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Diphosphates

Diphosphates are a class of organic compounds consisting of two phosphate groups linked together.
They play important roles in various biological processes, including energy metabolism, signal transduction, and the regulation of enzymatic activities.
Diphosphates can be found in a variety of natural and synthetic compounds, and they have numerous applications in research, medicine, and industry.
This MeSH term provides a comprehensive overview of the chemical structure, properties, and functions of diphosphates, helping researchers to effectively identify and utilize these important molecules in their work.

Most cited protocols related to «Diphosphates»

1
Fluorescent Probe Assay for Ferroptosis Regulators

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Publication 2014
beta-glycerol phosphate Biological Assay Buffers Cells Culture Media, Serum-Free Diphosphates Edetic Acid Fluorescein HEPES Lanugo Protease Inhibitors Proteins Serum Proteins Sodium Chloride Tablet Triton X-100
2
Molecular Dynamics Simulation of Protein-Ligand Complexes

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Publication 2016
Cuboid Bone dihydrofolate Diphosphates Electrostatics Friction glucosyltransferase D Halogens Homo sapiens Hydrogen Hydrogen Bonds inhibitors Ligands Mitogen-Activated Protein Kinase 10 NADP NADPH Dehydrogenase Oxidoreductase Pressure Proteins Sodium Chloride Staphylococcus aureus Tetrahydrofolate Dehydrogenase Thrombin Thymidine
3
Genome-wide CRISPR essential gene screen

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Publication 2016
Cell Motility Assays Chromatography, Affinity Diphosphates Gene Library Gene Regulatory Networks Genes Genes, Essential Human Body Inverse PCR Nickel spike protein, SARS-CoV-2 Strains
4
Viral Metagenomics of Oceanic Regions
Samples were collected from four oceanic regions (Figure 1). Briefly, the viral samples were concentrated on tangential flow filters (30–100-kD cutoff), distributed into 50-ml tubes and stored at 4 °C in the dark. A single sample was collected from the Sargasso Sea (labeled SAR) on 30 June 2005. Chloroform was added to this sample to stop microbial growth. Integrative samples, representing multiple sites and times, were assembled from the Gulf of Mexico (labeled GOM; 13 sites; 42 individual samples), the British Columbia coastal waters (labeled BBC; 38 sites; 85 individual samples), and the Arctic Ocean (labeled Arctic; 16 sites; 56 individual samples). These samples represent the combined viral assemblages of four oceanic regions over approximately one decade (sample details are described in Protocol S1).
Viral particles were purified using a combination of filtration and density-dependent centrifugation ([10 (link)]; http://scums.sdsu.edu/isolation.html, accessed 15 September 2006). The cesium chloride gradient was designed to recover virions with densities from 1.35 g ml−1 to 1.5 g ml−1. Viral DNA was isolated by a formamide/CTAB extraction [20 ], and the resulting DNA was amplified with Genomiphi and sequenced using pyrophosphate sequencing (454 Life Sciences, Branford, Connecticut, United States) [21 (link)] (see Protocol S1 for details on the technology). Each Genomiphi reaction started with 100–150 ng of DNA, above the 10 ng recommended by the manufacturer. A total of 181,044,179 base pairs (bp) of DNA sequence data was generated from the four libraries (SAR, 42 Mbp; GOM, 27 Mbp; BBC, 43 Mbp; and Arctic, 69 Mbp). The difference in library size was due to differences in number of successful reads during the pyrosequencing. The 1,768,297 sequences had an average length of 102 bp. The GOM, BBC, Arctic, and SAR metagenomes are deposited on the SDSU Center for Universal Microbe Sequencing website at (http://scums.sdsu.edu/phage/Oceans, accessed 15 September 2006).
Angly F.E., Felts B., Breitbart M., Salamon P., Edwards R.A., Carlson C., Chan A.M., Haynes M., Kelley S., Liu H., Mahaffy J.M., Mueller J.E., Nulton J., Olson R., Parsons R., Rayhawk S., Suttle C.A, & Rohwer F. (2006). The Marine Viromes of Four Oceanic Regions. PLoS Biology, 4(11), e368.
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Publication 2006
Bacteriophages Centrifugation cesium chloride Cetrimonium Bromide Chloroform Diphosphates DNA, Viral DNA Library Filtration formamide isolation Metagenome Virion
5
Quantifying HIV Proviral Load
Alu-HIV PCR was performed as described earlier (15 (link), 17 (link)) by use of 42 replicate reactions of a mix with gag-reverse HIV primer and Alu-forward primer as well as 42 replicates by use of only primers specific to HIV gag (HIV-only PCR). Samples were diluted to 2 or 10 μg DNA/mL and distributed in replicate PCR reactions containing 25 μL sample combined with 25 μL master mix, resulting in an equivalent of approximately 7500 cells (1 ng/μL PCR mix) or approximately 37 500 cells (5 ng/μL PCR mix) per 50 μL PCR replicate. All patient samples were run at 7500 cells/replicate PCR. We conducted the final nested qPCR in 20 μL with 10 μL of the first PCR product. This qPCR was optimized to enable robust amplification in a 1:1 dilution of PCR without PCR inhibition from pyrophosphates. We used master mixes and cycling conditions as previously described (15 (link)), and primer pairs are depicted in Supplemental Table 1, which accompanies the online version of this article at http://www.clinchem.org/content/vol60/issue6. Degenerate probes are no longer used for this assay, since they diminish robustness (unpublished data). PCR cycling was performed on an Applied Biosystems 7500 Real-Time PCR System, and Cq values were obtained by fit point analysis. Normalization to cell numbers was performed with a β-globin assay as described before (15 (link)).
De Spiegelaere W., Malatinkova E., Lynch L., Van Nieuwerburgh F., Messiaen P., O’Doherty U, & Vandekerckhove L. (2014). Quantification of Integrated HIV DNA by Repetitive-Sampling Alu-HIV PCR on the Basis of Poisson Statistics. Clinical chemistry, 60(6), 886-895.
Publication 2014
beta-Globins Biological Assay Cells Diphosphates Division, Cell DNA Replication Oligonucleotide Primers Patients Psychological Inhibition Technique, Dilution

