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Benzonase

Benzonase is a highly efficient endonuclease enzyme that cleaves DNA and RNA, making it a valuable tool in molecular biology and biochemistry research.
This enzyme is commonly used to degrade nucleic acids in samples, facilitating protein purification and other experimental procedures.
Benzonase's ability to rapidly and thoroughly digest nucleic acids has made it indispensable for a wide range of applications, including cell lysis, sample clarification, and nucleic acid removal.
Researchers can leverage the power of PubCompare.ai to optimize their Benzonase experiments, effortlessy locating relevant protocols from the literature and comparing methods to identify the most effective and reproducible approachs.
By enhancing reproducibility and accuracy, PubCompare.ai helps take Benzonase research to new hieghts, one step at a time.

Most cited protocols related to «Benzonase»

Automated GFP-tagged Protein Purification

Cell pellets were thawed on ice and incubated for 30 min at room temperature in 1 ml lysis buffer containing 150 mM NaCl, 50 mM Tris, pH 7.5, 5% glycerol, 1% IGEPAL-CA-630, 1 mM MgCl₂, 200 U benzonase (Merck), and EDTA-free complete protease inhibitor cocktail (Roche). When studying phospho-dependent interactions, phosphatase inhibitors (Roche) were added as well. Lysates were cleared by centrifugation at 4,000 g and 4°C for 15 min to remove remaining membrane and DNA, and the supernatant was incubated with 50 µl magnetic beads coupled to monoclonal mouse anti-GFP antibody (Miltenyi Biotec) for 15 min on ice. Because of the extremely small size of the beads (50 nm), they are nonsedimenting and show fast reaction kinetics. Magnetic columns were equilibrated using 250 µl lysis buffer. Cell lysates were added to the column after incubation and washed three times with 800 µl ice-cold wash buffer I containing 150 mM NaCl, 50 mM Tris, pH 7.5, 5% glycerol, and 0.05% IGEPAL-CA-630, and two times with 500 µl of wash buffer II containing 150 mM NaCl, 50 mM Tris, pH 7.5, and 5% glycerol. Purified proteins were predigested by adding 25 µl 2 M urea in 50 mM Tris, pH 7.5, 1 mM DTT, and 150 ng EndoLysC (Wako Chemicals USA, Inc.) for SILAC experiments or 150 ng trypsin (Promega) for label-free experiments. After in-column digestion for 30 min at room temperature, proteins were eluted by adding two times 50 µl 2 M urea in 50 mM Tris, pH 7.5, and 5 mM chloroacetamide. In SILAC experiments, heavy and light eluates of transgenic cell line and the corresponding WT cell line were combined immediately after elution from the columns. Proteins were digested overnight at room temperature. The digestion was stopped by adding 1 µl trifluoroacetic acid, and peptides of each experiment were split and purified on two C18 Stage Tips and stored at 4°C (Rappsilber et al., 2007 (link)).
Pull-downs can be performed manually on a hand magnet. In our laboratory, pull-downs were performed on the automated liquid-handling platform (Freedom EVO 200; Tecan) in a fully automated manner.

Hubner N.C., Bird A.W., Cox J., Splettstoesser B., Bandilla P., Poser I., Hyman A, & Mann M. (2010). Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. The Journal of Cell Biology, 189(4), 739-754.

Publication 2010

Animals, Transgenic Antibodies, Anti-Idiotypic Benzonase Buffers Cell Lines Cells Centrifugation chloroacetamide Cold Temperature Digestion Edetic Acid Glycerin Igepal CA-630 inhibitors Kinetics Lanugo Magnesium Chloride Mice, Laboratory Pellets, Drug Peptides Phosphoric Monoester Hydrolases Promega Protease Inhibitors Proteins Sodium Chloride Tissue, Membrane TNFSF14 protein, human Trifluoroacetic Acid Tromethamine Trypsin Urea

