terminal glycine of one UBIQUITIN molecule via an isopeptide bond to a lysine residue on a second ubiquitin molecule. It is structurally distinct from UBIQUITIN C, which is a single protein containing a tandemly arrayed ubiquitin peptide sequence.
A class of enzymes that catalyzes the ATP-dependent formation of a thioester bond between itself and UBIQUITIN. It then transfers the activated ubiquitin to one of the UBIQUITIN-PROTEIN LIGASES.
Enzymes that catalyze the joining of two molecules by the formation of a carbon-oxygen bond. EC 6.1.
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.
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.
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.
Proto-oncogene proteins that negatively regulate RECEPTOR PROTEIN-TYROSINE KINASE signaling. It is a UBIQUITIN-PROTEIN LIGASE and the cellular homologue of ONCOGENE PROTEIN V-CBL.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Cleavage of proteins into smaller peptides or amino acids either by PROTEASES or non-enzymatically (e.g., Hydrolysis). It does not include Protein Processing, Post-Translational.
A family of structurally-related proteins that were originally identified by their ability to complex with cyclin proteins (CYCLINS). They share a common domain that binds specifically to F-BOX MOTIFS. They take part in SKP CULLIN F-BOX PROTEIN LIGASES, where they can bind to a variety of F-BOX PROTEINS.
A family of structurally related proteins that are constitutively expressed and that negatively regulate cytokine-mediated SIGNAL TRANSDUCTION PATHWAYS. PIAS proteins inhibit the activity of signal transducers and activators of transcription.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
A 1.5-kDa small ubiquitin-related modifier protein that can covalently bind via an isopeptide link to a number of cellular proteins. It may play a role in intracellular protein transport and a number of other cellular processes.
A class of structurally related proteins of 12-20 kDa in size. They covalently modify specific proteins in a manner analogous to UBIQUITIN.
A type of POST-TRANSLATIONAL PROTEIN MODIFICATION by SMALL UBIQUITIN-RELATED MODIFIER PROTEINS (also known as SUMO proteins).
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
Adenine nucleotide containing one phosphate group esterified to the sugar moiety in the 2'-, 3'-, or 5'-position.
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.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Transport proteins that carry specific substances in the blood or across cell membranes.
Derangement in size and number of muscle fibers occurring with aging, reduction in blood supply, or following immobilization, prolonged weightlessness, malnutrition, and particularly in denervation.
Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.
Macromolecular complexes formed from the association of defined protein subunits.
Proteins that control the CELL DIVISION CYCLE. This family of proteins includes a wide variety of classes, including CYCLIN-DEPENDENT KINASES, mitogen-activated kinases, CYCLINS, and PHOSPHOPROTEIN PHOSPHATASES as well as their putative substrates such as chromatin-associated proteins, CYTOSKELETAL PROTEINS, and TRANSCRIPTION FACTORS.
Cell surface receptors for AUTOCRINE MOTILITY FACTOR, which is the secreted form of GLUCOSE-6-PHOSPHATE ISOMERASE. The receptor has an unusual composition in that it shares some structural similarities with G-PROTEIN-COUPLED RECEPTORS and functions as an ubiquitin protein ligase when internalized.
An E3 ubiquitin ligase primarily involved in regulation of the metaphase-to-anaphase transition during MITOSIS through ubiquitination of specific CELL CYCLE PROTEINS. Enzyme activity is tightly regulated through subunits and cofactors, which modulate activation, inhibition, and substrate specificity. The anaphase-promoting complex, or APC-C, is also involved in tissue differentiation in the PLACENTA, CRYSTALLINE LENS, and SKELETAL MUSCLE, and in regulation of postmitotic NEURONAL PLASTICITY and excitability.
A cell line generated from human embryonic kidney cells that were transformed with human adenovirus type 5.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
An essential amino acid. It is often added to animal feed.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
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.
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.
Established cell cultures that have the potential to propagate indefinitely.
Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.
Members of the peptidase C19 family which regulate signal transduction by removing UBIQUITIN from specific protein substrates via a process known as deubiquitination or deubiquitylation.
Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
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 protein constituents of muscle, the major ones being ACTINS and MYOSINS. More than a dozen accessory proteins exist including TROPONIN; TROPOMYOSIN; and DYSTROPHIN.
The aggregation of soluble ANTIGENS with ANTIBODIES, alone or with antibody binding factors such as ANTI-ANTIBODIES or STAPHYLOCOCCAL PROTEIN A, into complexes large enough to fall out of solution.
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.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
The facilitation of biochemical reactions with the aid of naturally occurring catalysts such as ENZYMES.
An enzyme that catalyzes the transfer of a phosphate group to the 5'-terminal hydroxyl groups of DNA and RNA. EC 2.7.1.78.
Hydrolases that specifically cleave the peptide bonds found in PROTEINS and PEPTIDES. Examples of sub-subclasses for this group include EXOPEPTIDASES and ENDOPEPTIDASES.
An E3 UBIQUITIN LIGASE that interacts with and inhibits TUMOR SUPPRESSOR PROTEIN P53. Its ability to ubiquitinate p53 is regulated by TUMOR SUPPRESSOR PROTEIN P14ARF.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.
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.
The process of moving proteins from one cellular compartment (including extracellular) to another by various sorting and transport mechanisms such as gated transport, protein translocation, and vesicular transport.
A degradation process whereby incorrectly folded proteins are selectively transported out of the ENDOPLASMIC RETICULUM and into the CYTOSOL. The misfolded proteins are subsequently ubiquitinated and degraded by the PROTEASOME.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
A thioester hydrolase which acts on esters formed between thiols such as DITHIOTHREITOL or GLUTATHIONE and the C-terminal glycine residue of UBIQUITIN.
A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.
The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
Systems of enzymes which function sequentially by catalyzing consecutive reactions linked by common metabolic intermediates. They may involve simply a transfer of water molecules or hydrogen atoms and may be associated with large supramolecular structures such as MITOCHONDRIA or RIBOSOMES.
The relationships of groups of organisms as reflected by their genetic makeup.
Together with the Apc2 subunit, forms the catalytic core of the E3 ubiquitin ligase, anaphase-promoting complex-cyclosome. It has a RING H2 domain which interacts with the cullin domain of Apc2. Apc11 also interacts with the E2 ubiquitin ligases involved in APC-C ubiquitination reactions.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
Proteins prepared by recombinant DNA technology.
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.
An order of stalked, sessile, single-celled EUKARYOTES. They are considered the transitional link between the flagellated protozoa and the SPONGES, the most primitive metazoans.
Proteins and peptides that are involved in SIGNAL TRANSDUCTION within the cell. Included here are peptides and proteins that regulate the activity of TRANSCRIPTION FACTORS and cellular processes in response to signals from CELL SURFACE RECEPTORS. Intracellular signaling peptide and proteins may be part of an enzymatic signaling cascade or act through binding to and modifying the action of other signaling factors.
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.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
Proteins covalently modified with UBIQUITINS or UBIQUITIN-LIKE PROTEINS.
A group of alicyclic hydrocarbons with the general formula R-C5H9.
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
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 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.
A single protein comprised of tandem repeats of the UBIQUITIN 78-amino acid sequence. It is a product of the polyubiquitin gene which contains multiple copies of the ubiquitin coding sequence. Proteolytic processing of ubiquitin C results in the formation of individual ubiquitin molecules. This protein is distinct from POLYUBIQUITIN, which is a protein formed through isopeptide linkage of multiple ubiquitin species.
A genus of ascomycetous fungi of the family Schizosaccharomycetaceae, order Schizosaccharomycetales.
Enzymes that catalyze the joining of two molecules by the formation of a carbon-sulfur bond. EC 6.2.
Methods for determining interaction between PROTEINS.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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).
ENDOPEPTIDASES which have a cysteine involved in the catalytic process. This group of enzymes is inactivated by CYSTEINE PROTEINASE INHIBITORS such as CYSTATINS and SULFHYDRYL REAGENTS.
Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.
Gram-negative aerobic rods found in warm water (40-79 degrees C) such as hot springs, hot water tanks, and thermally polluted rivers.