Most recents protocols related to «Diphosphates»

1
Generation and Maintenance of Haploid Human Embryonic Stem Cells
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Example 3

We generated and analyzed a collection of 14 early-passage (passage ≤9) human pES cell lines for the persistence of haploid cells. All cell lines originated from activated oocytes displaying second polar body extrusion and a single pronucleus. We initially utilized chromosome counting by metaphase spreading and G-banding as a method for unambiguous and quantitative discovery of rare haploid nuclei. Among ten individual pES cell lines, a low proportion of haploid metaphases was found exclusively in a single cell line, pES10 (1.3%, Table 1B). We also used viable FACS with Hoechst 33342 staining, aiming to isolate cells with a DNA content corresponding to less than two chromosomal copies (2c) from four additional lines, leading to the successful enrichment of haploid cells from a second cell line, pES12 (Table 2).

Two individual haploid-enriched ES cell lines were established from both pES10 and pES12 (hereafter referred to as h-pES10 and h-pES12) within five to six rounds of 1c-cell FACS enrichment and expansion (FIG. 1C (pES10), FIG. 5A (pES12)). These cell lines were grown in standard culture conditions for over 30 passages while including cells with a normal haploid karyotype (FIG. 1D, FIG. 5B). However, since diploidization occurred at a rate of 3-9% of the cells per day (FIG. 1E), cell sorting at every three to four passages was required for maintenance and analysis of haploid cells. Further, visualization of ploidy in adherent conditions was enabled by DNA fluorescence in situ hybridization (FISH) (FIG. 1F, FIG. 5c) and quantification of centromere protein foci (FIG. 1G, FIG. 5D; FIG. 6). In addition to their intact karyotype, haploid ES cells did not harbor significant copy number variations (CNVs) relative to their unsorted diploid counterparts (FIG. 5E). Importantly, we did not observe common duplications of specific regions in the two cell lines that would result in pseudo-diploidy. Therefore, genome integrity was preserved throughout haploid-cell isolation and maintenance. As expected, single nucleotide polymorphism (SNP) array analysis demonstrated complete homozygosity of diploid pES10 and pES12 cells across all chromosomes.