Isolation and Analysis of Protein Aggregates

50 OD₆₀₀ units of logarithmically growing cells in YPD medium were harvested, and cell pellets were frozen in liquid N₂. For preparation of cell lysates, the pellets were resuspended in lysis buffer (20 mM Na-phosphate, pH 6.8, 10 mM DTT, 1 mM EDTA, 0.1% Tween, 1 mM PMSF, protease inhibitor cocktail [Roche], 3 mg/ml zymolyase T20, and 1.25 U/ml benzonase) and incubated at room temperature for 20 min. Chilled samples were treated by tip sonication (Branson; eight times at level 4 and duty cycle 50%) and centrifuged for 20 min at 200 g at 4°C. Supernatants were adjusted to identical protein concentrations, and aggregated proteins were pelleted at 16,000 g for 20 min at 4°C. After removing supernatants, aggregated proteins were washed twice with 2% NP-40 (in 20 mM Na-phosphate, pH 6.8, 1 mM PMSF, and protease inhibitor cocktail), sonicated (six times at level 4 and duty cycle 50%), and centrifuged at 16,000 g for 20 min at 4°C. Aggregated proteins were washed in NP-40–deficient buffer (sonication, four times at level 2 and duty cycle 65%), boiled in SDS sample buffer, separated by SDS-PAGE (14%), and analyzed by Coomassie staining. Experiments were performed at least three times with similar results. Identification of isolated aggregates by mass spectrometry was performed according to previously described protocols (Kramer et al., 2002 (link); Wegrzyn et al., 2006 (link)). For significant protein identification, a score threshold of 200 was chosen.
For radioactive labeling of newly synthesized proteins, cells were starved for 1 h in methionine-free SC medium. The cells were labeled with 20 µCi/ml [³⁵S]methionine for 1 min, chilled quickly, and treated with 300 µg/ml cycloheximide to stop protein translation. ³⁵S-labeled aggregates were isolated, separated via SDS-PAGE, and visualized by autoradiography in FLA-9000 (Fujifilm).

Koplin A., Preissler S., Ilina Y., Koch M., Scior A., Erhardt M, & Deuerling E. (2010). A dual function for chaperones SSB–RAC and the NAC nascent polypeptide–associated complex on ribosomes. The Journal of Cell Biology, 189(1), 57-68.

Publication 2010

Autoradiography Benzonase Buffers Cells Cycloheximide Edetic Acid Freezing Mass Spectrometry Methionine Nonidet P-40 Pellets, Drug Phosphates Protease Inhibitors Protein Biosynthesis Proteins Radioactivity SDS-PAGE Tweens zymolyase

Isolation and Characterization of RNA-DNA Hybrids

Non-crosslinked HeLa cells were lysed in 85 mM KCl, 5 mM PIPES (pH 8.0), and 0.5% NP-40 for 10 min on ice. Pelleted nuclei were resuspended in RSB buffer (10 mM Tris-HCl pH 7.5, 200 mM NaCl, 2.5 mM MgCl2) with 0.2% sodium deoxycholate [NaDOC], 0.1% SDS, 0.05% sodium lauroyl sarcosinate [Na sarkosyl] and 0.5% Triton X-100, and extracts were sonicated for 10 min (Diagenode Bioruptor). Extracts were then diluted 1:4 in RSB with 0.5% Triton X-100 (RSB + T) and subjected to IP with the S9.6 antibody, bound to protein A dynabeads (Invitrogen), and preblocked with 0.5% BSA/PBS for 2 hr. CBP80 and IgG2a antibodies were used as control. RNase A (PureLink, Invitrogen) was added during IP at 0.1 ng RNase A per microgram genomic DNA. Beads were washed 4x with RSB + T; 2x with RSB; and eluted either in 2x LDS (Invitrogen), 100 mM DTT for 10 min at 70°C (for SDS-PAGE), or 1% SDS and 0.1 M NaHCO₃ for 30 min at room temperature (for RNA/DNA hybrid slot blot). Where indicated, nuclear extracts were treated with 1 U/μL benzonase (Sigma) for 30 min at 37°C before IP. Sequences and preparation of double-stranded competitors were described by Phillips et al. (2013) (link) and Rigby et al. (2014 (link)). For MS analysis, eluted samples were processed by filter-aided sample preparation (FASP) with trypsin (Wiśniewski et al., 2009 (link)). Table S1 provides the list of proteins that make up the RNA/DNA interactome.