Immunologic method used for detecting or quantifying immunoreactive substances. The substance is identified by first immobilizing it by blotting onto a membrane and then tagging it with labeled antibodies.
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 artificial induction of GENE SILENCING by the use of RNA INTERFERENCE to reduce the expression of a specific gene. It includes the use of DOUBLE-STRANDED RNA, such as SMALL INTERFERING RNA and RNA containing HAIRPIN LOOP SEQUENCE, and ANTI-SENSE OLIGONUCLEOTIDES.
Compounds that inhibit the function or proteolytic action of the PROTEASOME.
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
The rate dynamics in chemical or physical systems.
A family of large icosahedral DNA viruses infecting insects and poikilothermic vertebrates. Genera include IRIDOVIRUS; RANAVIRUS; Chloriridovirus; Megalocytivirus; and Lymphocystivirus.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
A ubiquitin-protein ligase that mediates OXYGEN-dependent polyubiquitination of HYPOXIA-INDUCIBLE FACTOR 1, ALPHA SUBUNIT. It is inactivated in VON HIPPEL-LINDAU SYNDROME.
A conserved class of proteins that control APOPTOSIS in both VERTEBRATES and INVERTEBRATES. IAP proteins interact with and inhibit CASPASES, and they function as ANTI-APOPTOTIC PROTEINS. The protein class is defined by an approximately 80-amino acid motif called the baculoviral inhibitor of apoptosis repeat.
Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.
A broad category of carrier proteins that play a role in SIGNAL TRANSDUCTION. They generally contain several modular domains, each of which having its own binding activity, and act by forming complexes with other intracellular-signaling molecules. Signal-transducing adaptor proteins lack enzyme activity, however their activity can be modulated by other signal-transducing enzymes
Nuclear phosphoprotein encoded by the p53 gene (GENES, P53) whose normal function is to control CELL PROLIFERATION and APOPTOSIS. A mutant or absent p53 protein has been found in LEUKEMIA; OSTEOSARCOMA; LUNG CANCER; and COLORECTAL CANCER.
Proteins obtained from the species Schizosaccharomyces pombe. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.
An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.
Interruptions in the sugar-phosphate backbone of DNA, across both strands adjacently.
The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)
Enzymes that catalyze the joining of either ammonia or an amide with another molecule, in which the linkage is in the form of a carbon-nitrogen bond. EC 6.3.1.
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 negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.
A system of cisternae in the CYTOPLASM of many cells. In places the endoplasmic reticulum is continuous with the plasma membrane (CELL MEMBRANE) or outer membrane of the nuclear envelope. If the outer surfaces of the endoplasmic reticulum membranes are coated with ribosomes, the endoplasmic reticulum is said to be rough-surfaced (ENDOPLASMIC RETICULUM, ROUGH); otherwise it is said to be smooth-surfaced (ENDOPLASMIC RETICULUM, SMOOTH). (King & Stansfield, A Dictionary of Genetics, 4th ed)
A guanine nucleotide containing one phosphate group esterified to the sugar moiety and found widely in nature.
PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.
The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.
A cell line derived from cultured tumor cells.
The complex series of phenomena, occurring between the end of one CELL DIVISION and the end of the next, by which cellular material is duplicated and then divided between two daughter cells. The cell cycle includes INTERPHASE, which includes G0 PHASE; G1 PHASE; S PHASE; and G2 PHASE, and CELL DIVISION PHASE.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
A part of the embryo in a seed plant. The number of cotyledons is an important feature in classifying plants. In seeds without an endosperm, they store food which is used in germination. In some plants, they emerge above the soil surface and become the first photosynthetic leaves. (From Concise Dictionary of Biology, 1990)
Release of a virus from the host cell following VIRUS ASSEMBLY and maturation. Egress can occur by host cell lysis, EXOCYTOSIS, or budding through the plasma membrane.
Proteins found in any species of bacterium.
A group of cell cycle proteins that negatively regulate the activity of CYCLIN/CYCLIN-DEPENDENT KINASE complexes. They inhibit CELL CYCLE progression and help control CELL PROLIFERATION following GENOTOXIC STRESS as well as during CELL DIFFERENTIATION.
A family of DNA plant viruses that infect eukaryotic algae.
Proteins produced from GENES that have acquired MUTATIONS.
A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.
Enzymes that catalyze the joining of glutamine-derived ammonia and another molecule. The linkage is in the form of a carbon-nitrogen bond. EC 6.3.5.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
A family of double-stranded DNA viruses infecting mammals (including humans), birds and insects. There are two subfamilies: CHORDOPOXVIRINAE, poxviruses of vertebrates, and ENTOMOPOXVIRINAE, poxviruses of insects.
Anaerobic hyperthermophilic species of ARCHAEA, isolated from hydrothermal fluid samples. It is obligately heterotrophic with coccoid cells that require TRYPTOPHAN for growth.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).
A subtype of striated muscle, attached by TENDONS to the SKELETON. Skeletal muscles are innervated and their movement can be consciously controlled. They are also called voluntary muscles.
Proteins to which calcium ions are bound. They can act as transport proteins, regulator proteins, or activator proteins. They typically contain EF HAND MOTIFS.
New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.
Proteins found in any species of virus.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.
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)
The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
Single chains of amino acids that are the units of multimeric PROTEINS. Multimeric proteins can be composed of identical or non-identical subunits. One or more monomeric subunits may compose a protomer which itself is a subunit structure of a larger assembly.
Large, multinucleate single cells, either cylindrical or prismatic in shape, that form the basic unit of SKELETAL MUSCLE. They consist of MYOFIBRILS enclosed within and attached to the SARCOLEMMA. They are derived from the fusion of skeletal myoblasts (MYOBLASTS, SKELETAL) into a syncytium, followed by differentiation.
Cellular uptake of extracellular materials within membrane-limited vacuoles or microvesicles. ENDOSOMES play a central role in endocytosis.
Proteins that are normally involved in holding cellular growth in check. Deficiencies or abnormalities in these proteins may lead to unregulated cell growth and tumor development.
A class of enzymes that transfers nucleotidyl residues. EC 2.7.7.
A non-essential amino acid that occurs in high levels in its free state in plasma. It is produced from pyruvate by transamination. It is involved in sugar and acid metabolism, increases IMMUNITY, and provides energy for muscle tissue, BRAIN, and the CENTRAL NERVOUS SYSTEM.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
A family of conserved cell surface receptors that contain EPIDERMAL GROWTH FACTOR repeats in their extracellular domain and ANKYRIN repeats in their cytoplasmic domains. The cytoplasmic domain of notch receptors is released upon ligand binding and translocates to the CELL NUCLEUS where it acts as transcription factor.
An inhibitory smad protein that associates with TRANSFORMING GROWTH FACTOR BETA RECEPTORS and BONE MORPHOGENETIC PROTEIN RECEPTORS. It negatively regulates SIGNAL TRANSDUCTION PATHWAYS by inhibiting PHOSPHORYLATION of RECEPTOR-REGULATED SMAD PROTEINS.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
A general term for single-celled rounded fungi that reproduce by budding. Brewers' and bakers' yeasts are SACCHAROMYCES CEREVISIAE; therapeutic dried yeast is YEAST, DRIED.
A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.
Technique for limiting use, activity, or movement by immobilizing or restraining animal by suspending from hindlimbs or tails. This immobilization is used to simulate some effects of reduced gravity and study weightlessness physiology.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.
Abscission-accelerating plant growth substance isolated from young cotton fruit, leaves of sycamore, birch, and other plants, and from potatoes, lemons, avocados, and other fruits.
A subclass of enzymes that aminoacylate AMINO ACID-SPECIFIC TRANSFER RNA with their corresponding AMINO ACIDS.
An inhibitor of apoptosis protein that is translated by a rare cap-independent mechanism. It blocks caspase-mediated cellular destruction by inhibiting CASPASE 3; CASPASE 7; and CASPASE 9.
Proteins found in any species of fungus.
An octanoic acid bridged with two sulfurs so that it is sometimes also called a pentanoic acid in some naming schemes. It is biosynthesized by cleavage of LINOLEIC ACID and is a coenzyme of oxoglutarate dehydrogenase (KETOGLUTARATE DEHYDROGENASE COMPLEX). It is used in DIETARY SUPPLEMENTS.