Both h-pES10 and h-pES12 exhibited classical human pluripotent stem cell features, including typical colony morphology and alkaline phosphatase activity (FIG. 2A, FIG. 2B). Single haploid ES cells expressed various hallmark pluripotency markers (NANOG, OCT4, SOX2, SSEA4 and TRA1-60), as confirmed in essentially pure haploid cultures by centromere foci quantification (>95% haploids) (FIG. 2C, FIG. 7). Notably, selective flow cytometry enabled to validate the expression of two human ES-cell-specific cell surface markers (TRA-1-60 and CLDN618) in single haploid cells (FIG. 2D). Moreover, sorted haploid and diploid ES cells showed highly similar transcriptional and epigenetic signatures of pluripotency genes (FIG. 2E, FIG. 2F). Since the haploid ES cells were derived as parthenotes, they featured distinct transcriptional and epigenetic profiles of maternal imprinting, owing to the absence of paternally-inherited alleles (FIG. 8).

Haploid cells are valuable for loss-of-function genetic screening because phenotypically-selectable mutants can be identified upon disruption of a single allele. To demonstrate the applicability of this principle in haploid human ES cells, we generated a genome-wide mutant library using a piggyBac transposon gene trap system that targets transcriptionally active loci (FIG. 2G, FIG. 8E), and screened for resistance to the purine analog 6-thioguanine (6-TG). Out of six isolated and analyzed 6-TG-resistant colonies, three harbored a gene trap insertion localizing to the nucleoside diphosphate linked moiety X-type motif 5 (NUDT5) autosomal gene (FIG. 2H). NUDT5 disruption was recently confirmed to confer 6-TG resistance in human cells,51 by acting upstream to the production of 5-phospho-D-ribose-1-pyrophosphate (PRPP), which serves as a phosphoribosyl donor in the hypoxanthine phosphoribosyltransferase 1 (HPRT1)-mediated conversion of 6-TG to thioguanosine monophosphate (TGMP) (FIG. 2I). Detection of a loss-of-function phenotype due to an autosomal mutation validates that genetic screening is feasible in haploid human ES cells.

US11859232B2. Screening for chemotherapy resistance in human haploid cells (2024-01-02). YISSUM RESEARCH DEVELOPMENT COMPANY OF THE HEBREW UNIVERSITY OF JERUSALEM LTD. [IL]. Inventors: Nissim Benvenisty [IL].
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Patent 2024
Alkaline Phosphatase Alleles Cell Lines Cell Nucleus Cells Cell Separation Centromere Chromosomes Copy Number Polymorphism Diphosphates Diploid Cell Diploidy Embryonic Stem Cells Flow Cytometry Fluorescent in Situ Hybridization Genes Genes, vif Genitalia Genome Genomic Library Haploid Cell HOE 33342 Homo sapiens Homozygote Human Embryonic Stem Cells Hypoxanthine Phosphoribosyltransferase isolation Jumping Genes Karyotype Metaphase Mothers Mutation Nucleosides Oocytes Phenotype Pluripotent Stem Cells Polar Bodies POU5F1 protein, human Proteins purine Ribose Single Nucleotide Polymorphism SOX2 protein, human stage-specific embryonic antigen-4 Tissue Donors Transcription, Genetic
2
Bacterial Identification via 16S rRNA Sequencing
The streak plate technique was employed to obtain the pure culture, and then the microbial classification was carried out according to the colony morphology. 16S rRNA gene sequence was used for the identification of bacterial strains. TIANamp Bacteria DNA Kit (China, TIANGEN) was used to extract the DNA. The extracted DNA of bacteria was used as the template to carry out the polymerase chain reaction (PCR), and P0 and P6 [34 (link)] (Table 1) were used as primers to amplify the 16S rRNA gene of bacteria. The total PCR reaction mixture was 25 μ L, i.e., 10× Taq Buffer 2.5 μ L, dNTP Mixture (2.5 mmol/L) 0.5 μ L, MgCl2 1.5 μ L, primer P0 0.5 μ L, primer P6 0.5 μ L, Taq enzyme (5 U / μ L) 0.3 μ L, template (total genomic DNA) 2 μ L, sterile water 17.2 μ L. The PCR amplification conditions were as follows:
95∘C1min30s-95∘C1min30s-56∘C30s-72∘C1min30s25cycles-72∘C10min-4∘C