Cristini A., Groh M., Kristiansen M.S, & Gromak N. (2018). RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage. Cell Reports, 23(6), 1891-1905.

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Publication 2018

Antibodies Benzonase Bicarbonate, Sodium Buffers Cell Nucleus Deoxycholic Acid, Monosodium Salt Genome HeLa Cells Hybrids IgG2A Immunoglobulins Magnesium Chloride Nonidet P-40 piperazine-N,N'-bis(2-ethanesulfonic acid) Proteins Ribonucleases SDS-PAGE Sodium Chloride sodium lauroyl sarcosinate Staphylococcal Protein A Triton X-100 Tromethamine Trypsin

Drosophila Embryo Lysis and Shearing

In all experiments involving the use of yeast, lysis was performed using a mechanical bead
beating procedure in 1% SDS-containing buffer. In all HeLa, mESC, and NP experiments, lysis
was performed using 1% SDS-containing buffer with Benzonase treatment to shear chromatin.
Details of yeast, HeLa, mESC, and NP lysis, reduction, and alkylation protocols are given in the
Supplementary Information.
Drosophila embryos were lysed using a solution-based procedure with sonication.
Single embryos in PCR tubes were re-suspended in 20 μl of lysis buffer containing
20 μg of SP3 beads. Lysis buffer was composed of 1% SDS (Bio-Rad), 1×
cOmplete Protease Inhibitor Cocktail-EDTA (Roche), 5 mM EDTA, 5 mM EGTA, 10 mM
NaOH, and 10 mM DTT, in 10 mM HEPES buffer at pH 8.5 (Sigma). The lysis solution was
combined with 20 μl of neat trifluoroethanol (Sigma) and sonicated for 15 min
in a Bioruptor (Diagenode) for 10 cycles (30 s on, 30 s off) on the setting
‘high’. The Bioruptor was operated in the absence of active cooling to allow the water
bath to heat and facilitate lysis and shearing of chromatin. To neutralize the lysis solution,
0.75 μl of 0.1% formic acid was added. Samples were then heated at 95°C
for 5 min and placed on ice before proceeding with reduction and alkylation steps. (Details
of reduction and alkylation can be found in the Supplementary Information.)

Hughes C.S., Foehr S., Garfield D.A., Furlong E.E., Steinmetz L.M, & Krijgsveld J. (2014). Ultrasensitive proteome analysis using paramagnetic bead technology. Molecular Systems Biology, 10(10), 1-10.

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Publication 2014

Alkylation Benzonase Buffers Chromatin Drosophila Edetic Acid Egtazic Acid Embryo formic acid HeLa Cells HEPES Mouse Embryonic Stem Cells Protease Inhibitors Trifluoroethanol Yeast, Dried

Recombinant AAV Production and Purification

Recombinant AAVs were generated by triple transfection of 293T cells (ATCC) using polyethylenimine (PEI)⁴⁶. Viral particles were harvested from the media at 72 hrs post transfection and from the cells and media at 120 hrs. Cell pellets were resuspended in 10mM Tris with 2mM MgCl₂, pH 8, freeze-thawed three times, and treated with 100 U/mL Benzonase (Epicentre) at 37°C for at least 1 hr. Viral media was concentrated by precipitation with 8% polyethylene glycol 8000 (Sigma-Aldrich) with 500 mM sodium chloride^{47 (link)}, resuspended in Tris-MgCl₂, and then added to the lysates. The combined stocks were then adjusted to 500 mM NaCl, incubated at 37°C for 30 minutes, and clarified by centrifugation at 2000 × g. The clarified stocks were then purified over iodixanol (Optiprep, Sigma; D1556) step gradients (15%, 25%, 40% and 60%)^{48 (link)}. Viruses were concentrated and formulated in phosphate buffered saline (PBS). Virus titers were determined by measuring the number of DNaseI-resistant vg using qPCR with linearized genome plasmid as a standard⁴⁶.
For capsid library virus generation, two modifications were made to the above virus production protocol to reduce the production of mosaic capsids that could arise from the presence of multiple capsid sequences in the same cell. First, only 10 ng of the rAAV-Cap-in-cis library plasmid was transfected (per 150 mm dish) to increase the likelihood that most transfected cells only received one capsid variant sequence. Second, the virus was collected at 48 hrs (media) and 60 hrs (cells and media), rather than at 72 hrs and 120 hrs as described above, to minimize the secondary transduction of producer cells with rAAV library virus released into the medium.