A broad category of proteins involved in the formation, transport and dissolution of TRANSPORT VESICLES. They play a role in the intracellular transport of molecules contained within membrane vesicles. Vesicular transport proteins are distinguished from MEMBRANE TRANSPORT PROTEINS, which move molecules across membranes, by the mode in which the molecules are transported.
CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.
Nuclear antigen with a role in DNA synthesis, DNA repair, and cell cycle progression. PCNA is required for the coordinated synthesis of both leading and lagging strands at the replication fork during DNA replication. PCNA expression correlates with the proliferation activity of several malignant and non-malignant cell types.
A phylum of anoxygenic, phototrophic bacteria including the family Chlorobiaceae. They occur in aquatic sediments, sulfur springs, and hot springs and utilize reduced sulfur compounds instead of oxygen.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.
Any of the hormones produced naturally in plants and active in controlling growth and other functions. There are three primary classes: auxins, cytokinins, and gibberellins.
The repair of DOUBLE-STRAND DNA BREAKS by rejoining the broken ends of DNA to each other directly.
Enzymes that catalyze the first step leading to the oxidation of succinic acid by the reversible formation of succinyl-CoA from succinate and CoA with the concomitant cleavage of ATP to ADP (EC 6.2.1.5) or GTP to GDP (EC 6.2.1.4) and orthophosphate. Itaconate can act instead of succinate and ITP instead of GTP.EC 6.2.1.-.
Hydroxycinnamic acid and its derivatives. Act as activators of the indoleacetic acid oxidizing system, thereby producing a decrease in the endogenous level of bound indoleacetic acid in plants.
That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.
Conversion of an inactive form of an enzyme to one possessing metabolic activity. It includes 1, activation by ions (activators); 2, activation by cofactors (coenzymes); and 3, conversion of an enzyme precursor (proenzyme or zymogen) to an active enzyme.
The process by which a DNA molecule is duplicated.
A hemoflagellate subspecies of parasitic protozoa that causes nagana in domestic and game animals in Africa. It apparently does not infect humans. It is transmitted by bites of tsetse flies (Glossina).
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
A group of acylated oligopeptides produced by Actinomycetes that function as protease inhibitors. They have been known to inhibit to varying degrees trypsin, plasmin, KALLIKREINS, papain and the cathepsins.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
Viruses whose nucleic acid is DNA.
Peptides composed of two amino acid units.
DNA ligase III along with its cofactor XRCC1 catalyzes the nick-sealing step in short-patch BER in humans. DNA ligase I ligates ... Pascucci, Barbara (1999). "Long Patch Base Excision Repair with Purified Human Proteins DNA LIGASE I AS PATCH SIZE MEDIATOR FOR ... Cappelli, Enrico (1997). "Involvement of XRCC1 and DNA Ligase III Gene Products in DNA Base Excision Repair". Journal of ... Caldecott, Keith (1995). "Characterization of the XRCC1-DNA ligase III complex in vitro and its absence from mutant hamster ...
The single-strand viral DNA ends are ligated by host DNA ligase. It is not generally appreciated that the 12 bp lambda cohesive ...
... the processed coding ends are ligated together by DNA ligase IV. All of these processing events result in a paratope that is ... The blunt signal ends are flush ligated together to form a circular piece of DNA containing all of the intervening sequences ... DNA ligase IV, non-homologous end-joining factor 1 (NHEJ1; also known as Cernunnos or XRCC4-like factor [XLF]), the recently ... DNA ligase IV, Cernunnos, and several DNA polymerases. DNA-PK forms a complex that leads to its autophosphorylation, resulting ...
The USER enzyme treated fragments are mixed and ligated using T4 DNA ligase and subjected to Dpn1 digestion to remove the ... Fragments with complementary overhangs are hybridized and ligated using T4 DNA ligase. Finally these constructs are then ... half strands using T4 DNA ligase in the presence of 0.1 mM ATP. Ligated products are then amplified by two types of PCR to ... Next the products from this cleavage are ligated together, resulting in the insertion of the gene into the target plasmid. An ...
Instead the DNA ligase from phage T4 is used as it can ligate blunt-ended DNA as well as single-stranded DNA. Factors that ... The DNA ligase from E. coli cannot ligate blunt-ended DNA except under conditions of molecular crowding, and it is therefore ... The DNA ligase first reacts with ATP or NAD+, forming a ligase-AMP intermediate with the AMP linked to the ε-amino group of ... Without a phosphate group at the ends the vector cannot ligate to itself, but can be ligated to an insert with a phosphate ...
Right and left adapters will need to be attached by T7 DNA Polymerase and T4 DNA ligase after sonification. Strands that fail ... to have adapters ligated are washed away. Adapters contain three different segments: the sequence complementary to solid ...
This sequence is recognized by the so-called WW domains in a special E3 ubiquitin-protein ligase named Nedd4-2. Nedd4-2 ligates ... In the absence of a recognizable PY motif, ubiquitin-protein ligase Nedd4-2 cannot bind to the ENaC subunit and hence cannot ... McDonald FJ, Western AH, McNeil JD, Thomas BC, Olson DR, Snyder PM (September 2002). "Ubiquitin-protein ligase WWP2 binds to ...
Oligonucleotides are annealed and ligated; the preferential ligation by DNA ligase for matching sequences results in a signal ... DNA nanoballs are simply formed by denaturing double stranded, adapter ligated libraries and ligating the forward strand only ...
Ligase chain reaction, a method that amplifies the nucleic acid used as the probe. For each of the two DNA strands, two partial ... probes are ligated to form the actual one; thus, LCR uses two enzymes: a DNA polymerase (used for initial template ... Wiedmann, M (February 1994). "Ligase chain reaction (LCR) -- Overview and applications". PCR Methods and Applications. 3 (4): ... amplification and then inactivated) and a thermostable DNA ligase. Transcription-mediated amplification, an isothermal, single- ...
DNA ligase is then added to join the dye-labelled probe to the primer. Non-ligated probes are washed away, followed by ... The flow cell is exposed to reagents for polymerase-based extension, and priming occurs as the free/distal end of a ligated ... In this approach, the sequence extension reaction is not carried out by polymerases but rather by DNA ligase and either one- ... fluorescence imaging to determine the identity of the ligated probe. The cycle can be repeated either by using cleavable probes ...
The removal of the RNA primer allows DNA ligase to ligate the DNA-DNA nick between the new fragment and the previous strand. ...
... a piece of mRNA is ligated with a single stranded DNA with the help from T4 DNA ligase. This is not a standard T4 DNA ligase ... Once the mRNA library is generated, it will be Urea-PAGE purified and ligated using T4 DNA ligase to the DNA spacer linker ... The ligated mRNA-DNA-puromycin library is translated in Red Nova Lysate (Novagen) or E. Coli S30 Extract System (Promega), ... ligation reaction, where two pieces of double stranded DNA are ligated together. To increase the yield of this special ligation ...
The cut site is then radiolabeled with phosphorus-32 and splint-ligated to a 116nt ssDNA oligonucleotide using DNA ligase. ... After degradation, the labelled residue is purified together with the ligated DNA oligonucleotide and finally hydrolyzed and ... that exploits the ligase sensitivity to 3' and 5' nucleotides (so far used for m6A, 2'-O-Me, Ψ) Microarray modification ...
First benzoate is ligated to CoASH to form the high-energy benzoyl-CoA thioester. This reaction is catalyzed by the HXM-A and ... HXM-B medium-chain acid:CoA ligases and requires energy in the form of ATP. ... The benzoyl-CoA is then conjugated to glycine ...
CYP2D6, dopamine β-hydroxylase (DBH), flavin-containing monooxygenase 3 (FMO3), butyrate-CoA ligase (XM-ligase), and glycine N- ... First benzoate is ligated to CoASH to form the high-energy benzoyl-CoA thioester. This reaction is catalyzed by the HXM-A and ... HXM-B medium-chain acid:CoA ligases and requires energy in the form of ATP. ... The benzoyl-CoA is then conjugated to glycine ...
