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Gel electrophoresis is a method for separation and analysis of biomacromolecules and their fragments, based on their size and charge. It is used in clinical chemistry to separate proteins by charge or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge.
Southern blot is a method used in molecular biology for the detection and quantification of a specific DNA sequence in DNA samples. Southern blotting combines the transfer of electrophoresis-separated DNA fragments to a filter membrane in a process called blotting, and the subsequent fragment detection by probe hybridization.
Sodium laureth sulfate (SLES), an accepted contraction of sodium lauryl ether sulfate (SLES), also called sodium alkylethersulfate, is an anionic detergent and surfactant found in many personal care products and for industrial uses. SLES is an inexpensive and very effective foaming agent. SLES, sodium lauryl sulfate (SLS), ammonium lauryl sulfate (ALS), and sodium pareth sulfate are surfactants that are used in many cosmetic products for their cleaning and emulsifying properties. It is derived from palm kernel oil or coconut oil. In herbicides, it is used as a surfactant to improve absorption of the herbicidal chemicals and reduces time the product takes to be rainfast, when enough of the herbicidal agent will be absorbed.
Sodium dodecyl sulfate (SDS) or sodium lauryl sulfate (SLS), sometimes written sodium laurilsulfate, is an organic compound with the formula CH3(CH2)11OSO3Na. It is an anionic surfactant used in many cleaning and hygiene products. This compound is the sodium salt of the 12-carbon an organosulfate. Its hydrocarbon tail combined with a polar "headgroup" give the compound amphiphilic properties that make it useful as a detergent. SDS is also component of mixtures produced from inexpensive coconut and palm oils. SDS is a common component of many domestic cleaning, personal hygiene and cosmetic, pharmaceutical, and food products, as well as of industrial and commercial cleaning and product formulations.
Sodium hydroxide, also known as lye and caustic soda, is an inorganic compound with the formula NaOH. It is a white solid ionic compound consisting of sodium cations Na+ and hydroxide anions OH−.
Polyacrylamide gel electrophoresis (PAGE) is a technique widely used in biochemistry, forensic chemistry, genetics, molecular biology and biotechnology to separate biological macromolecules, usually proteins or nucleic acids, according to their electrophoretic mobility. Electrophoretic mobility is a function of the length, conformation, and charge of the molecule. Polyacrylamide gel electrophoresis is a powerful tool used to analyze RNA samples. When polyacrylamide gel is denatured after electrophoresis, it provides information on the sample composition of the RNA species.
Potassium hydroxide is an inorganic compound with the formula KOH, and is commonly called caustic potash.
A lysis buffer is a buffer solution used for the purpose of breaking open cells for use in molecular biology experiments that analyze the labile macromolecules of the cells. Most lysis buffers contain buffering salts and ionic salts to regulate the pH and osmolarity of the lysate. Sometimes detergents are added to break up membrane structures. For lysis buffers targeted at protein extraction, protease inhibitors are often included, and in difficult cases may be almost required. Lysis buffers can be used on both animal and plant tissue cells.
Protein purification is a series of processes intended to isolate one or a few proteins from a complex mixture, usually cells, tissues or whole organisms. Protein purification is vital for the specification of the function, structure and interactions of the protein of interest. The purification process may separate the protein and non-protein parts of the mixture, and finally separate the desired protein from all other proteins. Ideally, to study a protein of interest, it must be separated from other components of the cell so that contaminants won't interfere in the examination of the protein of interest's structure and function. Separation of one protein from all others is typically the most laborious aspect of protein purification. Separation steps usually exploit differences in protein size, physico-chemical properties, binding affinity and biological activity. The pure result may be termed protein isolate.
The first isolation of deoxyribonucleic acid (DNA) was done in 1869 by Friedrich Miescher. Currently, it is a routine procedure in molecular biology or forensic analyses. For the chemical method, many different kits are used for extraction, and selecting the correct one will save time on kit optimization and extraction procedures. PCR sensitivity detection is considered to show the variation between the commercial kits.
Immunoprecipitation (IP) is the technique of precipitating a protein antigen out of solution using an antibody that specifically binds to that particular protein. This process can be used to isolate and concentrate a particular protein from a sample containing many thousands of different proteins. Immunoprecipitation requires that the antibody be coupled to a solid substrate at some point in the procedure.