Deverman B.E., Pravdo P.L., Simpson B.P., Kumar S.R., Chan K.Y., Banerjee A., Wu W.L., Yang B., Huber N., Pasca S.P, & Gradinaru V. (2016). Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain. Nature biotechnology, 34(2), 204-209.

Publication 2015

Benzonase Capsid Capsid Proteins Centrifugation DNA Library Freezing Genome HEK293 Cells Hyperostosis, Diffuse Idiopathic Skeletal iodixanol Magnesium Chloride Pellets, Drug Phosphates Plasmids polyethylene glycol 8000 Polyethyleneimine Saline Solution Sodium Sodium Chloride Transfection Tromethamine Virion Virus

Most recents protocols related to «Benzonase»

Intracellular Staining and Mass Cytometry of Cryopreserved Splenocytes

For intracellular staining, short-term reactivation of cryopreserved splenocytes and subsequent mass cytometry analysis were performed as described previously^{94 (link)}. In short, cells were kept at −80 °C for less than 2 months before thawing in a 37 °C water bath. Cells were then immediately resuspended in cell culture medium supplemented with 1:10,000 benzonase (Sigma-Aldrich), and centrifuged at 300 g for 7 min at 24 °C. Samples were then left overnight at 37 °C before restimulation with 50 ng/mL phorbol 12-myristate 13-acetate (Sigma-Aldrich) and 500 ng/mL ionomycin (Sigma-Aldrich) in the presence of 1× brefeldin A (BD Biosciences) and 1× monensin (Biolegend) for 4 h at 37 °C. For splenocytes, one anchor sample to correct batch effect among different acquisitions and one non-stimulated control sample were also included. For both PBMCs and reactivated cryopreserved splenocytes, surface staining was performed for 30 min at 4 °C. To identify dead cells, 2.5 μM cisplatin (Sigma-Aldrich) was added for 5 min on ice. To minimize technical variability, an equal number of cells from each sample were barcoded using Cell-ID 20-Plex (Fluidigm). Cells from all samples were then combined in one single tube. The combined sample was then processed for Live/Dead and surface staining. For intracellular cytokine staining of reactivated cryopreserved splenocytes, after surface staining, cells were fixed and permeabilized with FOXP3 staining kit (Invitrogen) and stained for intracellular markers and cytokines. The antibodies used are reported in Supplementary Table 2. Because CD4 molecules are internalized during phorbol 12-myristate 13-acetate/ionomycin stimulation^{95 (link)}, the anti-CD4 antibody was used in both the surface staining and the intracellular staining steps. After washing, the combined sample was incubated with 4% PFA overnight at 4 °C. Prior to acquisition in a Helios™ II CyTOF® system, samples were washed with cell staining buffer and mass cytometry grade water. Multidimensional datasets were analyzed using FlowJo and R (R Core Team, 2017).

Suzzi S., Croese T., Ravid A., Gold O., Clark A.R., Medina S., Kitsberg D., Adam M., Vernon K.A., Kohnert E., Shapira I., Malitsky S., Itkin M., Brandis A., Mehlman T., Salame T.M., Colaiuta S.P., Cahalon L., Slyper M., Greka A., Habib N, & Schwartz M. (2023). N-acetylneuraminic acid links immune exhaustion and accelerated memory deficit in diet-induced obese Alzheimer’s disease mouse model. Nature Communications, 14, 1293.

