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Artificial Gene Synthesis
Artificial gene synthesis, or simply gene synthesis, refers to a group of methods that are used in synthetic biology to construct and assemble genes from nucleotides ''de novo''. Unlike DNA synthesis in living cells, artificial gene synthesis does not require template DNA, allowing virtually any DNA sequence to be synthesized in the laboratory. It comprises two main steps, the first of which is solid-phase DNA synthesis, sometimes known as DNA printing. This produces oligonucleotide fragments that are generally under 200 base pairs. The second step then involves connecting these oligonucleotide fragments using various DNA assembly methods. Because artificial gene synthesis does not require template DNA, it is theoretically possible to make a completely synthetic DNA molecule with no limits on the nucleotide sequence or size. Synthesis of the first complete gene, a yeast tRNA, was demonstrated by Har Gobind Khorana and coworkers in 1972. Synthesis of the first peptide- and protein-c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Synthetic Biology
Synthetic biology (SynBio) is a multidisciplinary field of science that focuses on living systems and organisms. It applies engineering principles to develop new biological parts, devices, and systems or to redesign existing systems found in nature. It is a branch of science that encompasses a broad range of methodologies from various disciplines, such as biochemistry, biotechnology, biomaterials, Materials science, material science/engineering, genetic engineering, molecular biology, molecular engineering, systems biology, Model lipid bilayer, membrane science, biophysics, Biological engineering, chemical and biological engineering, Electrical engineering, electrical and computer engineering, control engineering and evolutionary biology. It includes designing and constructing BioBrick, biological modules, biological systems, and biological machines, or re-designing existing biological systems for useful purposes. Additionally, it is the branch of science that focuses on the ne ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
High-performance Liquid Chromatography
High-performance liquid chromatography (HPLC), formerly referred to as high-pressure liquid chromatography, is a technique in analytical chemistry used to separate, identify, and quantify specific components in mixtures. The mixtures can originate from food, chemicals, pharmaceuticals, biological, environmental and agriculture, etc., which have been dissolved into liquid solutions. It relies on high pressure pumps, which deliver mixtures of various solvents, called the mobile phase, which flows through the system, collecting the sample mixture on the way, delivering it into a cylinder, called the column, filled with solid particles, made of adsorbent material, called the stationary phase. Each component in the sample interacts differently with the adsorbent material, causing different migration rates for each component. These different rates lead to separation as the species flow out of the column into a specific detector such as UV detectors. The output of the detecto ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Aromatic Hydrocarbon
Aromatic compounds or arenes are organic compounds "with a chemistry typified by benzene" and "cyclically conjugated." The word "aromatic" originates from the past grouping of molecules based on odor, before their general chemical properties were understood. The current definition of aromatic compounds does not have any relation to their odor. Aromatic compounds are now defined as cyclic compounds satisfying Hückel's rule. Aromatic compounds have the following general properties: * Typically unreactive * Often non polar and hydrophobic * High carbon-hydrogen ratio * Burn with a strong sooty yellow flame, due to high C:H ratio * Undergo electrophilic substitution reactions and nucleophilic aromatic substitutions Arenes are typically split into two categories - benzoids, that contain a benzene derivative and follow the benzene ring model, and non-benzoids that contain other aromatic cyclic derivatives. Aromatic compounds are commonly used in organic synthesis and are involved in m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNaM
dNaM is an artificial nucleobase containing a 3-methoxy-2-naphthyl group instead of a natural base. When it was originally successfully introduced into DNA for replication in an E. coli semi-synthetic organism, it was paired up with d5SICS. For short it is called ''X'' whilst the d5SICS being called Y. d5SICS was replaced by dTPT3 in revised versions due to its improved ability to replicate in a wider range of sequence contexts. X pairs with Y using hydrophobic and packing interactions instead of hydrogen bonding, which occurs in natural base pairs. Inside the semi-synthetic organism, methyl directed mismatch repair pathway ( MMR) actually fixes unnatural-natural mispairs, whereas recombinational repair actually cuts out the unnatural. The E. coli semi-synthetic organism managed to hold onto the new base for an extended time both while on a plasmid as well as when stored in the chromosome. In free DNA, rings of d5SICS and dNaM are placed in parallel planes instead of the sa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
D5SICS
d5SICS is an artificial nucleoside containing 6-methylisoquinoline-1-thione-2-yl group instead of a base. It pairs up with dNaM in a hydrophobic interaction. It was not able to be removed by the error-correcting machinery of the ''E. coli'' into which it was inserted. The pairing of d5SICS–dNaM is mediated by packing and hydrophobic forces instead of hydrogen bonding In chemistry, a hydrogen bond (H-bond) is a specific type of molecular interaction that exhibits partial covalent character and cannot be described as a purely electrostatic force. It occurs when a hydrogen (H) atom, Covalent bond, covalently b ..., which occurs in natural base pairs. Therefore, in free DNA, rings of d5SICS and dNaM are placed in parallel planes instead of the same plane. The d5SICS-dNaM pairing replaced an older dNaM- dTPT3 pairing. References Nucleosides Synthetic biology Thioketones Nitrogen heterocycles Heterocyclic compounds with 2 rings Hydroxymethyl compounds {{mole ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scripps Research Institute
