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Ligation (molecular Biology)
In molecular biology, ligation is the joining of two nucleic acid fragments through the action of an enzyme. It is an essential laboratory procedure in the molecular cloning of DNA, whereby DNA fragments are joined to create recombinant DNA molecules (such as when a foreign DNA fragment is inserted into a plasmid). The ends of DNA fragments are joined by the formation of phosphodiester bonds between the 3'-hydroxyl of one DNA terminus with the 5'-phosphoryl of another. RNA may also be ligated similarly. A co-factor is generally involved in the reaction, and this is usually ATP or NAD+. Ligation in the laboratory is normally performed using T4 DNA ligase. However, procedures for ligation without the use of standard DNA ligase are also popular. Ligation reaction The mechanism of the ligation reaction was first elucidated in the laboratory of I. Robert Lehman. Two fragments of DNA may be joined by DNA ligase which catalyzes the formation of a phosphodiester bond between the 3 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ligation
Ligation may refer to: * Ligation (molecular biology), the covalent linking of two ends of DNA or RNA molecules * In medicine, the making of a ligature (tie) * Chemical ligation, the production of peptides from amino acids * Tubal ligation, a method of female sterilization * Rubber band ligation, a treatment for hemorrhoids * In coordination chemistry, making a bond between a ligand and a Lewis acid * In orthodontics, a method of attaching the archwires to the brackets * KAHA Ligation * Ligation-independent cloning * Typographic ligature In writing and typography, a ligature occurs where two or more graphemes or letters are joined to form a single glyph. Examples are the characters æ and œ used in English and French, in which the letters 'a' and 'e' are joined for the first li ... forming {{disambiguation pl:Ligacja ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Intramolecular Reaction
Intramolecular in chemistry describes a process or characteristic limited within the structure of a single molecule, a property or phenomenon limited to the extent of a single molecule. Examples * intramolecular hydride transfer (transfer of a hydride ion from one part to another within the same molecule) * intramolecular hydrogen bond (a hydrogen bond formed between two functional groups of the same molecule) *cyclization of ω-haloalkylamines and alcohols to form the corresponding saturated nitrogen and oxygen heterocycles, respectively (an SN2 reaction within the same molecule) In intramolecular organic reactions, two reaction sites are contained within a single molecule. This creates a very high effective concentration (resulting in high reaction rates), and, therefore, many intramolecular reactions that would not occur as an intermolecular reaction between two compounds take place. Examples of intramolecular reactions are the Smiles rearrangement, the Dieckmann condensation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Calf-intestinal Alkaline Phosphatase
Calf-intestinal alkaline phosphatase (CIAP/CIP) is a type of alkaline phosphatase that catalyzes the removal of phosphate groups from the 5' end of DNA strands and phosphomonoesters from RNA. This enzyme is frequently used in DNA sub-cloning, as DNA fragments that lack the 5' phosphate groups cannot ligate. This prevents recircularization of the linearized DNA vector Vector most often refers to: *Euclidean vector, a quantity with a magnitude and a direction *Vector (epidemiology), an agent that carries and transmits an infectious pathogen into another living organism Vector may also refer to: Mathematic ... and improves the yield of the vector containing the appropriate insert. References Enzymes Genetics techniques {{Enzyme-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
EcoRI
''Eco''RI (pronounced "eco R one") is a restriction endonuclease enzyme isolated from species '' E. coli.'' It is a restriction enzyme that cleaves DNA double helices into fragments at specific sites, and is also a part of the restriction modification system. The ''Eco'' part of the enzyme's name originates from the species from which it was isolated - "E" denotes generic name which is "Escherichia" and "co" denotes species name, "coli" - while the R represents the particular strain, in this case RY13, and the I denotes that it was the first enzyme isolated from this strain. In molecular biology it is used as a restriction enzyme. ''Eco''RI creates 4 nucleotide sticky ends with 5' end overhangs of AATT. The nucleic acid recognition sequence where the enzyme cuts is G↓AATTC, which has a palindromic, complementary sequence of CTTAA↓G. Other restriction enzymes, depending on their cut sites, can also leave 3' overhangs or blunt ends with no overhangs. Structure Primary str ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NdeI
''Nde''I is an endonuclease isolated from '' Neisseria denitrificans''. In molecular biology, it is commonly used as a restriction enzyme. Recognition sequence Recognition sequence of ''Nde''I: 5'CATATG 3'GTATAC The ends generated by ''Nde''I digest: 5'---CA TATG---3' 3'---GTAT AC---5' Use in molecular biology ''Nde''I is a specific Type II restriction enzyme that cuts open specific target sequences, unlike exonucleases. This enzyme is used in gene cloning to cut open reading frames in the plasmid of certain bacteria such as E. coli and insert a foreign gene, such as the gfpuv gene that codes for bio fluorescence of the jelly fish ''Aequorea victoria''. ''Nde''I is useful in generating heterologous DNA construct because it contains the start codon ATG. It therefore can be used in some expression vectors, such as those in the pET series of vectors, for the ligation of the start of a gene when making an expression construct. Note however that ''Nde''I generates onl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ionic Strength
The ionic strength of a solution is a measure of the concentration of ions in that solution. Ionic compounds, when dissolved in water, dissociate into ions. The total electrolyte concentration in solution will affect important properties such as the dissociation constant or the solubility of different salts. One of the main characteristics of a solution with dissolved ions is the ionic strength. Ionic strength can be molar (mol/L solution) or molal (mol/kg solvent) and to avoid confusion the units should be stated explicitly. The concept of ionic strength was first introduced by Lewis and Randall in 1921 while describing the activity coefficients of strong electrolytes. Quantifying ionic strength The molar ionic strength, ''I'', of a solution is a function of the concentration of ''all'' ions present in that solution. :I = \begin\frac\end\sum_^ c_i z_i^ where one half is because we are including both cations and anions, ''c''i is the molar concentration of ion i (M, mol/L), ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Melting