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Publication 2023

Antibodies Antibodies, Anti-Idiotypic Bath Benzonase Brefeldin A Buffers CD4 Antigens Cell Culture Techniques Cells Cisplatin Culture Media Cytokine Ionomycin Monensin Protoplasm Tetradecanoylphorbol Acetate

Western Blotting of Testis Lysates

Testes were lysed in RIPA buffer (Pierce) plus HALT protease inhibitor (Thermo Fisher Scientific), homogenized with an electronic pestle for 1 min, incubated at 4°C with agitation for 30 min, sonicated for 3 × 30 s, and then clarified at 14,000 × g at 4°C for 20 min. RPE lysates were collected in 2× SDS–polyacrylamide gel electrophoresis (PAGE) buffer and treated with benzonase nuclease (Millipore-Sigma) for 5 min. Samples were loaded into NuPAGE precast gels, transferred onto polyvinylidene fluoride (PVDF) membrane (Amersham Hybond P, Cytiva), and then rinsed in water then TBST, and then blocked in 5% milk in TBS plus 0.1% Tween. Membranes were then incubated overnight at 4°C in primary antibodies (Supplementary file 3) diluted in 5% milk TBST. Membranes were then washed 3 × 10 min TBST, incubated in Horse Radish Peroxidase (HRP)-conjugated secondary antibodies detailed in Supplementary file 4 for 1 hr at room temperature and developed using Pierce SuperSignal Pico Plus (Pierce) or ECL (GE Healthcare) reagent and imaged on ImageQuant.

Hall E.A., Kumar D., Prosser S.L., Yeyati P.L., Herranz-Pérez V., García-Verdugo J.M., Rose L., McKie L., Dodd D.O., Tennant P.A., Megaw R., Murphy L.C., Ferreira M.F., Grimes G., Williams L., Quidwai T., Pelletier L., Reiter J.F, & Mill P. (2023). Centriolar satellites expedite mother centriole remodeling to promote ciliogenesis. eLife, 12, e79299.

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Publication 2023

Antibodies Benzonase Buffers Gels Horseradish Peroxidase Milk, Cow's polyvinylidene fluoride Protease Inhibitors Radioimmunoprecipitation Assay SDS-PAGE Testis Tissue, Membrane Tweens

Glycoproteome Profiling in MCF7 Cells

MCF7 cells (from the American Type Culture Collection, ATCC) were
grown in DMEM medium (Sigma-Aldrich) containing 10% fetal bovine serum
(FBS, Thermo) at 37 °C with 5.0% CO₂ in a humidified
incubator. When the confluency reached 80%, the medium was replaced
using a heavy lysine (K8) and arginine (R6) containing medium, and
250 μM N-azidoacetylgalactosamine-tetraacetylated
(Ac₄GalNAz, Click Chemistry Tools) and 50 μM puromycin
(Puro, Santa Cruz Biotechnology) were added to the medium. For the
control samples, Puro was not added. Then, cells were treated for
1 h. For the boosting sample, cells were cultured in the medium containing
heavy lysine and arginine for 2 weeks for complete labeling of proteins
with heavy K and R in the cells. Then the cells were treated with
250 μM Ac₄GalNAz for 48 h to label O-GlcNAcylated proteins.
Cells from different samples were harvested
and washed with ice-cold PBS twice. They were lysed with a buffer
containing 50 mM HEPES, pH = 7.4, 150 mM NaCl, 0.5% SDC, 0.1% SDS,
1% NP-40, 50 μM Thiamet G, 50 units/mL Benzonase nuclease (Millipore),
and 1 tablet/10 mL EDTA-free protease inhibitor for 2 h at 4 °C.
Then the lysates were centrifuged for 10 min at 4696g, and the debris was discarded. The labeled glycopeptides or glycoproteins
were reacted with a biotin probe through a click chemistry reaction.
In the cell lysate, 250 μM photocleavable (PC) biotin-alkyne
(Click Chemistry Tools), 1 mM CuSO₄, 5 mM Tris(3-hydroxypropyltriazolylmethyl)
amine (THPTA, Click Chemistry Tools), 5% dimethyl sulfoxide (DMSO),
15 mM sodium l-ascorbate (Sigma), and 15 mM aminoguanidine
hydrochloride (Sigma) were added, and the reaction lasted for 2 h
at room temperature.

