|
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] |
Base Pair
A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, "Watson–Crick" (or "Watson–Crick–Franklin") base pairs (guanine–cytosine and adenine–thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The Complementarity (molecular biology), complementary nature of this based-paired structure provides a Redundancy (information theory), redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and ... [...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] |
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] |
Nucleoside
Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase (also termed a nitrogenous base) and a five-carbon sugar (ribose or 2'-deoxyribose) whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups. In a nucleoside, the anomeric carbon is linked through a glycosidic bond to the N9 of a purine or the N1 of a pyrimidine. Nucleotides are the molecular building blocks of DNA and RNA. List of nucleosides and corresponding nucleobases ''This list does not include modified nucleobases and the corresponding nucleosides'' Each chemical has a short symbol, useful when the chemical family is clear from the context, and a longer symbol, if further disambiguation is needed. For example, long nucleobase sequences in genomes are usually described by CATG symbols, not Cyt-Ade-Thy-Gua (see '' Nucleic acid sequence § Notation''). Sources Nucleosides can ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Isoquinoline
Isoquinoline is an individual chemical specimen - a heterocyclic aromatic organic compound - as well as the name of a family of many thousands of natural plant alkaloids, any one of which might be referred to as "an isoquinoline". It is a structural isomer of quinoline. Isoquinoline and quinoline are benzopyridines, which are composed of a benzene ring fused to a pyridine ring. In a broader sense, the term isoquinoline is used to make reference to isoquinoline derivatives. 1-Benzylisoquinoline is the structural backbone in many naturally occurring alkaloids such as papaverine. The isoquinoline ring in these natural compound derives from the aromatic amino acid tyrosine. Properties Isoquinoline is a colorless hygroscopic liquid at temperatures above its melting point with a penetrating, unpleasant odor. Impure samples can appear brownish, as is typical for nitrogen heterocycles. It crystallizes in form of platelets that have a low solubility in water but dissolve well in et ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrophobic Force
The hydrophobic effect is the observed tendency of nonpolar substances to aggregate in an aqueous solution and to be excluded by water#Properties, water. The word hydrophobic literally means "water-fearing", and it describes the Segregation in materials, segregation of water and nonpolar substances, which maximizes the entropy of water and minimizes the area of contact between water and nonpolar molecules. In terms of thermodynamics, the hydrophobic effect is the free energy change of water surrounding a solute. A positive free energy change of the surrounding solvent indicates hydrophobicity, whereas a negative free energy change implies hydrophilicity. The hydrophobic effect is responsible for the separation of a mixture of oil and water into its two components. It is also responsible for effects related to biology, including: cell membrane and vesicle formation, protein folding, insertion of membrane proteins into the nonpolar lipid environment and protein-small molecule asso ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 bonded to a more Electronegativity, electronegative donor atom or group (Dn), interacts with another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac). Unlike simple Dipole–dipole attraction, dipole–dipole interactions, hydrogen bonding arises from charge transfer (nB → σ*AH), Atomic orbital, orbital interactions, and quantum mechanical Delocalized electron, delocalization, making it a resonance-assisted interaction rather than a mere electrostatic attraction. The general notation for hydrogen bonding is Dn−H···Ac, where the solid line represents a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond. The most frequent donor and acceptor atoms are nitrogen (N), oxyg ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ring (chemistry)
In chemistry, a ring is an ambiguous term referring either to a simple cycle of atoms and bonds in a molecule or to a connected set of atoms and bonds in which every atom and bond is a member of a cycle (also called a ring system). A ring system that is a simple cycle is called a monocycle or simple ring, and one that is not a simple cycle is called a polycycle or polycyclic ring system. A simple ring contains the same number of sigma bonds as atoms, and a polycyclic ring system contains more sigma bonds than atoms. A molecule containing one or more rings is called a cyclic compound, and a molecule containing two or more rings (either in the same or different ring systems) is termed a polycyclic compound. A molecule containing no rings is called an acyclic or open-chain compound. Homocyclic and heterocyclic rings A homocycle or homocyclic ring is a ring in which all atoms are of the same chemical element. A heterocycle or heterocyclic ring is a ring containing atoms of at least ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleosides
Nucleosides are glycosylamines that can be thought of as nucleotides without a phosphate group. A nucleoside consists simply of a nucleobase (also termed a nitrogenous base) and a five-carbon sugar (ribose or 2'-deoxyribose) whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups. In a nucleoside, the anomeric carbon is linked through a glycosidic bond to the N9 of a purine or the N1 of a pyrimidine. Nucleotides are the molecular building blocks of DNA and RNA. List of nucleosides and corresponding nucleobases ''This list does not include Nucleobase#Modified nucleobases, modified nucleobases and the corresponding nucleosides'' Each chemical has a short symbol, useful when the chemical family is clear from the context, and a longer symbol, if further disambiguation is needed. For example, long nucleobase sequences in genomes are usually described by CATG symbols, not Cyt-Ade-Thy-Gua (see ''Nucleic acid sequence#Notation, Nucle ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Thioketones
In organic chemistry, thioketones (; also known as thiones or thiocarbonyls) are organosulfur compounds related to conventional ketones in which the oxygen has been replaced by a sulfur. Instead of a structure of , thioketones have the structure , which is reflected by the prefix "thio-" in the name of the functional group. Thus the simplest thioketone is thioacetone, the sulfur analog of acetone. Unhindered alkylthioketones typically tend to form polymers or rings. Structure and bonding The C=S bond length of thiobenzophenone is 1.63 Å, which is comparable to 1.64 Å, the C=S bond length of thioformaldehyde, measured in the gas phase. Due to steric interactions, the phenyl groups are not coplanar and the dihedral angle SC-CC is 36°. Unhindered dialkylthiones polymerize or oligomerize but thiocamphor is well characterized red solid. Consistent with the double bond rule, most alkyl thioketones are unstable with respect to dimerization.Organosulfur Chemistry I: Topics in Curr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nitrogen Heterocycles
Nitrogen is a chemical element; it has symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at seventh in total abundance in the Milky Way and the Solar System. At standard temperature and pressure, two atoms of the element bond to form N2, a colourless and odourless diatomic gas. N2 forms about 78% of Earth's atmosphere, making it the most abundant chemical species in air. Because of the volatility of nitrogen compounds, nitrogen is relatively rare in the solid parts of the Earth. It was first discovered and isolated by Scottish physician Daniel Rutherford in 1772 and independently by Carl Wilhelm Scheele and Henry Cavendish at about the same time. The name was suggested by French chemist Jean-Antoine-Claude Chaptal in 1790 when it was found that nitrogen was present in nitric acid and nitrates. Antoine Lavoisier suggested instead the nam ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
