Identifiers | |
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ECHA InfoCard | 100.120.143 |
EC Number |
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CompTox Dashboard (EPA) | |
Properties | |
C72H42N6Na4O18RuS6 | |
Molar mass | 1664.54 g·mol−1 |
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). |
Tetrasodium tris(bathophenanthroline disulfonate)ruthenium(II) (Na4Ru(bps)3) is a sodium salt of coordination compound. In this form, it is the salt of a sulfonic acid. This compound is an extension of the phenanthroline series of coordination compounds. Ruthenium(II) tris(bathophenanthroline disulfonate), referring to the anionic fragment, is used as a protein dye in biochemistry for differentiating and detecting different proteins in laboratory settings.
In recent years, 2-D electrophoresis has been widely accepted as a standard procedure to separate complex protein mixtures in proteome studies (Proteomics). Protein visualisation by Ruthenium(II) tris(bathophenthroline disulfonate) has become a firmly established and widely used method in proteomic analysis [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] and a crucial step in gene expression profiling.
For protein detection, it is advantageous to use fluorescent labels containing chromophores which have longer excitation wavelength and emission wavelength than the aromatic amino acids. The dyes used for this important step should combine attributes like good signal to background ratio (contrast), broad linear dynamic range, broad application range, photochemical stability and compatibility to protein identification techniques, e.g. mass spectrometry (MS) or Western blotting.
Originally, the ruthenium transition metal complex, ruthenium(II) tris(4,7-diphenyl-1,10-phenanthroline disulfonate) also termed as ruthenium(II) tris(bathophentroline disulfonate) (RuBPS) was synthesized by Bannwarth [17] as a precursor molecule for a dye that was used as a non-radioactive label for oligo nucleotides. [18] Within 5 years, similar transition metal complexes had been recognized as workable protein detection reagents, [19] and shortly afterwards the europium analog of RuBPS was demonstrated as an effective fluorescent protein detection reagent. [20] The first reported use of RuBPS for protein detection appears to be the commercial release of the proprietary Sypro Ruby protein staining solution in 1999. [21] [22] While Sypro Ruby is proprietary & is not stated to have RuBPS as the major component, it is stated to have ruthenium, and Rabilloud et al. synthesized RuPBS and compared it to Sypro Ruby, finding them to be highly similar, albeit not identical, reagents for fluorescent detection of proteins in polyacrylamide gels. [21] [23] Notably, Rabilloud et al. made their comparisons against the first formulation of Sypro Ruby, the second (and presumed current) formulation of Sypro Ruby has the same product numbers (but distinct lot numbers) and an increased performance with diverse fixative solutions. [24] [25]
The fact that RuBPS is not only easy to synthesize but also easy to handle, induced further developments in this field.
Lamanda et al. improved the RuBPS staining protocol by selectively destaining the polyacrylamide matrix while the protein content remained tinctured. This new technique entailed a variety of advantages like strong signals, ameliorated signal to background ratio, better linearity and advanced baseline resolution. [25] More recently, heteroleptic ruthenium(II) complexes highly similar to RuBPS were shown to have some improved properties, specifically a broader pH range where they could be used. [26]
The isoelectric point (pI, pH(I), IEP), is the pH at which a molecule carries no net electrical charge or is electrically neutral in the statistical mean. The standard nomenclature to represent the isoelectric point is pH(I). However, pI is also used. For brevity, this article uses pI. The net charge on the molecule is affected by pH of its surrounding environment and can become more positively or negatively charged due to the gain or loss, respectively, of protons (H+).
Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body.
The western blot, or western blotting, is a widely used analytical technique in molecular biology and immunogenetics to detect specific proteins in a sample of tissue homogenate or extract. Besides detecting the proteins, this technique is also utilized to visualize, distinguish, and quantify the different proteins in a complicated protein combination.
Two-dimensional gel electrophoresis, abbreviated as 2-DE or 2-D electrophoresis, is a form of gel electrophoresis commonly used to analyze proteins. Mixtures of proteins are separated by two properties in two dimensions on 2D gels. 2-DE was first independently introduced by O'Farrell and Klose in 1975.
Protein electrophoresis is a method for analysing the proteins in a fluid or an extract. The electrophoresis may be performed with a small volume of sample in a number of alternative ways with or without a supporting medium, namely agarose or polyacrylamide. Variants of gel electrophoresis include SDS-PAGE, free-flow electrophoresis, electrofocusing, isotachophoresis, affinity electrophoresis, immunoelectrophoresis, counterelectrophoresis, and capillary electrophoresis. Each variant has many subtypes with individual advantages and limitations. Gel electrophoresis is often performed in combination with electroblotting or immunoblotting to give additional information about a specific protein.