Xu S., Yin K, & Wu R. (2023). Combining Selective Enrichment and a Boosting Approach to Globally and Site-Specifically Characterize Protein Co-translational O-GlcNAcylation. Analytical Chemistry, 95(9), 4371-4380.

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Publication 2023

Alkynes Amines Arginine Benzonase Biotin Cells Cold Temperature Culture Media Edetic Acid Glycopeptides HEPES Lysine MCF-7 Cells Nonidet P-40 Proteins Puromycin SERPINA1 protein, human Sodium Ascorbate Sodium Chloride Somatostatin-Secreting Cells Sulfoxide, Dimethyl Tablet thiamet G Tromethamine

Liver Proteomics: iTRAQ Labeling and Mass Spectrometry

iTRAQ labeling with two 8-plex iTRAQ kits was performed in the Proteomic facility of the Institute of Biomedicine of Seville using their standard protocols. Individual liver samples were isolated in urea lysis buffer (8 M urea, 25 mM Tris, 100 mM NaCl, 25 mM NaF, 10 mM Na₄P₂O₇, 50 mM β-glycerophospate, 1 mM Na₃VO₄, 1:100 protease inhibitors, and 1:100 deacetylase inhibitors, pH 8). Samples were sonicated for 10 s and centrifuged at 20,000 × g for 15 min at 4 °C. The supernatant was harvested and stored at −80 °C. Then, samples were reduced with 50 mM tris-(2-carboxyethyl)phosphine (AB Sciex) at 60 °C for 1 h with shaking and were subsequently alkylated using 200 mM S-methyl methanethiosulfonate (AB Sciex) for 30 min at room temperature. Samples were then trypsinized at 37 °C in a 10:1 ratio (w/w) of substrate/enzyme in a water bath overnight (Promega). Then, samples were speed-vac dried. The iTRAQ-labeling assay was conducted according to the manufacturer’s instructions (iTRAQ 8-plex, AB Sciex). Briefly, peptides were reconstituted in 1 M triethylammonium bicarbonate (Sigma-Aldrich St. Louis, MO, USA), 0.05% SDS, 1:100 phosphatase inhibitor cocktail, 1:100 protease inhibitor cocktail, and 0.002% benzonase (Novagen, Argentina) and labeled with one isobaric amine-reactive tag. After 2 h of incubation, labeled samples were pooled, dried at 45 °C, and stored overnight at 4 °C. iTRAQ-labeled samples were desalted using Oasis HLB C18 cartridges (Waters, Milford, MA, USA) and dried using a vacuum centrifuge. Peptides were then prefractionated using MCX Oasis columns (Waters) and increasing concentrations (50–2000 mM) of ammonium formate. Fractions were collected, individually washed using C18 cartridges, and dried. Peptides from each fraction were separated using nano-liquid chromatography (nano LC 1000, Thermo Scientific) and analyzed by means of nano-electrospray ionization (Proxeon Biosystems, Odense, Denmark) connected to a Q Exactive Plus Orbitrap mass spectrometer (Thermo Scientific). Briefly, 13 µl of each fraction was loaded, preconcentrated, and washed in an Acclaim PepMap (75 µm × 2 cm, nanoViper, C18, 3 µm, 100 Å) precolumn (Thermo Scientific). Peptides were separated in an analytical column (75 µm × 15 cm, nanoViper, C18, 2 µm, 100 Å, Acclaim PepMap RSLC) for 240 min at 200 nL/minute (Thermo Scientific). Peptides were eluted with a gradient of buffer A (0.1% formic acid, 100% H₂O) to buffer B (0.1% formic acid, 100% acetonitrile). The Q Exactive system was used for MS/MS analysis in the positive ion and information-dependent acquisition mode. Proteins were identified and quantified using Proteome Discoverer (v2.1, Thermo Fisher Scientific), using three embedded search nodes; Mascot^{72 (link)} (v2.5.1), Sequest HT (Thermo Fisher Scientific), and MS Amanda^{73 (link)} (v2.1.5) search algorithms. The Percolator algorithm was used to calculate the false discovery rate (FDR) of peptide spectrum matches, set to a q-value of 0.05^{74 (link)}. Entrez labels and gene names were retrieved with the R interface to Uniprot web services R package version 2.20.0. Raw counts were normalized using the weighted trimmed mean of M-values method^{75 (link)}, and the batch effect for the two iTRAQ experiments was removed using ComBat^{76 (link)}. The contrast between different conditions was carried out with the quasi-likelihood test implemented in edgeR^{77 (link)}. Raw data are accessible at 10.5281/zenodo.6140992.