Phosphate-buffered saline (PBS) is a buffer solution commonly used in biological research. It is a water-based salt solution containing disodium hydrogen phosphate, sodium chloride and, in some formulations, potassium chloride and potassium dihydrogen phosphate. The buffer helps to maintain a constant pH. The osmolarity and ion concentrations of the solutions match those of the human body (isotonic).
A plasmid preparation is a method of DNA extraction and purification for plasmid DNA, it is an important step in many molecular biology experiments and is essential for the successful use of plasmids in research and biotechnology. Many methods have been developed to purify plasmid DNA from bacteria.
Ethanol precipitation is a method used to purify and/or concentrate RNA, DNA, and polysaccharides such as pectin and xyloglucan from aqueous solutions by adding ethanol as an antisolvent.
Buffer P2 is a lysis buffer solution produced by Qiagen. It contains 1% sodium dodecyl sulfate (SDS) (w/v) to puncture holes in cellular membranes, and 200mM NaOH. It is used in conjunction with other resuspension buffers and lysis buffers to release DNA from cells, often as part of the alkaline lysis method of purifying plasmid DNA from bacterial cell culture.
NUN buffer is a solution that makes it possible to purify proteins located in the nucleus of eukaryotic cells. Although other procedures are available they result in loss of albumin D-box binding protein (DBP) which is unwanted if nuclear signal pathways are to be investigated. Therefore, a new extraction procedure was developed in 1993 to increase recovery of nonhistone proteins using a (NUN) solution containing 0.3 M NaCl, 1 M urea, and 1% nonionic detergent Nonidet P-40, which destabilize salt bridges, hydrogen bonds, and hydrophobic interactions, respectively; resulting in a disruption of interaction between proteins and DNA. By incubating nuclei in NUN buffer and centrifuging the solution, the supernatant will therefore contain nuclear proteins.
Calcium chloride (CaCl2) transformation is a laboratory technique in prokaryotic (bacterial) cell biology. The addition of calcium chloride to a cell suspension promotes the binding of plasmid DNA to lipopolysaccharides (LPS). Positively charged calcium ions attract both the negatively charged DNA backbone and the negatively charged groups in the LPS inner core. The plasmid DNA can then pass into the cell upon heat shock, where chilled cells (+4 degrees Celsius) are heated to a higher temperature (+42 degrees Celsius) for a short time.
Spin column-based nucleic acid purification is a solid phase extraction method to quickly purify nucleic acids. This method relies on the fact that nucleic acid will bind to the solid phase of silica under certain conditions.
Radioimmunoprecipitation assay buffer is a lysis buffer used to lyse cells and tissue for the radio immunoprecipitation assay (RIPA). This buffer is more denaturing than NP-40 or Triton X-100 because it contains the ionic detergents SDS and sodium deoxycholate as active constituents and is particularly useful for disruption of nuclear membranes in the preparation of nuclear extracts. The stronger detergents in RIPA buffer cause greater protein denaturation and decrease protein-protein interactions.
Polyvalent DNA gold nanoparticles, now more commonly referred to as spherical nucleic acids, are colloidal gold particles densely modified with short, highly oriented, synthetic DNA strands. They were invented by Chad Mirkin et al. at Northwestern University in 1996. Paul Alivisatos et al. at the University of California, Berkeley introduced a related monovalent structure the same year. Due to the strong interaction between gold and thiols (-SH), the first polyvalent DNA gold nanoparticles were obtained by capping the gold nanoparticles with a dense monolayer of thiol-modified DNA. The dense packing and negative charge of the phosphate backbones of DNA orients it into solution with a footprint that is dependent on factors including the particle size and radius of curvature.
References
- ↑ {Cloninger, 2008 #100}
- Alkaline Lysis at Mama Ji's Molecular Kitchen
- Birnboim HC, Doly J (November 1979). "A rapid alkaline extraction procedure for screening recombinant plasmid DNA". Nucleic Acids Res. 7 (6): 1513–23. doi:10.1093/nar/7.6.1513. PMC 342324 . PMID 388356.
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