Coomassie brilliant blue is the name of two similar triphenylmethane dyes that were developed for use in the textile industry but are now commonly used for staining proteins in analytical biochemistry. Coomassie brilliant blue G-250 differs from Coomassie brilliant blue R-250 by the addition of two methyl groups. The name "Coomassie" is a registered trademark of Imperial Chemical Industries.
In pathology, silver staining is the use of silver to selectively alter the appearance of a target in microscopy of histological sections; in temperature gradient gel electrophoresis; and in polyacrylamide gels.
Cyanines, also referred to as tetramethylindo(di)-carbocyanines are a synthetic dye family belonging to the polymethine group. Although the name derives etymologically from terms for shades of blue, the cyanine family covers the electromagnetic spectrum from near IR to UV.
QPNC-PAGE, or Quantitative Preparative Native Continuous PolyAcrylamide Gel Electrophoresis, is a bioanalytical, one-dimensional, high-resolution and high-precision technique applied in biochemistry and bioinorganic chemistry to separate proteins quantitatively by isoelectric point and by continuous elution from a gel column. This standardized variant of native gel electrophoresis and subset of preparative polyacrylamide gel electrophoresis is used by biologists to isolate macromolecules in solution, for example, active or native metalloproteins in biological samples or properly and improperly folded metal cofactor-containing proteins or protein isoforms in complex protein mixtures.
Top-down proteomics is a method of protein identification that either uses an ion trapping mass spectrometer to store an isolated protein ion for mass measurement and tandem mass spectrometry (MS/MS) analysis or other protein purification methods such as two-dimensional gel electrophoresis in conjunction with MS/MS. Top-down proteomics is capable of identifying and quantitating unique proteoforms through the analysis of intact proteins. The name is derived from the similar approach to DNA sequencing. During mass spectrometry intact proteins are typically ionized by electrospray ionization and trapped in a Fourier transform ion cyclotron resonance, quadrupole ion trap or Orbitrap mass spectrometer. Fragmentation for tandem mass spectrometry is accomplished by electron-capture dissociation or electron-transfer dissociation. Effective fractionation is critical for sample handling before mass-spectrometry-based proteomics. Proteome analysis routinely involves digesting intact proteins followed by inferred protein identification using mass spectrometry (MS). Top-down MS (non-gel) proteomics interrogates protein structure through measurement of an intact mass followed by direct ion dissociation in the gas phase.
Bottom-up proteomics is a common method to identify proteins and characterize their amino acid sequences and post-translational modifications by proteolytic digestion of proteins prior to analysis by mass spectrometry. The major alternative workflow used in proteomics is called top-down proteomics where intact proteins are purified prior to digestion and/or fragmentation either within the mass spectrometer or by 2D electrophoresis. Essentially, bottom-up proteomics is a relatively simple and reliable means of determining the protein make-up of a given sample of cells, tissues, etc.
Within chemistry for acid–base reactions, Immobilized pH gradient (IPG) gels are the acrylamide gel matrix co-polymerized with the pH gradient, which result in completely stable gradients except the most alkaline (>12) pH values. The immobilized pH gradient is obtained by the continuous change in the ratio of Immobilines. An Immobiline is a weak acid or base defined by its pK value. Immobilized pH gradients (IPG) are made by mixing two kinds of acrylamide mixture, one with Immobiline having acidic buffering property and other with basic buffering property. The concentrations of the buffers in the two solutions define the range and shape of the pH gradient produced. Both solutions contain acrylamide monomers and catalysts. During polymerization, the acrylamide portion of the buffers co polymerize with the acrylamide and bisacrylamide monomers to form a polyacrylamide gel. These polymerised gels are backed with plastic based backing that allow ease in handling and improve IPG's performance. The gel is then washed to remove catalysts and unpolymerized monomers, which interfere with isoelectric separation. IPG increased reproducibility of Isoelectric focusing and 2D-Gel Electrophoresis. Other advantages are increased resolution, reproducible separation of alkaline proteins and increased loading capacity.