Primers sequence

PrimersSeqence
P05′-GAGAGTTTGATCCTGGCTCAG-3’
P65′-CTACGGCTACCT TGTTACGA-3’
The full-length sequence of 16S rRNA gene was sequenced by pyrophosphate sequencing and spliced. In the analysis and comparison of the microbial sequence, only those with 100% consistent sequence are considered to be the same microorganism. To identify the microbial species, the full-length base sequences of 16S rRNA gene were compared in the NCBI database. Researchers generally believe that the similarity of bacterial 16S rRNA below 98.7% can be considered a new bacterial species, and less than 94.50% can be considered a new bacterial genus [35 (link)].
The 16S rRNA sequences of all strains obtained were uploaded to NCBI GenBank, and the registration numbers are listed in the Supplementary Information Tables.
Zhao J., Shakir Y., Deng Y, & Zhang Y. (2023). Use of modified ichip for the cultivation of thermo-tolerant microorganisms from the hot spring. BMC Microbiology, 23, 56.
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Publication 2023
Bacteria Base Sequence Buffers Diphosphates DNA, Bacterial Enzymes Genes Genes, Bacterial Genome Magnesium Chloride Oligonucleotide Primers Polymerase Chain Reaction Ribosomal RNA Genes RNA, Ribosomal, 16S Sterility, Reproductive Strains
3
Enzymatic Synthesis of Selenium-Doped Manganese Phosphate Nanoparticles
The nanoparticles of Se-MnP were synthesized by an enzymatic reaction, using an organic phosphorylated molecules of Fructose disodium diphosphate (C6H12Na2O12P2, Na2FDP) (Sigma-Aldrich Co., US) to instead traditional phosphate salts. In a typical process in synthesis of Se-MnP, 0.66 g of Na2FDP was dissolved in 40 mL of deionized water, 0.02 g of Na2SeO3 (Sigma-Aldrich Co., US) was dissolved in 40 mL of deionized water, separately. Then, the above solutions were mixed and stirred for 5 min at 37 °C within a water bath. Thereafter, 1 mL of ALP aqueous solution (20 U/mL) was added to the mixed solution and magnetically stirred. Then, 0.19 g of MnCl2·4H2O (Aladdin Biochemical Technology Co., China) dissolved in 20 mL of water was dropwise added into the above solution. During the whole reaction process, the pH value of the reaction solution was kept between 8.0 and 8.5 by continually adding a dilute NaOH aqueous solution (0.5 M). Finally, the as-prepared samples were collected by centrifugation and washed with ethanol twice, deionized water twice, and freeze-dried into powders for further use. The MnP without Se element was used as a control sample. The synthesis procedure of the MnP sample is as follows: 0.66 g of Na2FDP was dissolved in 80 mL of deionized water and then mixed with 1 mL of ALP (20 U/mL) aqueous solution. The rest of process is same to the preparation of Se-MnP sample.
Pei M., Liu K., Qu X., Wang K., Chen Q., Zhang Y., Wang X., Wang Z., Li X., Chen F., Qin H, & Zhang Y. (2023). Enzyme-catalyzed synthesis of selenium-doped manganese phosphate for synergistic therapy of drug-resistant colorectal cancer. Journal of Nanobiotechnology, 21, 72.
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Publication 2023
Anabolism Bath Centrifugation Diphosphates Enzymes Ethanol Freezing Fructose manganese chloride Phosphates Powder Salts Selenium
4
Biochemical Analysis of Fish Muscle
The TVB-N content was assessed as described previously [27 (link)]. For this, a fish muscle fraction (10 g) was extracted with 6% perchloric acid and brought up to 50 mL. TVB-N value was determined by titration of the distillate with 10 mM HCl after steam-distillation of the acid extracts rendered alkaline to pH 13 with 20% NaOH. The resulting values were expressed as mg TVB-N·kg−1 fish muscle.
