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Netropsin
Netropsin (also termed congocidine or sinanomycin) is a polyamide with antibiotic and antiviral activity. Netropsin was discovered by Finlay ''et al.'', and first isolated from the actinobacterium '' Streptomyces netropsis''. It belongs to the class of pyrrole-amidine antibiotics. DNA binding properties Netropsin binds to the minor groove of AT-rich sequences of double stranded DNA. In contrast, netropsin does not bind single stranded DNA or double stranded RNA. Crystallographic structures of DNA-bound Netropsin have been obtained and elucidate details of how the drug binds in the minor groove. In the bound structure, the drug makes hydrogen bonding interactions with four subsequent base pairs of the DNA duplex, locally displacing the water molecules of the spine of hydration. Using gel mobility and analytical ultracentrifugation, it was shown that Netropsin binding to DNA increases the twist per base by similar to 9˚ per molecule bound. Thus, it removes supercoils when i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Netropsin DNA Bound
Netropsin (also termed congocidine or sinanomycin) is a polyamide with antibiotic and antiviral activity. Netropsin was discovered by Finlay ''et al.'', and first isolated from the actinobacterium ''Streptomyces netropsis''. It belongs to the class of pyrrole-amidine antibiotics. DNA binding properties Netropsin binds to the minor groove of AT-rich sequences of double stranded DNA. In contrast, netropsin does not bind single stranded DNA or double stranded RNA. Crystallographic structures of DNA-bound Netropsin have been obtained and elucidate details of how the drug binds in the minor groove. In the bound structure, the drug makes hydrogen bonding interactions with four subsequent base pairs of the DNA duplex, locally displacing the water molecules of the spine of hydration. Using gel mobility and analytical ultracentrifugation, it was shown that Netropsin binding to DNA increases the twist per base by similar to 9˚ per molecule bound. Thus, it removes supercoils when ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hoechst 33258
Hoechst stains are part of a family of blue fluorescent dyes used to stain DNA. These bis-benzimides were originally developed by Hoechst AG, which numbered all their compounds so that the dye Hoechst 33342 is the 33,342nd compound made by the company. There are three related Hoechst stains: Hoechst 33258, Hoechst 33342, and Hoechst 34580. The dyes Hoechst 33258 and Hoechst 33342 are the ones most commonly used and they have similar excitation– emission spectra. Molecular characteristics Both dyes are excited by ultraviolet light at around 350 nm, and both emit blue-cyan fluorescent light around an emission spectrum maximum at 461 nm. Unbound dye has its maximum fluorescence emission in the 510–540 nm range. Hoechst stains can be excited with a xenon- or mercury-arc lamp or with an ultraviolet laser. There is a considerable Stokes shift between the excitation and emission spectra that makes Hoechst dyes useful in experiments in which multiple fluorophores ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pentamidine
Pentamidine is an antimicrobial medication used to treat African trypanosomiasis, leishmaniasis, '' Balamuthia'' infections, babesiosis, and to prevent and treat pneumocystis pneumonia (PCP) in people with poor immune function. In African trypanosomiasis it is used for early disease before central nervous system involvement, as a second line option to suramin. It is an option for both visceral leishmaniasis and cutaneous leishmaniasis. Pentamidine can be given by injection into a vein or muscle or by inhalation. Common side effects of the injectable form include low blood sugar, pain at the site of injection, nausea, vomiting, low blood pressure, and kidney problems. Common side effects of the inhaled form include wheezing, cough, and nausea. It is unclear if doses should be changed in those with kidney or liver problems. Pentamidine is not recommended in early pregnancy but may be used in later pregnancy. Its safety during breastfeeding is unclear. Pentamidine is in the aro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DAPI
DAPI (pronounced 'DAPPY', /ˈdæpiː/), or 4′,6-diamidino-2-phenylindole, is a fluorescent stain that binds strongly to adenine–thymine-rich regions in DNA. It is used extensively in fluorescence microscopy. As DAPI can pass through an intact cell membrane, it can be used to stain both live and fixed cells, though it passes through the membrane less efficiently in live cells and therefore provides a marker for membrane viability. History DAPI was first synthesised in 1971 in the laboratory of Otto Dann as part of a search for drugs to treat trypanosomiasis. Although it was unsuccessful as a drug, further investigation indicated it bound strongly to DNA and became more fluorescent when bound. This led to its use in identifying mitochondrial DNA in ultracentrifugation in 1975, the first recorded use of DAPI as a fluorescent DNA stain. Strong fluorescence when bound to DNA led to the rapid adoption of DAPI for fluorescent staining of DNA for fluorescence microscopy. Its use ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sigma-Aldrich
Sigma-Aldrich (formally MilliporeSigma) is an American chemical, life science, and biotechnology company that is owned by the German chemical conglomerate Merck Group. Sigma-Aldrich was created in 1975 by the merger of Sigma Chemical Company and Aldrich Chemical Company. It grew through various acquisitions until it had over 9,600 employees and was listed on the Fortune 1000. The company is headquartered in St. Louis and has operations in approximately 40 countries. In 2015, the German chemical conglomerate Merck Group acquired Sigma-Aldrich for $17 billion. The company is currently a part of Merck's life science business and in combination with Merck's earlier acquired Millipore Corporation, Millipore, operates as MilliporeSigma. History Sigma Chemical Company of St. Louis and Aldrich Chemical Company of Milwaukee were both American specialty chemical companies when they merged in August 1975. The company grew throughout the 1980s and 1990s, with significant expansion in fac ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Antibiotics
