Mechanism
The acid converts deoxyribose to a molecule that binds with diphenylamine to form a blue substance. The reagent does not interact with RNA, so can be used to distinguish DNA from RNA. [2] [3]
The Dische test, or Dische reaction, is used to distinguish DNA from RNA. It was invented by Zacharias Dische.
Dische's diphenylamine reagent consists of diphenylamine, glacial acetic acid, sulfuric acid, and ethanol. [1]
When heated with DNA, it turns blue in the presence of DNA. A more intense blue color indicates a greater concentration of DNA.
The acid converts deoxyribose to a molecule that binds with diphenylamine to form a blue substance. The reagent does not interact with RNA, so can be used to distinguish DNA from RNA. [2] [3]
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" base pairs allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based-paired structure provides a 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 RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base-pairing patterns that identify particular regulatory regions of genes.
Methylation, in the chemical sciences, is the addition of a methyl group on a substrate, or the substitution of an atom by a methyl group. Methylation is a form of alkylation, with a methyl group replacing a hydrogen atom. These terms are commonly used in chemistry, biochemistry, soil science, and biology.
In chemistry, a reagent or analytical reagent is a substance or compound added to a system to cause a chemical reaction, or test if one occurs. The terms reactant and reagent are often used interchangeably, but reactant specifies a substance consumed in the course of a chemical reaction. Solvents, though involved in the reaction mechanism, are usually not called reactants. Similarly, catalysts are not consumed by the reaction, so they are not reactants. In biochemistry, especially in connection with enzyme-catalyzed reactions, the reactants are commonly called substrates.
Viral load, also known as viral burden, is a numerical expression of the quantity of virus in a given volume of fluid, including biological and environmental specimens. It is not to be confused with viral titre or viral titer, which depends on the assay. When an assay for measuring the infective virus particle is done, viral titre often refers to the concentration of infectious viral particles, which is different from the total viral particles. Viral load is measured using body fluids sputum and blood plasma. As an example of environmental specimens, the viral load of norovirus can be determined from run-off water on garden produce. Norovirus has not only prolonged viral shedding and has the ability to survive in the environment but a minuscule infectious dose is required to produce infection in humans: less than 100 viral particles.
A nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nucleotides. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, with its double helix, there are two possible directions for the notated sequence; of these two, the sense strand is used. Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure.
Protein sequencing is the practical process of determining the amino acid sequence of all or part of a protein or peptide. This may serve to identify the protein or characterize its post-translational modifications. Typically, partial sequencing of a protein provides sufficient information to identify it with reference to databases of protein sequences derived from the conceptual translation of genes.
RiboGreen is a proprietary fluorescent dye that is used in the detection and quantification of nucleic acids, including both RNA and DNA. It is synthesized and marketed by Molecular Probes/Invitrogen of Eugene, Oregon, United States. In its free form, RiboGreen exhibits little fluorescence and possesses a negligible absorbance signature. When bound to nucleic acids, the dye fluoresces with an intensity that, according to the manufacturer, is several orders of magnitude greater than the unbound form. The fluorescence can be detected by a sensor and the nucleic acid can be quantified. The presence of protein contaminants in the sample of nucleic acids to be tested does not make significant contributions to the absorbance, and thus allows for the addition of deoxyribonucleases to the protocol in order to degrade DNA, in the instances where one is only interested in detecting or quantifying RNA.
Dimethyl sulfate (DMS) is a chemical compound with formula (CH3O)2SO2. As the diester of methanol and sulfuric acid, its formula is often written as (CH3)2SO4 or Me2SO4, where CH3 or Me is methyl. Me2SO4 is mainly used as a methylating agent in organic synthesis.
Diphenylamine is an organic compound with the formula (C6H5)2NH. The compound is a derivative of aniline, consisting of an amine bound to two phenyl groups. The compound is a colorless solid, but commercial samples are often yellow due to oxidized impurities. Diphenylamine dissolves well in many common organic solvents, and is moderately soluble in water. It is used mainly for its antioxidant properties. Diphenylamine is widely used as an industrial antioxidant, dye mordant and reagent and is also employed in agriculture as a fungicide and antihelmintic.
A nitrate test is a chemical test used to determine the presence of nitrate ion in solution. Testing for the presence of nitrate via wet chemistry is generally difficult compared with testing for other anions, as almost all nitrates are soluble in water. In contrast, many common ions give insoluble salts, e.g. halides precipitate with silver, and sulfate precipitate with barium.