Nucleotide extracts were obtained following the method proposed by Ryder [28 (link)]. The analysis was carried out by HPLC following the procedure proposed by Aubourg et al. [29 (link)]. The K value (%) was calculated on the basis of the following molar concentration ratio, in which the concentrations of the different molecules involved in the adenosine-triphosphate degradation pathway are taken into account: K value (%) = 100 × [hypoxanthine + inosine]/[adenosine-triphosphate + adenosine-diphosphate + adenosine-monophosphate + inosine-monophosphate + inosine + hypoxanthine].
Malga J.M., Roco T., Silva A., Tabilo-Munizaga G., Pérez-Won M, & Aubourg S.P. (2023). Effect of Rigor Stage and Pressurisation on Lipid Damage, Total Volatile Amine Formation and Autolysis Development in Palm Ruff Stored on Ice. Foods, 12(4), 799.
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Publication 2023
Acids Adenosine Triphosphate adenosine triphosphate monophosphate Diphosphates Distillation Fishes High-Performance Liquid Chromatographies Hypoxanthine Inosine Inosine Monophosphate Molar Muscle Tissue Nucleotides Perchloric Acid Steam Titrimetry
5
Bile Acids, Phospholipids, and Cholesterol Analysis
For bile acid analysis [30 (link)], 1 μL of bile sample was diluted with 99 μL of Milli-Q® water and then incubated with the reagent solution (6 mg NAD, 0.5 M hydrazine hydrate buffer, 0.05 M Na-pyrophosphate) for 4 min. The mix was then incubated with the solution (0.03 M Tris-EDTA; 0.3 U/mL 3-alpha-OH steroid dehydrogenase), and the bile acid concentration was determined by spectrophotometry (excitation of 340/330 nm/emission of 440/420 nm, CLARIOstar Plus microplate reader, BMG Labtech, Ortenberg, Germany). For phospholipid (PL) analysis, 1 μL of bile sample was diluted with 49 μL of Milli-Q® water and then incubated with the reagent solution (100 mM MOPS, pH 8; 0.55 mM HVA; 20 mM CaCl2; 11 U/mL phospholipase-D; 1.66 U/mL peroxidase; 0.1% Triton X-100) for 4 min. The mix was then incubated with a start reagent (1 M MOPS, pH 8, 50 U/mL choline oxidase), and the PL concentration was determined by spectrophotometry (excitation 340/330 nm/emission 440/420 nm using a CLARIOstar Plus microplate reader, BMG Labtech, Ortenberg, Germany). For cholesterol analysis, 1 μL of bile sample was diluted with 29 μL of Milli-Q® water and then incubated with the reagent solution (100 mM MOPS, pH 8, 0.25 mM HVA; 0.1% Triton X-100) for 4 min. The mix was then incubated with a start reagent (0.1 M MOPS, pH 8, 0.06 U/mL cholesterol oxidase, 0.15 U/mL cholesterol esterase, 0.45 U/mL peroxidase, 0.06 mM taurocholate), and the cholesterol concentration was determined by spectrophotometry (excitation of 330/340 nm/emission of 420/440 nm, CLARIOstar Plus microplate reader, BMG Labtech, Ortenberg, Germany).
Mérian J., Ghezali L., Trenteseaux C., Duparc T., Beuzelin D., Bouguetoch V., Combes G., Sioufi N., Martinez L.O, & Najib S. (2023). Intermittent Fasting Resolves Dyslipidemia and Atherogenesis in Apolipoprotein E-Deficient Mice in a Diet-Dependent Manner, Irrespective of Sex. Cells, 12(4), 533.
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Publication 2023
Bile Bile Acids Buffers Cholesterol Cholesterol Oxidase choline oxidase Diphosphates Edetic Acid hydrazine hydrate morpholinopropane sulfonic acid Oxidoreductase Peroxidase Phospholipase D Phospholipids Spectrophotometry Steroids Sterol Esterase Taurocholate Triton X-100 Tromethamine

Top products related to «Diphosphates»