Both the cDNA and the linker have blunt ends which can be ligated together using a high concentration of T4 DNA ligase. Then ... Restriction endonucleases and DNA ligase are then used to clone the sequences into bacterial plasmids. The cloned bacteria are ...
DNA ligase is then used to ligate a DNA sequence or gene of interest into the linearized DNA, forming a single large, circular ... which is then ligated into a bacterial plasmid. By inserting large fragments of DNA, from 100-1000 kb, the inserted sequences ...
Blunt ends are much less likely to be ligated by a DNA ligase because the blunt end doesn't have the overhanging base pair that ... The overhang can then be used to ligate in (see DNA ligase) a piece of DNA with a complementary overhang (another EcoRI-cut ... For example, a sticky end trailing with AATTG is more likely to bind with a ligase than a blunt end where both the 5' and 3' ... Sticky ends of DNA however are more likely to successfully bind with the help of a DNA ligase because of the exposed and ...
NHEJ is referred to as "non-homologous" because the break ends are directly ligated without the need for a homologous template ... The NHEJ pathway depends on several proteins including ligase 4, DNA polymerase mu and NHEJ factor 1 (NHEJ1, also known as ... "A human iPSC model of Ligase IV deficiency reveals an important role for NHEJ-mediated-DSB repair in the survival and genomic ... Cernunnos or XLF). DNA ligase 4 (Lig4) has a highly specific role in the repair of double-strand breaks by NHEJ. Lig4 ...
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. ... The kinase phosphorylates the 5'-end of the analyte and the ligase will join the capture probe to the analyte to the detection ... Stringent, low/no salt wash will remove un-ligated products. The ligation of the analyte to the ligation probe makes the method ... Further, more exotic nucleic acid chemistries with oligonucleotide drugs may impact upon the activity of the ligase, which ...
Gap filling The gap is filled by DNA polymerase using free nucleotides and the ends of the probe are ligated by ligase, ... Ligase and DNA polymerase concentrations Enrichment of the captured target by either rolling circle amplification or ...
... dependent upon the size of the strands being ligated; for more information see DNA ligase), the insert should become ... The insert and the destination vector are then mixed together with DNA ligase. A typical molar ratio of insert genes to ...
The transposase makes a staggered cut at the target site producing sticky ends, cuts out the DNA transposon and ligates it into ... A DNA polymerase fills in the resulting gaps from the sticky ends and DNA ligase closes the sugar-phosphate backbone. This ...
It is a double-stranded DNA that originates in a linear form that is ligated by means of DNA ligase to a covalently closed ring ... DNA ligase 1 and DNA ligase 3 directly reduce the formation of cccDNA, whereas DNA ligase 4 is crucial for cccDNA formation in ... "The role of host DNA ligases in hepadnavirus covalently closed circular DNA formation". PLOS Pathogens. 13 (12): e1006784. doi: ... it is known that ligase inhibitors play a crucial role as knockout experiments support. ...
These oligomeric plus strands are cleaved by a host RNase and ligated by a host RNA ligase to reform the monomeric plus strand ... T4 DNA ligase) or template-free ligation using special DNA ligases (i.e., CircLigase). Primer-induced single-strand DNA ... DNA polymerase I removes the primer, replacing it with DNA, and DNA ligase joins the ends to make another molecule of double- ... Another is circle to circle amplification or C2CA, where the RCA products are digested with a restriction enzyme and ligated ...
... units are then polymerised in the periplasm by the Wzy polymerase and ligated to the lipid A-core moiety by the WaaL ligase. ...
Oligonucleotides are annealed and ligated; the preferential ligation by DNA ligase for matching sequences results in a signal ...
They are covalently ligated together through the standard 3' to 5' phosphodiester bonds of DNA. DNA ligase can ligate ... 2. DNA ligase During normal DNA replication, DNA ligase catalyzes end-to-end joining (ligation) of short fragments of DNA, ... For the purposes of DNA cloning, purified DNA ligase is used to covalently join the ends of a restriction fragment and vector ... "Structure and Function of Mammalian DNA Ligases." Mutation Research/DNA Repair 407.1 (1998): 1-9. Print. Hung, Mien-Chie, and ...
... ligase, and nuclease in the process to unravel the strands involved, replicate the helitron, and subsequently ligate the ... Non-autuonomous helitrons may lack a transposase, a helicase, a ligase, or a nuclease. All are thought to be necessary for this ...
Large inserts of DNA can be ligated into the middle of the YAC so that there is an "arm" of the YAC on either side of the ... The fragments are then inserted into the vector using DNA ligase. Next, the vector DNA can be taken up by a host organism - ... Use the enzyme DNA ligase to seal the DNA fragments into the vector. This creates a large pool of recombinant molecules. These ... Once inside the host, the cosmids circularize with the aid of the host's DNA ligase and then function as plasmids. Cosmids are ...
Once a protein is tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin ... Ubiquitin contains seven lysine residues to which another ubiquitin can be ligated, resulting in different types of ... Bashir T, Dorrello NV, Amador V, Guardavaccaro D, Pagano M (March 2004). "Control of the SCF(Skp2-Cks1) ubiquitin ligase by the ... The tagging reaction is catalyzed by enzymes called ubiquitin ligases. ...
ligase activity. • protein binding. • protein heterodimerization activity. • acid-amino acid ligase activity. • NEDD8 ... "A new NEDD8-ligating system for cullin-4A". Genes Dev. 12 (15): 2263-8. doi:10.1101/gad.12.15.2263. PMC 317039. PMID 9694792 ... and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E1 ubiquitin-activating enzyme family. The encoded ...
... and the remaining nick is sealed by DNA ligase, which then ligates these fragments to form the lagging strand. ...
A DNA polymerase fills in the resulting gaps from the sticky ends and DNA ligase closes the sugar-phosphate backbone. This ... The transposase makes a staggered cut at the target site producing sticky ends, cuts out the DNA transposon and ligates it into ...
Yeast tRNA ligase adds an adenosine monophosphate group to the 5' end of the 3'-half and joins the two halves together.[21] NAD ... U2/U5/U6 remain bound to the lariat, and the 3' site is cleaved and exons are ligated using ATP hydrolysis. The spliced RNA is ... U4 is released, U6/U2 catalyzes transesterification, making the 5'-end of the intron ligate to the A on intron and form a ... "Structure and function of the yeast tRNA ligase gene". The Journal of Biological Chemistry. 263 (7): 3171-6. PMID 3277966 ...
... dependent upon the size of the strands being ligated; for more information see DNA ligase), the insert should become ... The insert and the destination vector are then mixed together with DNA ligase. A typical molar ratio of insert genes to ...
The Met20 loop is observed in its occluded conformation in the three product ligating intermediates, where the nicotinamide ...
The lagging strand is synthesized in short fragments called the Okazaki fragments, which are then ligated by ligases (ligase I ... the E3 ligase CRL4Cdt2 can degrade POLD4/p12 during normal DNA replication and in the presence of DNA damage.[70] POLD4/p12 can ... The production of the heterotrimer depends on p12 degradation by the E3 ligase RNF8, a protein involved in DSBs repair and ... "The tail that wags the dog: p12, the smallest subunit of DNA polymerase δ, is degraded by ubiquitin ligases in response to DNA ...
... present in two successive nucleotides of either parent DNA or newly formed DNA and thereafter the ligating activity ligates ... are filled with deoxyribonucleotides and sealed by the enzyme ligase. The rate of DNA replication in a living cell was first ...
The E6 proteins of HPV will bind to the N-terminus of the cellular E6-AP E3 ubiquitin ligase, redirecting the complex to bind ... These modifiers have their own specific E1 (activating), E2 (conjugating) and E3 (ligating) enzymes that conjugate the UBLs to ... Ligation: E3 ubiquitin ligases catalyse the final step of the ubiquitination cascade. Most commonly, they create an isopeptide ... Identification of E3 ligase substrates is critical to understand its implication in human diseases since deregulation of E3- ...