An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting bacterial infections, and antibiotic medications are widely used in the treatment and prevention of such infections. They may either kill or inhibit the growth of bacteria. A limited number of antibiotics also possess antiprotozoal activity. Antibiotics are not effective against viruses such as the common cold or influenza; drugs which inhibit viruses are termed antiviral drugs or antivirals rather than antibiotics. Sometimes, the term ''antibiotic''—literally "opposing life", from the Greek roots ἀντι ''anti'', "against" and βίος ''bios'', "life"—is broadly used to refer to any substance used against microbes, but in the usual medical usage, antibiotics (such as penicillin) are those produced naturally (by one microorganism fighting another), whereas non-antibiotic antibacterials (such as sulfonamides and antisep ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Guanidines
Guanidine is the compound with the formula HNC(NH2)2. It is a colourless solid that dissolves in polar solvents. It is a strong base that is used in the production of plastics and explosives. It is found in urine predominantly in patients experiencing renal failure. A guanidine moiety also appears in larger organic molecules, including on the side chain of arginine. Structure Guanidine can be thought of as a nitrogenous analogue of carbonic acid. That is, the C=O group in carbonic acid is replaced by a C=NH group, and each OH is replaced by a group. Isobutene can be seen as the carbon analogue in much the same way. A detailed crystallographic analysis of guanidine was elucidated 148 years after its first synthesis, despite the simplicity of the molecule. In 2013, the positions of the hydrogen atoms and their displacement parameters were accurately determined using single-crystal neutron diffraction. Production Guanidine can be obtained from natural sources, being first isolat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amidines
Amidines are organic compounds with the functional group RC(NR)NR2, where the R groups can be the same or different. They are the imine derivatives of amides (RC(O)NR2). The simplest amidine is formamidine, HC(=NH)NH2. Examples of amidines include: * DBU * diminazene * benzamidine * Pentamidine * Paranyline Preparation A common route to primary amidines is the Pinner reaction. Reaction of the nitrile with alcohol in the presence of acid gives an iminoether. Treatment of the resulting compound with ammonia then completes the conversion to the amidine. Instead of using a Bronsted acid, Lewis acids such as aluminium trichloride promote the direct amination of nitriles. They are also generated by amination of an imidoyl chloride. They are also prepared by the addition of organolithium reagents to diimines, followed by protonation or alkylation. Dimethylformamide acetal reacts with primary amines to give amidines: :Me2NC(H)(OMe)2 + RNH2 → Me2NC=NHR + 2 MeOH Properties and appl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Comparison Of Nucleic Acid Simulation Software
This is a list of notable computer programs that are used for nucleic acids simulations. See also References Computational chemistry software Software comparisons Molecular dynamics software Molecular modelling software {{science-software-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Single-strand Binding Protein
Single-strand DNA-binding protein (SSB) is a protein found in ''Escherichia coli'' (''E. coli'') bacteria, that binds to single-stranded regions of deoxyribonucleic acid ( DNA). Single-stranded DNA is produced during all aspects of DNA metabolism: replication, recombination, and repair. As well as stabilizing this single-stranded DNA, SSB proteins bind to and modulate the function of numerous proteins involved in all of these processes. Active ''E. coli'' SSB is composed of four identical 19 kDa subunits. Binding of single-stranded DNA to the tetramer can occur in different "modes", with SSB occupying different numbers of DNA bases depending on a number of factors, including salt concentration. For example, the (SSB)65 binding mode, in which approximately 65 nucleotides of DNA wrap around the SSB tetramer and contact all four of its subunits, is favoured at high salt concentrations ''in vitro''. At lower salt concentrations, the (SSB)35 binding mode, in which about 35 nucleotides ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA-binding Protein
DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair. However, there are some known minor groove DNA-binding ligands such as netropsin, distamycin, Hoechst 33258, pentamidine, DAPI and others. Examples DNA-binding proteins include transcription factors which modulate the process of transcription, various polymerases, nucleases which cleave DNA molecules, and histones which are involved in chromosome packaging and transcription in the cell nucleus. DNA-binding proteins can incorporate such domains as the zinc finger, the helix-turn-helix, and the leucine zipper (among many others) that facilitate binding to nucleic acid. There are also more unusual examples such as transcription activator like effectors. Non-specific DNA-pr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lexitropsin
Lexitropsins are members of a family of semi-synthetic DNA-binding ligands. They are structural analogs of the natural antibiotics netropsin and distamycin. Antibiotics of this group can bind in the minor groove of DNA with different sequence-selectivity. Lexitropsins form a complexes with DNA with stoichiometry 1:1 and 2:1. Based on the 2:1 complexes were obtained ligands with high sequence-selectivity. See also * Hoechst 33258 * Pentamidine * DNA binding ligand * Single-strand binding protein * Comparison of nucleic acid simulation software This is a list of notable computer programs that are used for nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a ... References {{Reflist Molecular biology DNA-binding substances ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