1
Protease inhibitor cocktail by Merck Group
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The Protease Inhibitor Cocktail is a laboratory product designed to inhibit the activity of proteases, which are enzymes that can degrade proteins. It is a combination of various chemical compounds that work to prevent the breakdown of proteins in biological samples, allowing for more accurate analysis and preservation of protein integrity.
2
Protease inhibitor cocktail by Roche
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Protease inhibitor cocktail is a laboratory reagent used to inhibit the activity of proteases, which are enzymes that break down proteins. It is commonly used in protein extraction and purification procedures to prevent protein degradation.
3
Enzchek pyrophosphate assay kit by Thermo Fisher Scientific
Sourced in Singapore, United States
The EnzChek Pyrophosphate Assay Kit is a fluorescence-based assay designed to detect and quantify the presence of pyrophosphate (PPi) in various biological samples. The kit provides the necessary reagents and protocols to measure PPi levels using a fluorescence microplate reader.
4
Protease inhibitor by Roche
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Protease inhibitors are a class of laboratory equipment used in the field of biochemistry and molecular biology. These inhibitors are designed to specifically target and inactivate proteases, which are enzymes that break down proteins. Protease inhibitors play a crucial role in various experimental and analytical procedures, such as protein extraction, purification, and stabilization.
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Complete protease inhibitor cocktail by Roche
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The Complete Protease Inhibitor Cocktail is a laboratory product designed to inhibit a broad spectrum of proteases. It is a concentrated solution containing a mixture of protease inhibitors effective against a variety of protease classes. This product is intended to be used in research applications to preserve the integrity of target proteins by preventing their degradation by proteolytic enzymes.
6
Adenosine triphosphate (atp) by Merck Group
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ATP is a laboratory instrument used to measure the presence and concentration of adenosine triphosphate (ATP) in various samples. ATP is a key molecule involved in energy transfer within living cells. The ATP product provides a reliable and accurate method for quantifying ATP levels, which is useful in applications such as microbial detection, cell viability assessment, and ATP-based assays.
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9
Cq diphosphate salt by Merck Group
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CQ diphosphate salt is a chemical compound used in various laboratory applications. It serves as a core component in specific experimental procedures, providing a functional role in the research and analysis processes. The detailed applications and intended uses of this product are not available for an unbiased, factual description.
10
Protease and phosphatase inhibitor by Roche
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Protease and phosphatase inhibitors are a class of lab equipment used to prevent the degradation of proteins and protein modifications during sample preparation and analysis. They work by inhibiting the activity of enzymes that can cleave or alter proteins, helping to preserve the integrity of the samples for further study.

More about "Diphosphates"

Diphosphates are a class of organic compounds composed of two phosphate groups linked together.
They play crucial roles in various biological processes, including energy metabolism, signal transduction, and the regulation of enzymatic activities.
Diphosphates can be found in a variety of natural and synthetic compounds, and they have numerous applications in research, medicine, and industry.
These versatile molecules, also known as pyrophosphates or bisphosphates, are structurally similar to ATP (Adenosine Triphosphate) and serve as important energy carriers and signaling molecules within cells.
They are involved in the regulation of enzyme activity, calcium homeostasis, and the formation of bone and tooth enamel.
Diphosphates can be found in a wide range of natural and synthetic compounds, such as the CQ diphosphate salt, which is used in the treatment of malaria.
They are also used in the EnzChek Pyrophosphate Assay Kit, a tool for measuring the activity of enzymes that produce or consume pyrophosphate.
In research settings, diphosphates are often used in conjunction with protease inhibitors and phosphatase inhibitors to preserve the integrity of proteins and enzymatic activities during sample preparation and analysis.
This is particularly important when working with β-actin, a ubiquitous cytoskeletal protein, and when using PVDF membranes for Western blotting.
By understanding the structure, properties, and functions of diphosphates, researchers can effectively identify and utilize these important molecules in their work, leading to advancements in fields such as biochemistry, cell biology, and pharmacology.
Ultimately, the insights gained from the study of diphosphates can contribute to the development of new therapeutic strategies and the optimization of research protocols.