In NHEJ, DNA Ligase IV, a specialized DNA ligase that forms a complex with the cofactor XRCC4, directly joins the two ends. To ... This is followed by recruitment of XRCC1-LIG3 to the site for ligating the DNA ends, leading to an intact DNA. MMEJ is always ... MMEJ removes the extra nucleotides (flaps) where strands are joined, and then ligates the strands to create an intact DNA ... The gap is then sealed by enzyme DNA ligase. Nucleotide excision repair (NER): bulky, helix-distorting damage, such as ...
When the PCNA binding site on DNA ligase I is inactive, DNA ligase I's ability to connect Okazaki fragments is severely ... For Okazaki maturation to occur, RNA primers must create segments on the fragments to be ligated. This is used as a building ... Then, DNA ligase I binds to the PCNA, which is clamped to the nicks of the lagging strand, and catalyzes the formation of ... DNA ligase seals the nick made by the FEN1 and it creates a functional continuous double strand of DNA. PCNA simulates ...
Osaka F, Kawasaki H, Aida N, Saeki M, Chiba T, Kawashima S, Tanaka K, Kato S (August 1998). "A new NEDD8-ligating system for ... Wu K, Chen A, Tan P, Pan ZQ (January 2002). "The Nedd8-conjugated ROC1-CUL1 core ubiquitin ligase utilizes Nedd8 charged ... The primary known substrates of NEDD8 modification are the Cullin subunits of Cullin-based E3 ubiquitin ligases, which are ... Their NEDDylation is critical for the recruitment of E2 to the ligase complex, thus facilitating ubiquitin conjugation. NEDD8 ...
So S, Adachi N, Lieber MR, Koyama H (2004). "Genetic interactions between BLM and DNA ligase IV in human cells". J. Biol. Chem ... DNA and passing either a single stranded or a double stranded DNA segment through the transient break and finally re-ligating ... XRCC4-DNA ligase 4 complex). X4L4 stimulates WRN exonuclease activity that likely facilitates DNA end processing prior to final ... "Werner protein cooperates with the XRCC4-DNA ligase IV complex in end-processing". Biochemistry. 47 (28): 7548-56. doi:10.1021/ ...
First benzoate is ligated to CoASH to form the high-energy benzoyl-CoA thioester. This reaction is catalyzed by the HXM-A and ... Butyrate-CoA ligase, also known as xenobiotic/medium-chain fatty acid-ligase (XM-ligase), is an enzyme (EC 6.2.1.2) that ... This enzyme belongs to the family of ligases, specifically those forming carbon-sulfur bonds as acid-thiol ligases. This enzyme ... 3-hydroxybutyryl CoA ligase, xenobiotic/medium-chain fatty acid ligase, and short-chain acyl-CoA synthetase. ACSM1 ACSM2A ...
... are ligated to the 5' and 3' ends of the RNA fragments thanks to the activity of the T4 RNA ligase 2 truncated. After the ... the RNA fragments are firstly ligated to the adapters and then attached to the surface of a plate): generally, universal ... adapters are ligated to both ends of the small RNAs, retrotranscription occurs producing complementary DNA molecules (cDNAs) ...
LCR can also be used to amplify template molecules that have been successfully ligated for the purpose of assessing ligation ... The ligase chain reaction (LCR) is an amplification process that differs from PCR in that it involves a thermostable ligase to ... A mismatch at the 3′ end of the discriminating primer prevents the DNA ligase from joining the two fragments together. By using ... Gene amplification Wiedmann, M; Wilson, WJ; Czajka, J; Luo, J; Barany, F; Batt, CA (Feb 1994). "Ligase chain reaction (LCR)-- ...
In order to copy RNA, fragments or monomers (individual building blocks) that have 5′-triphosphates must be ligated together. ... Other examples of RNA ligases include the L1 ligase (Robertson and Ellington), the R3C ligase (Joyce), the DSL ligase (Inoue). ... The most active ligase known to date is the Class I ligase, isolated from random sequence (work of David Bartel, while in the ... The RNA Ligase ribozyme was the first of several types of synthetic ribozymes produced by in vitro evolution and selection ...
... click-ligated' to 5' alkyne-modified DNA adaptors via copper-catalysed azide-alkyne cycloaddition (CuAAC). This generates ssDNA ... mechanical or enzymatic fragmentation of the sample RNA Removal of RNA/DNA ligase enzymes: In ClickSeq, there are no RNA or DNA ...
... then a PCR-amplified target gene also digested with the same enzymes is ligated into the vectors using DNA ligase. The target ... Another method of cloning without the use of DNA digest and ligase is by DNA recombination, for example as used in the Gateway ... Other cloning vectors may use topoisomerase instead of ligase and cloning may be done more rapidly without the need for ... vector may then accept a PCR product by ligating both the 5' ends of the PCR product, releasing the topoisomerase and forming a ...
Select from our array of cloning enzymes such as ligases, polymerases and PNK, DNA modifying enzymes (e.g., phosphatases and ... How to Ligate an Insert into a Vector. Tool. Find Cloning Products Using the CloneWeaver™ Tool. ... Ligase Nuclease Polynucleotide Kinase RNA Polymerase RNase Inhibitors TdT Primers. Phage Promoter Primers pUC/M13 Reporter ... Promega offers a variety of cloning enzymes including DNA and RNA ligases and polymerases. T7, T3, and SP6 RNA Polymerases are ...
A commonly used enzyme for this reaction is bacteriophage T4 DNA ligase, which requires ATP as the energy source to catalyze ... terminus of the deoxyribozyme ligase limit the range of sequences that can be ligated. ... Ligating DNA with DNA J Am Chem Soc. 2004 Mar 24;126(11):3454-60. doi: 10.1021/ja039713i. ... The self-ligating deoxyribozyme has also been reconfigured to generate a trans-acting construct that joins separate DNA ...
... ligated_DNA + ADP + P) ? T4 ligase, AFAIK, does not have nuclease activity. If so, absense of ATP would mean no ligation ... T4 ligase question. Dima Klenchin klenchin at REMOVE_TO_REPLY.facstaff.wisc.edu Mon Aug 6 00:03:11 EST 2001 *Previous message: ... will ligase start eating up DNA and act as a DNAse ,(considering the ligation reaction being a real chemical ,reaction DNA1 + ...
Kahle PJ, Haass C (July 2004). "How does parkin ligate ubiquitin to Parkinsons disease?". EMBO Reports. 5 (7): 681-5. doi: ... "Structure and function of Parkin E3 ubiquitin ligase reveals aspects of RING and HECT ligases". Nature Communications. 4: 1982 ... Parkin (ligase) has been shown to interact with: Alpha-synuclein, CASK, CUL1, FBXW7 and GPR37, HSPA1A, HSPA8, Multisynthetase ... Like other members of the RING-between-RING (RBR) family of E3 ligases, parkin possesses two RING finger domains and an in- ...
The two fragments were mixed and ligated with T4 DNA ligase and subsequently digested with ClaI. This created a chimeric sbss- ... The mixture was ligated with T4 DNA ligase. The resulting mixture of fragments and plasmids was used to transform E. coli cells ... which had been ligated and EcoRI-cleaved as described in the previous paragraph. The fragments were ligated, and inserted into ... ethanol precipitated and resuspended in 20 ul of DNA ligase buffer with ATP. T4 DNA ligase (20 units) was added and the mixture ...
High fidelity polymerases are everywhere-but why would you need a high fidelity ligase? And what do we even mean by ... which a high fidelity ligase will not ligate. Thats filled in first by the polymerase and then the HiFi ligase will ligate the ... which is a ligase from a different organism, an ATP-dependent ligase or ATP-ligase, attack ligase, or NAD-dependent. And you ... Ligase is going to have a lot of trouble with that. You know, T4 can ligate across gaps and ligase mismatches, but its got ...
... ligated with T4 DNA ligase (Promega); and directly used for natural transformation of S. mutans (Fig.1). ... Ligated DNA product (10 to 20 μl) along with 500 ng of freshly prepared CSP per ml was added to each tube and incubated a ... A) A PCR construct was made by ligating the amplified Erm cassette (Erm CSTP1-CSTP2) and left (P1-P2) and right (P3-P4) ... Ligated products from the allelic-exchange mutagenesis step (containing the left and right flanking regions and the Erm ...