Scripps Research is a nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California, the institute has over 170 laboratories employing 2,100 scientists, technicians, graduate students, and administrative and other staff. The institute holds over 1,100 patents, has produced 11 FDA-approved therapeutics, and has generated over 50 spin-off companies. The Scripps Research graduate program is ranked 9th nationally in the biological sciences, 6th for organic chemistry, and 6th for biochemistry. In 2022, their Jupiter, Florida, campus became a part of the University of Florida. Jupiter-based graduate students remain part of the Scripps Research graduate program. History Scripps Research began with the Scripps Metabolic Clinic, founded near the current site in the La Jolla area of San Diego in 1924 by philanthropist Ellen Browning Scripps, who was inspired by the discovery of insulin. In 1946, the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MutS-1
MutS is a mismatch DNA repair protein, originally described in ''Escherichia coli''. Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element (Klenow fragment) of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of ''Escherichia coli'' involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognizes and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base. MutS can also collaborate with methyltransferases in th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polymerase Chain Reaction
The polymerase chain reaction (PCR) is a method widely used to make millions to billions of copies of a specific DNA sample rapidly, allowing scientists to amplify a very small sample of DNA (or a part of it) sufficiently to enable detailed study. PCR was invented in 1983 by American biochemist Kary Mullis at Cetus Corporation. Mullis and biochemist Michael Smith (chemist), Michael Smith, who had developed other essential ways of manipulating DNA, were jointly awarded the Nobel Prize in Chemistry in 1993. PCR is fundamental to many of the procedures used in genetic testing and research, including analysis of Ancient DNA, ancient samples of DNA and identification of infectious agents. Using PCR, copies of very small amounts of DNA sequences are exponentially amplified in a series of cycles of temperature changes. PCR is now a common and often indispensable technique used in medical laboratory research for a broad variety of applications including biomedical research and forensic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ligase Chain Reaction
The ligase chain reaction (LCR) is a method of DNA amplification. The ligase chain reaction (LCR) is an amplification process that differs from polymerase chain reaction (PCR) in that it involves a thermostable ligase to join two probes or other molecules together which can then be amplified by standard PCR cycling. Each cycle results in a doubling of the target nucleic acid molecule. A key advantage of LCR is greater specificity as compared to PCR. Thus, LCR requires two completely different enzymes to operate properly: ligase, to join probe molecules together, and a thermostable polymerase (e.g., ''Taq'' polymerase) to amplify those molecules involved in successful ligation. The probes involved in the ligation are designed such that the 5′ end of one probe is directly adjacent to the 3′ end of the other probe, thereby providing the requisite 3′-OH and 5′-PO4 group substrates for the ligase. LCR was originally developed to detect point mutations; a single base mismatch ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Enzyme
An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different molecules known as product (chemistry), products. Almost all metabolism, metabolic processes in the cell (biology), cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called ''enzymology'' and the field of pseudoenzyme, pseudoenzyme analysis recognizes that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts include Ribozyme, catalytic RNA molecules, also called ribozymes. They are sometimes descr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ligase
In biochemistry, a ligase is an enzyme that can catalyze the joining ( ligation) of two molecules by forming a new chemical bond. This is typically via hydrolysis of a small pendant chemical group on one of the molecules, typically resulting in the formation of new C-O, C-S, or C-N bonds. For example, DNA ligase can join two complementary fragments of nucleic acid by forming phosphodiester bonds, and repair single stranded breaks that arise in double stranded DNA during replication. In general, a ligase catalyzes the following dehydration reaction, thus joining molecules A and B: A-OH + B-H → A–B + H2O Nomenclature The naming of ligases is inconsistent and so these enzymes are commonly known by several different names. Generally, the common names of ligases include the word "ligase", such as in DNA ligase, an enzyme commonly used in molecular biology laboratories to join together DNA fragments. However, many common names use the term "synthetase" or "synthase" instead, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polymerase
In biochemistry, a polymerase is an enzyme (Enzyme Commission number, EC 2.7.7.6/7/19/48/49) that synthesizes long chains of polymers or nucleic acids. DNA polymerase and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by copying a DNA template strand using Base pair, base-pairing interactions or RNA by half ladder replication. A DNA polymerase from the thermophile, thermophilic bacterium, ''Thermus aquaticus'' (''Taq'') (Protein Data Bank, PDB]1BGX EC 2.7.7.7) is used in the polymerase chain reaction, an important technique of molecular biology. A polymerase may be template-dependent or template-independent. Polynucleotide adenylyltransferase, Poly-A-polymerase is an example of template independent polymerase. Terminal deoxynucleotidyl transferase also known to have template independent and template dependent activities. By function *DNA polymerase (DNA-directed DNA polymerase, DdDP) **Family A: DNA polymerase I; Pol POLG, γ, POLQ, θ, DNA polymer ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