Acid guanidinium thiocyanate-phenol-chloroform extraction is a liquid–liquid extraction technique in biochemistry. It is widely used in molecular biology for isolating RNA. This method may take longer than a column-based system such as the silica-based purification, but has higher purity and the advantage of high recovery of RNA: an RNA column is typically unsuitable for purification of short RNA species, such as siRNA, miRNA, gRNA and tRNA.
Aminoallyl nucleotide is a nucleotide with a modified base containing an allylamine. They are used in post-labeling of nucleic acids by fluorescence detection in microarray. They are reactive with N-Hydroxysuccinimide ester group which helps attach a fluorescent dye to the primary amino group on the nucleotide. These nucleotides are known as 5-(3-aminoallyl)-nucleotides since the aminoallyl group is usually attached to carbon 5 of the pyrimidine ring of uracil or cytosine. The primary amine group in the aminoallyl moiety is aliphatic and thus more reactive compared to the amine groups that are directly attached to the rings (aromatic) of the bases. Common names of aminoallyl nucleosides are initially abbreviated with aa- or AA- to indicate aminoallyl. The 5-carbon sugar is indicated with or without the lowercase "d" indicating deoxyribose if included or ribose if not. Finally the nitrogenous base and number of phosphates are indicated.
New England Biolabs (NEB) is an American life sciences company which produces and supplies recombinant and native enzyme reagents for life science research. It also provides products and services supporting genome editing, synthetic biology and next-generation sequencing. NEB also provides free access to research tools such as REBASE, InBASE, and Polbase.
Nuclease S1 is an endonuclease enzyme that splits single-stranded DNA (ssDNA) and RNA into oligo- or mononucleotides. This enzyme catalyses the following chemical reaction
Bial's test is a chemical test for the presence of pentoses originally developed for the diagnosis of Pentosuria. It is named after Manfred Bial, a German physician. The components include orcinol, hydrochloric acid, and ferric chloride. A pentose, if present, will be dehydrated to form furfural which then reacts with the orcinol to generate a colored substance. The solution will turn bluish and a precipitate may form. The solution shows two absorption bands, one in the red between Fraunhofer lines B and C and the other near the D line. An estimate of the relevant wavelengths can be made by referring to the Fraunhofer lines article.
The IMViC tests are a group of individual tests used in microbiology lab testing to identify an organism in the coliform group. A coliform is a gram negative, aerobic, or facultative anaerobic rod, which produces gas from lactose within 48 hours. The presence of some coliforms indicate fecal contamination.
Experimental approaches of determining the structure of nucleic acids, such as RNA and DNA, can be largely classified into biophysical and biochemical methods. Biophysical methods use the fundamental physical properties of molecules for structure determination, including X-ray crystallography, NMR and cryo-EM. Biochemical methods exploit the chemical properties of nucleic acids using specific reagents and conditions to assay the structure of nucleic acids. Such methods may involve chemical probing with specific reagents, or rely on native or analogue chemistry. Different experimental approaches have unique merits and are suitable for different experimental purposes.
Forensic serology is the detection, identification, classification, and study of various bodily fluids such as blood, semen, saliva, and urine, and their relationship to a crime scene. A forensic serologist may also be involved in DNA analysis and bloodstain pattern analysis. Serology testing begins with presumptive tests which gives the analyst an indication that a specific bodily fluid may be present, but cannot completely confirm its presence. Following the presumptive tests, confirmatory tests are done on the same sample to confirm what the unknown substance actually is.
Optimer ligands are short synthetic oligonucleotide molecules composed of DNA or RNA that bind to a specific target molecule. They are engineered to bind their target molecules with affinity typically in the low nanomolar range. Optimers can be used as antibody mimetics in a range of applications, and have been optimized to increase their stability, reduce their molecular weight, and offer increased scalability and consistency in manufacture compared to standard aptamer molecules.
Zacharias Dische was an American biochemist of Ukrainian-Jewish origin. He worked as a biochemical researcher in Vienna before being forced by the Anschluss to become a refugee, first in France and then in the US, where he joined the faculty of Columbia University in 1943. During his time in Marseilles he made a major discovery that is little known and usually attributed to others.