Step 4: Ligate & Inactivate. The substrate for ligase is a bridge structure formed by hybridization of a third oligonucleotide ... Products for Step 4: Ligate & Inactivate. TaqMan® Protein Expression Core Reagents Kit with Master Mix The TaqMan® Protein ... Protein Expression Fast Master Mix are optimized for the amplification of ligated oligonucleotide target sequences prepared ...
Ligases also vary in their type of activity. The specificity and accuracy of the ligation depends upon ligase selection and ... With the right ligase, conditions and probes, even single-base variations in sequence can be reliably detected. ... DNA ligases vary in their ability to join fragments, add adaptors, repair nicks or breaks, link vectors and inserts, and to ... However, ligases can ligate some mismatches to a significant degree, and very active ligases, such as T4 DNA Ligase, can ligate ...
The two fragments were then ligated with a T4 DNA ligase (NEB). ... LBAC-A was prepared by ligating a 4,282-bp DIG-labeled PCR ...
SCF UBIQUITIN LIGASE. Multiprotein complex that ligates ubiquitin to proteins that will be degraded by the proteasome. SCF ... Phosphorylation-dependent ubiquitination of cyclin E by the SCFFbw7 ubiquitin ligase. Science 294, 173-177 (2001). ...
Ligases have many other uses, such as being used to isotopically label RNA fragments by ligating labelled and unlabelled ... Ligases are vital for the production of recombinant DNA used to insert genes into plasmids, which are important tools in ... Many biotechnological companies investigate ligases due to their importance in the regulation of gene expression. The optimised ... There is an ever-increasing demand for more efficient and diverse ligases. ...
The PCR product was then ligated into the vector using T4 DNA ligase. The ligation mixture was used to transform DH5α cells by ... the use of DNA polymerases and ligases, and other techniques. Using an amino acid sequence encoding a metal binding protein or ...
Fragment F2 and the dephosphorylated plasmid V2 were ligated with T4 DNA ligase. E. coli HB101 cells are then transformed and ... Fragment F2 and the dephosphorylated plasmid V2 were ligated with T4 DNA ligase. E. coli HB1O1 cells were then transformed and ... "ligase") per 0.5 μg of approximately equimolar amounts of the DNA fragments to be ligated. ... The amplified sequences are ligated into pQE-9 and are inserted in frame with the sequence encoding for the histidine tag and ...
The amplified products were digested with DpnI (NEB) and ligated with T4 DNA ligase (NEB). To transfer the PTEN coding regions ...
This disgest was followed by phosphatasing the vector and ligating the two parts with qucik ligase. I plated on AC to select ... This disgest was followed by phosphatasing the vector and ligating the two parts with qucik ligase. I plated on AC to select ...
DNA ligase III along with its cofactor XRCC1 catalyzes the nick-sealing step in short-patch BER in humans. DNA ligase I ligates ... Pascucci, Barbara (1999). "Long Patch Base Excision Repair with Purified Human Proteins DNA LIGASE I AS PATCH SIZE MEDIATOR FOR ... Cappelli, Enrico (1997). "Involvement of XRCC1 and DNA Ligase III Gene Products in DNA Base Excision Repair". Journal of ... Caldecott, Keith (1995). "Characterization of the XRCC1-DNA ligase III complex in vitro and its absence from mutant hamster ...
AraCMP-terminated fragments were ligated more slowly than control fragments by T4 DNA ligase. AraCMP located at an ...
The final PCR fragment was digested with BssHII/NotI and ligated to the digested pFastBac1 vector with T4 DNA ligase (Promega ... Vector and insert were ligated by T4 DNA ligase (Promega). Correct insertion was verified by diagnostic digests and sequencing ...
Oligonucleotides are annealed and ligated; the preferential ligation by DNA ligase for matching sequences results in a signal ... 0093] Other suitable amplification methods include, but are not limited to, ligase chain reaction (LCR) (see Wu and Wallace ( ... 0099] Sequencing by ligation uses a DNA ligase to determine the target sequence. ...
Equimolar ratios of the oligonucleotides were mixed and ligated using the thermostable ligase. "Ampligase" according to the ... 5, 241 (1993)) was ligated into the Sacl and EcoRI sites of pUC19 (Gibco-BRL, Bethesda, Md.) to give PUC-V. A 950 bp fragment ... The LT-B coding region was obtained on a 410 bp fragment from pLTB11 by digestion with BamHI and DraI, and ligated with pBI221 ... The 3′ end of the LT-A coding sequence was obtained by digestion of pDF82 with XbaI and SacI, and ligated with pLTA210.5 ...
Both the insert and vector were ligated using T4-Ligase Rapid kit (Fermentas). Ligation product was transformed overnight in ...
Most ligases Ive used have optimal temperature at RT. Why do you ligate at 4? Also, my favorite ligase was from Roche/ ... Most likely there is so much insert in your solution that the inserts ligate with each other and messes up the whole reaction. ...
Add 1 ul NEB T4 DNA ligase buffer •Add 0.5 ul T4 DNA ligase •Add water to 10 ul if necessary •ligate 16C/30 min, heat kill 80C/ ... Below is a modification of this protocol to describe how to ligate in a single Biobrick part as well as renaming the use as ... PstI and DpnI to leave two ends ready to be ligated to a Biobrick™ part". Used in this way, it effectively incapacitates the ...
Then, insert DNA is ligated into plasmid vector by DNA ligase. Although this method works efficiently, shortage of suitable ... If the vector is ligated without gene, 5500 bp and 2300 bp DNA pieces were observed in gel (Fig.5b). pAHC25 vector was also ... 4). Ligation of binary vector with TaNAC69-1 and TtNAM-B2 genes was achieved using T4 DNA ligase. Ligation products belonging ... Finally, ligation reaction was performed to ligate genes into pAHC25 vector. The second approach contains TOPO Cloning and ...
... a SUMO-conjugating enzyme that ligates directly to its protein substrate, such as RanGAP1; and (iv) an E3-like SUMO ligase (10 ... SUMO has been shown to ligate to numerous proteins and modulate their translocation, activity, or stability (6-9). In view of ... Immunofluorescence showed that Myc-SUMO and its ligated proteins are mainly localized in the nucleus (Fig. 2), which is in ... and SUMO protein ligases, in a manner similar to ubiquitinylation. Identification of SUMO-regulated proteins is hampered by the ...
Reading frame cassette A (Invitrogen) was ligated with T4 DNA ligase into peGFP-C1. After selection with chloramphenicol and ... pDEST102 was similarly digested, and the insert, comprising EGFP and cassette A with termini, was gel purified and ligated into ... and ligated with the reading frame B cassette (Invitrogen). Colonies were selected in ccdB survival E. coli as above but with ...
... because you CIP your insert in the ligase buffer). I agree with this, since theoretically the double-cut vector cannot re- ... ligate to itself. KpnI and PstI should work together, so your incomplete digestion may be due to inadequate enzyme or digest ...
chemical reactions such as cutting and ligating. Ligase. In biochemistry, ligase is an enzyme that can catalyse the joining of ...
Ligate the fragments together using T4 ligase. To do this, mix 50 ng of digested pgrg36 and 6 ng of PCR insert in a reaction ... Ligate the annealed oligo and the purified fragment using T4 ligase at 37 °C: mix 50 ng of digested pRG2 and 1 ng of annealed ... Transform the ligated plasmid into DH5-α competent cells. Grow the resulting transformants on Luria broth (LB) agar plates ... volume of 20 μL containing 1x ligase buffer and 0.5 U ligase enzyme. Incubate at room temperature (RT) overnight. ...