An electrophoretic color marker is a chemical used to monitor the progress of agarose gel electrophoresis and polyacrylamide gel electrophoresis (PAGE) since DNA, RNA, and most proteins are colourless. The color markers are made up of a mixture of dyes that migrate through the gel matrix alongside the sample of interest. They are typically designed to have different mobilities from the sample components and to generate colored bands that can be used to assess the migration and separation of sample components.
The Proteomics Standards Initiative (PSI) is a working group of the Human Proteome Organization. It aims to define data standards for proteomics to facilitate data comparison, exchange and verification.
Affinity electrophoresis is a general name for many analytical methods used in biochemistry and biotechnology. Both qualitative and quantitative information may be obtained through affinity electrophoresis. Cross electrophoresis, the first affinity electrophoresis method, was created by Nakamura et al. Enzyme-substrate complexes have been detected using cross electrophoresis. The methods include the so-called electrophoretic mobility shift assay, charge shift electrophoresis and affinity capillary electrophoresis. The methods are based on changes in the electrophoretic pattern of molecules through biospecific interaction or complex formation. The interaction or binding of a molecule, charged or uncharged, will normally change the electrophoretic properties of a molecule. Membrane proteins may be identified by a shift in mobility induced by a charged detergent. Nucleic acids or nucleic acid fragments may be characterized by their affinity to other molecules. The methods have been used for estimation of binding constants, as for instance in lectin affinity electrophoresis or characterization of molecules with specific features like glycan content or ligand binding. For enzymes and other ligand-binding proteins, one-dimensional electrophoresis similar to counter electrophoresis or to "rocket immunoelectrophoresis", affinity electrophoresis may be used as an alternative quantification of the protein. Some of the methods are similar to affinity chromatography by use of immobilized ligands.
A gel doc, also known as a gel documentation system, gel image system or gel imager, refers to equipment widely used in molecular biology laboratories for the imaging and documentation of nucleic acid and protein suspended within polyacrylamide or agarose gels. Genetic information is stored in DNA. Polyacrylamide or agarose gel electrophoresis procedures are carried out to examine nucleic acids or proteins in order to analyze the genetic data. For protein analysis, two-dimensional gel electrophoresis is employed (2-DGE) which is one of the methods most frequently used in comparative proteomic investigations that can distinguish thousands of proteins in a single run. Proteins are separated using 2-DGE first, based on their isoelectric points (pIs) in one dimension and then based on their molecular mass in the other. After that, a thorough qualitative and quantitative analysis of the proteomes is performed using gel documentation with software image assessment methods on the 2-DGE gels stained for protein visibility. Gels are typically stained with Ethidium bromide or other nucleic acid stains such as GelGreen.
The New South Wales Systems Biology Initiative, directed by Marc Wilkins is a non-profit facility within the School of Biotechnology and Biomolecular Sciences at the University of New South Wales. Their focus is undertaking basic and applied research in the development and application of bioinformatics for genomics and proteomics.
Epicocconone is a long Stokes' shift fluorogenic natural product found in the fungus Epicoccum nigrum. Though weakly fluorescent in water it reacts covalently yet reversibly with primary amines such as those in proteins to yield a product with a strong orange-red emission (610 nm). Epicoconone is notable because it the first covalent/reversible/turn-on fluorophore to be discovered and is a natural product with a new fluorescent scaffold. It is also cell membrane permeable, unlike many other fluorophores, and subsequently can be used in in vivo applications. Additionally, this dye can be used as a sensitive total protein stain for 1D and 2D electrophoresis, quantitative determination of protein concentration, making it a powerful loading control for Western blots.
Normalization of Western blot data is an analytical step that is performed to compare the relative abundance of a specific protein across the lanes of a blot or gel under diverse experimental treatments, or across tissues or developmental stages. The overall goal of normalization is to minimize effects arising from variations in experimental errors, such as inconsistent sample preparation, unequal sample loading across gel lanes, or uneven protein transfer, which can compromise the conclusions that can be obtained from Western blot data. Currently, there are two methods for normalizing Western blot data: (i) housekeeping protein normalization and (ii) total protein normalization.
SDS-PAGE is a discontinuous electrophoretic system developed by Ulrich K. Laemmli which is commonly used as a method to separate proteins with molecular masses between 5 and 250 kDa. The combined use of sodium dodecyl sulfate and polyacrylamide gel eliminates the influence of structure and charge, and proteins are separated by differences in their size. At least up to 2012, the publication describing it was the most frequently cited paper by a single author, and the second most cited overall.
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