Nucleic acid thermodynamics is the study of how temperature affects the nucleic acid structure of double-stranded DNA (dsDNA). The melting temperature (''Tm'') is defined as the temperature at which half of the DNA strands are in the random coil or single-stranded (ssDNA) state. ''Tm'' depends on the length of the DNA molecule and its specific nucleotide sequence. DNA, when in a state where its two strands are dissociated (i.e., the dsDNA molecule exists as two independent strands), is referred to as having been denatured by the high temperature. Concepts Hybridization Hybridization is the process of establishing a non-covalent, sequence-specific interaction between two or more complementary strands of nucleic acids into a single complex, which in the case of two strands is referred to as a duplex. Oligonucleotides, DNA, or RNA will bind to their complement under normal conditions, so two perfectly complementary strands will bind to each other readily. In order to reduce the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transformation (genetics)
In molecular biology and genetics, transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s). For transformation to take place, the recipient bacterium must be in a state of competence, which might occur in nature as a time-limited response to environmental conditions such as starvation and cell density, and may also be induced in a laboratory. Transformation is one of three processes that lead to horizontal gene transfer, in which exogenous genetic material passes from one bacterium to another, the other two being conjugation (transfer of genetic material between two bacterial cells in direct contact) and transduction (injection of foreign DNA by a bacteriophage virus into the host bacterium). In transformation, the genetic material passes through the intervening medium, and uptake is completely dependent on the recipient bacterium. As of 2014 about 8 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Concatemers
A concatemer is a long continuous DNA molecule that contains multiple copies of the same DNA sequence linked in series. These polymeric molecules are usually copies of an entire genome linked end to end and separated by ''cos'' sites (a protein binding nucleotide sequence that occurs once in each copy of the genome). Concatemers are frequently the result of rolling circle replication, and may be seen in the late stage of bacterial infection by phages. As an example, if the genes in the phage DNA are arranged ABC, then in a concatemer the genes would be ABCABCABCABC and so on (assuming synthesis was initiated between genes C and A). They are further broken by ribozymes. During active infection, some species of viruses have been shown to replicate their genetic material via the formation of concatemers. In the case of ''human herpesvirus-6'', its entire genome is made over and over on a single strand. These long concatemers are subsequently cleaved between the pac-1 and pac-2 region ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polyethylene Glycol
Polyethylene glycol (PEG; ) is a polyether compound derived from petroleum with many applications, from industrial manufacturing to medicine. PEG is also known as polyethylene oxide (PEO) or polyoxyethylene (POE), depending on its molecular weight. The structure of PEG is commonly expressed as H−(O−CH2−CH2)n−OH. Uses Medical uses * Pharmaceutical-grade PEG is used as an excipient in many pharmaceutical products, in oral, topical, and parenteral dosage forms. * PEG is the basis of a number of laxatives (as ''MiraLax''). Whole bowel irrigation with polyethylene glycol and added electrolytes is used for bowel preparation before surgery or colonoscopy. * PEG is used in medicines for treating disimpaction and maintenance therapy for children with constipation. * When attached to various protein medications or drug carriers, polyethylene glycol of suitable length slows down their clearance from the blood. * The possibility that PEG could be used to fuse axons is being ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Macromolecular Crowding
The phenomenon of macromolecular crowding alters the properties of molecules in a solution when high concentrations of macromolecules such as proteins are present. Such conditions occur routinely in living cells; for instance, the cytosol of ''Escherichia coli'' contains about 300– of macromolecules. Crowding occurs since these high concentrations of macromolecules reduce the volume of solvent available for other molecules in the solution, which has the result of increasing their effective concentrations. Crowding can promote formation of a biomolecular condensate by colloidal phase separation. This crowding effect can make molecules in cells behave in radically different ways than in test-tube assays. Consequently, measurements of the properties of enzymes or processes in metabolism that are made in the laboratory (''in vitro'') in dilute solutions may be different by many orders of magnitude from the true values seen in living cells (''in vivo''). The study of biochemical pro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Spermidine
Spermidine is a polyamine compound () found in ribosomes and living tissues and having various metabolic functions within organisms. It was originally isolated from semen. Function Spermidine is an aliphatic polyamine. Spermidine synthase (SPDS) catalyzes its formation from putrescine. It is a precursor to other polyamines, such as spermine and its structural isomer thermospermine. Spermidine synchronizes an array of biological processes, (such as Ca2+, Na+, K+ -ATPase) thus maintaining membrane potential and controlling intracellular pH and volume. Spermidine regulates biological processes, such as Ca2+ influx by glutamatergic N-methyl-d-aspartate receptor (NMDA receptor), which has been associated with nitric oxide synthase (NOS) and cGMP/PKG pathway activation and a decrease of Na+,K+-ATPase activity in cerebral cortex synaptosomes. Spermidine is a longevity agent in mammals due to various mechanisms of action, which are just beginning to be understood. Autophagy is the main m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