  • We have used the action of two catalytic DNAs, an ATP-dependent self-adenylating deoxyribozyme (AppDNA) and a self-ligating deoxyribozyme, to create a ligation system that covalently joins oligonucleotides via the formation of a 3',5'-phosphodiester linkage. (nih.gov)
  • The final ligation step of the deoxyribozyme-catalyzed sequence of reactions mimics the final step of the T4 DNA ligase reaction. (nih.gov)
  • Under these conditions, the ligase deoxyribozyme promotes DNA ligation at least 10(5)-fold faster than that generated by a simple DNA template. (nih.gov)
  • In this webinar, NEB Scientist and ligase expert Greg Lohman discusses mismatch ligation by DNA ligases and the molecular diagnostics applications that depend on the use of high-fidelity DNA ligases like NEB's HiFi Taq DNA Ligase to detect single base differences in DNA. (neb.com)
  • What applications there are that require high fidelity ligation, and what ligases you might want to use for them. (neb.com)
  • The specificity and accuracy of the ligation depends upon ligase selection and careful optimization of reaction conditions. (neb.com)
  • In vitro , ligases (notably T4 DNA Ligase) are critical reagents for many molecular biology protocols, including vector-insert joining for recombinant plasmid construction, adaptor ligation for next-generation sequencing (NGS) library construction, and circularization of dsDNA (6). (neb.com)
  • By creating a very short overhang on a PCR of a plasmid backbone, the remnant, when cut with EcoRI and PstI is sufficiently short that it will not anneal at ligation temperature, and will therefore not ligate. (openwetware.org)
  • Yeast tRNA ligase (Trl1) is an essential trifunctional enzyme that catalyzes exon-exon ligation during tRNA biogenesis and the non-conventional splicing of HAC1 mRNA during the unfolded protein response (UPR). (elifesciences.org)
  • Exon ligation progresses via a covalent ligase-AMP intermediate (LIG-AMP) and a 5'−5' RNA-adenylate. (elifesciences.org)
  • Typically, DNA and plasmid vector are individually cut to yield complementary ends, then both are added to a ligation reaction to be circularised by DNA ligase. (openwetware.org)
  • Lei Zhang et al, Archaeal RNA Ligase from Thermoccocus Kodakarensis for Template Dependent Ligation, RNA Biology (2016). (phys.org)
  • Unexpectedly, ligation reactions also occurred in the absence of the exogenous ligase. (mdc-berlin.de)
  • Finally, DNA ligase IV, XRCC4, and XLF form the ligation complex which ligates the double-strand break. (usc.edu)
  • DNA ligases vary in their ability to join fragments, add adaptors, repair nicks or breaks, link vectors and inserts, and to circularize dsDNA. (neb.com)
  • T4 DNA Ligase (NEB #M0202 ) is incredibly efficient at sealing nicks, as well as joining or circularizing DNA fragments with blunt or cohesive (short complementary) ends. (neb.com)
  • T4 DNA Ligase can ligate a wide variety of DNA structures, including modified bases and the ends of double stranded fragments. (neb.com)
  • Final joining is accomplished by a nick-selective ligase, such as Taq DNA Ligase, which only reacts with substrates containing no gaps, and will not join any fragments end-to-end without the exo/polymerase generation of annealed complemen-tary regions. (neb.com)
  • 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)
  • AraCMP-terminated fragments were ligated more slowly than control fragments by T4 DNA ligase. (nih.gov)
  • With proper design of the cleavage sites, two fragments cut by type IIs restriction enzymes can be ligated into a product lacking the original restriction site. (nih.gov)
  • Short single stranded DNA fragments will not ligate to 4 bp overhangs. (openwetware.org)
  • T4 DNA ligase is used to join the DNA fragments. (openwetware.org)
  • This enzyme will ligate DNA fragments having blunt or overhanging, cohesive, 'sticky' ends. (openwetware.org)
  • DNA ligases are enzymes that seal breaks in DNA by joining 5´-phosphorylated DNA termini to 3´-OH DNA termini (1-4). (neb.com)
  • Ligases are enzymes that serve critical functions in cells, helping to fuse together broken strands of DNA and RNA. (phys.org)
  • As our designs became more complex, we grew increasingly frustrated at the lack of specialized enzymes, such as ligases. (phys.org)
  • Then, insert DNA is ligated into plasmid vector by DNA ligase. (thefreelibrary.com)
  • Activity 2 will help students conceptualize the mechanics involved in cutting and ligating DNAs into a plasmid vector with "sticky ends" of complementary DNA base pairs. (accessexcellence.org)
  • There exists a multitude of E3 ligases, which differ in structure and substrate specificity to allow selective targeting of proteins to intracellular degradation. (wikipedia.org)
  • however, the protein is a component of a multiprotein E3 ubiquitin ligase complex which in turn is part of the ubiquitin-proteasome system that mediates the targeting of proteins for degradation. (wikipedia.org)
  • While human cells utilize both short- and long-patch BER, the yeast Saccharomyces cerevisiae was long thought to lack a short-patch pathway because it does not have homologs of several mammalian short-patch proteins, including pol β, DNA ligase III, XRCC1, and the kinase domain of PNKP. (wikipedia.org)
  • Ligases are, therefore, commercially-valuable proteins. (uea.ac.uk)
  • 10 known ubiquitin-like proteins that have been shown to ligate to other target protein molecules. (pnas.org)
  • SUMO has been shown to ligate to numerous proteins and modulate their translocation, activity, or stability ( 6 - 9 ). (pnas.org)
  • However, the majority of the E3 ligases consist of a protein complex where the tasks of substrate- and E2 binding are subdivided between separate proteins ( Deshaies, 1999 ). (biologists.org)
  • The SSB is then ligated, a process that employs proteins also involved in SSB repair, e.g. (diva-portal.org)
  • In contrast to the large number of ubiquitin ligases that have been found, three SUMO E3s have been identified so far. (pnas.org)
  • A well-known group of multi-subunit E3 ligases are the Cullin-Ring ubiquitin ligases (CLRs), which are based around a Cullin core. (biologists.org)
  • This disgest was followed by phosphatasing the vector and ligating the two parts with qucik ligase. (igem.org)
  • I agree with this, since theoretically the double-cut vector cannot re-ligate to itself. (bio.net)
  • Entry clone (A) and expression vector (B) are mixed in one tube together with BsaI and ligase. (nih.gov)
  • In the case of transformation, the fragment may be ligated into a cloning vector using T4 DNA ligase, Catalog Number KEM0019 . (sigmaaldrich.com)
  • In vivo , ligases are important for the repair of nicks, breaks in one strand of a dsDNA molecule, DNA formed during replication (i.e. (neb.com)
  • The E3 ligases, which bind to a substrate and attach the ubiquitin molecule, are believed to provide substrate specificity. (biologists.org)
  • If the mutation is not present, the structure of the hybrid molecule is disrupted and the ligase will not seal the nick. (phys.org)
  • A commonly used enzyme for this reaction is bacteriophage T4 DNA ligase, which requires ATP as the energy source to catalyze the otherwise unfavorable formation of a phosphodiester bond. (nih.gov)
  • Most likely there is so much insert in your solution that the inserts ligate with each other and messes up the whole reaction. (protocol-online.org)
  • The sumoylation reaction is catalyzed by the SUMO protease, which exposes the C-terminal active glycine residue of the nascent SUMO, the heterodimeric SUMO activating enzyme, the SUMO conjugating enzyme, Ubc9, and SUMO protein ligases, in a manner similar to ubiquitinylation. (pnas.org)
  • The salts and whatever in your restriction buffer might not make your ligase happy and you have not even diluted them (80% of your reaction is basically in the restriction buffer). (biology-online.org)
  • Okay, so the T4 DNA ligase and other DNA ligases, as you likely know, seal breaks in double-stranded DNA. (neb.com)
  • And so, you'd need a very active ligase to seal these double-stranded breaks, especially the blunt ends. (neb.com)
  • With the right ligase, conditions and probes, even single-base variations in sequence can be reliably detected. (neb.com)
  • When probe extension is complete, the ligated probes are removed and the process is started over with a linker to offset the template. (news-medical.net)
  • For their paper, Zhang and Tripathi used KOD1Rnl to ligate engineered probes in the detection of lab-made Ebola RNA transcripts. (phys.org)
  • The probes are then paired or "hybridized" with a target RNA strand in the presence of template dependent ligase. (phys.org)
  • If the mutation is present in the target strand, the RNA probes will hybridize properly, and the nick will be sealed by the ligase. (phys.org)
  • Five components of the classical NHEJ (Ku70, Ku80, DNA-PKcs, DNA ligase IV, and XRCC4) have been shown to be important for CSR ( 11 - 16 ). (rupress.org)
  • The DNA ligase is locked on a variety of DNA structures. (neb.com)
  • Taq Ligase is a NAD+-dependent DNA ligase from a thermostable bacterium that can survive high temperatures (up to 95°C) and is active over a range of elevated temperatures (37-75°C). However, it only has significant activity on nicked DNA, and negligible activity on short cohesive and blunt substrates in end-joining reactions. (neb.com)
  • In particular, there are few RNA ligases that are thermostable, that is, ones that can operate at high temperatures. (phys.org)
  • Blunt-end cloning involves ligating dsDNA into a plasmid where both the insert and linearized plasmid have no overhanging bases at their termini. (idtdna.com)
  • Ligases are very, very active on nicks. (neb.com)
  • As you go down this list, nicks are very easy to ligate and are the highest activity substrate available. (neb.com)
  • Less commonly utilized in vitro , Taq DNA Ligase (NEB #M0208 ) will ligate only nicks (9-12). (neb.com)
  • 2005), Mind bomb-2 is an E3 ligase for Notch ligand. (xenbase.org)
  • The substrate for ligase is a bridge structure formed by hybridization of a third oligonucleotide to the oligonucleotide ends of the assay probe pair. (appliedbiosystems.com)
  • DNA ligase preferentially binds the oligonucleotide that matches the template sequence. (news-medical.net)
  • In the second step, quantum dots derivatized with HaloTag, a modified haloalkane dehalogenase, react with the ligated bromodecanoic acid to form a covalent adduct. (mit.edu)
  • Parkin is a 465-residue E3 ubiquitin ligase that plays a critical role in ubiquitination- the process whereby molecules are covalently labelled with ubiquitin (Ub) and directed towards degradation in proteasomes or lysosomes. (wikipedia.org)
  • By tracking the fitness decline of ligase ribozyme populations with bottleneck sizes between 100 and 3000 molecules, we detected the appearance and subsequent fixation of both slightly deleterious mutations and advantageous mutations. (genetics.org)
  • The problem is that the temperatures needed to straighten out the RNA are often too high for the ligase to be effective in fusing molecules. (phys.org)
  • However, the sequence requirements of the AppDNA and that of the 3' terminus of the deoxyribozyme ligase limit the range of sequences that can be ligated. (nih.gov)
  • A concatamer is a 500-1000bp of the Nla(ss) - (N)10 - (N)10 - Nla(ss) sequences ligated together. (studentdoctor.net)
  • because you CIP your insert in the ligase buffer). (bio.net)
  • in parallel I also did a gel purification exp and ligated with simliar amounts. (biology-online.org)
  • 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)
  • 11. The recombinant cell of claim 9 or claim 10 wherein the cell exhibits increased activity compared to a wild-type control of one or more of: a thiolase, 3-hydroxy-3-methyl-glutaryl (HMG)-CoA synthase, HMG-CoA reductase, acyl-CoA ligase, or enoyl-CoA hydratase. (sumobrain.com)
  • 18. The recombinant cell of claim 11 wherein the acyl-CoA ligase comprises Sidl. (sumobrain.com)
  • Most ligases I've used have optimal temperature at RT. (protocol-online.org)
  • Derived from a microbe that thrives near volcanic thermal vents, the new ligase, called KOD1Rnl, can work at the high temperature desirable for some laboratory procedures. (phys.org)
  • Ub is then transferred to an E2 ubiquitin-conjugating enzyme before being conjugated to the target protein via an E3 ubiquitin ligase. (wikipedia.org)
  • The fungal tRNA ligase Trl1 (previously named Rlg1) is encoded by an essential gene and is involved in tRNA splicing and the unfolded protein response (UPR). (elifesciences.org)
  • In the first step, Escherichia coli lipoic acid ligase (LplA) site-specifically attaches 10-bromodecanoic acid onto a 13 amino acid recognition sequence that is genetically fused to a protein of interest. (mit.edu)
  • The self-ligating deoxyribozyme has also been reconfigured to generate a trans-acting construct that joins separate DNA oligonucleotides of defined sequence. (nih.gov)
  • So now I know that I need to incorporate these restriction sites on my primer if I want to ligate my PCR product to my plasmid. (thescienceforum.com)
  • It will also efficiently ligate many undesirable structures, including substrates containing gaps of one or more nucleotides and nicked substrates that contain DNA base pair mismatches (12-15). (neb.com)
  • These data suggest that Mib2 has functional similarities to Mib1 , but might have distinct roles in Notch signaling as an E3 ubiquitin ligase. (xenbase.org)
  • Cohesive ends are between 10 and 100 times slower to ligate than a nick. (neb.com)
  • It does not benefit from the hydrogen bond stabilization associated with the complementary overhanging bases used in cohesive-end cloning, but the transient associations of the available 5' phosphate and 3' hydroxyl groups are sufficient to produce successful clones in the presence of T4 ligase [1]. (idtdna.com)
  • This is ligated with T4 DNA ligase which catalyzes the bonding. (majortests.com)
  • The initial rate constant (k(obs)) of the optimized deoxyribozyme ligase was found to be 1 x 10(-)(4) min(-)(1). (nih.gov)
  • Many E3 ligases have been found to be involved in developmental processes. (biologists.org)
  • RNA ligases are found in all domains of life. (elifesciences.org)
  • We found that this is a highly specific RNA ligase," Zhang said of KOD1Rnl. (phys.org)
  • We found this targeting method to be specific, fast, and fully orthogonal to a previously reported and analogous quantum dot targeting method using E. coli biotin ligase and streptavidin. (mit.edu)
  • Parkin also contains an N-terminal Ub-like domain (Ubl) for specific substrate recognition, a unique RING0 domain and a repressor (REP) region that tonically suppresses ligase activity. (wikipedia.org)
  • T4 ligase, AFAIK, does not have nuclease activity. (bio.net)
  • So here is the activity of T4 ligase on nicked DNA. (neb.com)
  • Ligases also vary in their type of activity. (neb.com)
  • Both Mib1 and Mib2 have an E3 ubiquitin ligase activity in their C-terminal RING domain and interact with Xenopus Delta (XD) via their N-terminal region. (xenbase.org)
  • This all depends on the extent to which the ligase is template dependent and its structural specificity. (phys.org)
  • Instead of DNA polymerase, it makes use of DNA ligase to identify the unknown bases in a strand. (news-medical.net)
  • Hi there, Today I used my PCR product (that was cleaned up) to ligate into PET expression. (biology-online.org)
  • I did also use the gel purified DNA but also was told to try ligating the pcr product straight into the vecotr. (biology-online.org)
  • A template-dependent RNA ligase will fuse two RNA strands only when one strand is aligned adjacently with the other strand onto a template. (phys.org)
  • Some ligases are inherently more specific than others. (phys.org)
  • Maybe they prefer a more specific ligase action or something, but i wouldn't bother. (thescienceforum.com)
  • To directly and unambiguously identify miRNA:target site interactions, we modified our CLIP methodology in C. elegans to experimentally ligate miRNAs to their target sites. (mdc-berlin.de)
  • The ligase/adenylyltransferase domain (LIG) is shown in blue, the polynucleotide kinase domain (KIN) in white, the cyclic phosphodiesterase domain (CPD) in green. (elifesciences.org)
  • After removal of the intron (gray), the exon ends are first modified ('healed') by the CPD and KIN domains and finally ligated ('sealed') by the LIG domain. (elifesciences.org)
  • High fidelity polymerases are everywhere-but why would you need a high fidelity ligase? (neb.com)
  • Structurally, E3 ligases can be subdivided into Ring-domain or HECT-domain based ligases. (biologists.org)
  • Here we report the crystal structure of Trl1 RNA ligase domain from Chaetomium thermophilum at 1.9 Å resolution. (elifesciences.org)
  • We describe the identification of Xenopus Cullin-1 , an E3 ubiquitin ligase, and show that blocking the function of endogenous Cullin-1 leads to pleiotropic defects in development. (biologists.org)