Sola-García A., Cáliz-Molina M.Á., Espadas I., Petr M., Panadero-Morón C., González-Morán D., Martín-Vázquez M.E., Narbona-Pérez Á.J., López-Noriega L., Martínez-Corrales G., López-Fernández-Sobrino R., Carmona-Marin L.M., Martínez-Force E., Yanes O., Vinaixa M., López-López D., Reyes J.C., Dopazo J., Martín F., Gauthier B.R., Scheibye-Knudsen M., Capilla-González V, & Martín-Montalvo A. (2023). Metabolic reprogramming by Acly inhibition using SB-204990 alters glucoregulation and modulates molecular mechanisms associated with aging. Communications Biology, 6, 250.

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Publication 2023

acetonitrile Amines Bath Benzonase Biological Assay Buffers CREB3L1 protein, human Enzymes formic acid formic acid, ammonium salt Genes inhibitors Liquid Chromatography Liver methyl methanethiosulfonate Na4P2O7 Peptides phosphine Phosphoric Monoester Hydrolases Promega Protease Inhibitors Proteins Proteome Sodium Chloride Tandem Mass Spectrometry triethylammonium bicarbonate Tromethamine Urea Vacuum

Chromatin Fractionation and Enrichment

Chromatin fractions were prepared as described previously^{53 (link)} with some modifications. In brief, cells were lysed by swelling and mechanical force in buffer A (10 mM ammonium bicarbonate pH 8.0, 1.5 mM MgCl₂, 10 mM KCl, 10 mM sodium ascorbate, 5 mM Trolox, 10 mM sodium azide, 1× protease inhibitor cocktail and 0.2% NP40). Nuclei were then collected by centrifugation and chemically lysed in buffer C (20 mM ammonium bicarbonate pH 8.0, 420 mM NaCl₂, 20% (v/v) glycerol, 2 mM MgCl₂, 0.2 mM EDTA, 0.1% NP40, 10 mM sodium ascorbate, 5 mM Trolox, 10 mM sodium azide, 1× protease inhibitor cocktail and 0.5 mM DTT). Lysates were centrifuged at 20,800g for 45 min at 4 °C. The pellet contains the insoluble chromatin fraction and consists of DNA and proteins tightly bound to chromatin. To solubilize the chromatin pellet, 750 U Benzonase (Sigma-Aldrich) was added, followed by 10 min incubation on ice and 5 min of agitation at room temperature. Clarified lysate was collected and the protein concentration was quantified using Bio-Rad Bradford’s reagent. Approximately 4 mg lysates from SILAC heavy or light cells were mixed 1:1 and incubated with 50 μl Streptavidin magnetic beads (Pierce, 88817) at 4 °C on a rotating wheel overnight. The beads were washed four times with RIPA buffer.

Wang H., Fan Z., Shliaha P.V., Miele M., Hendrickson R.C., Jiang X, & Helin K. (2023). H3K4me3 regulates RNA polymerase II promoter-proximal pause-release. Nature, 615(7951), 339-348.

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Publication 2023

ammonium bicarbonate Benzonase Buffers Cell Nucleus Cells Centrifugation Chromatin Edetic Acid Glycerin Light Magnesium Chloride Protease Inhibitors Proteins Radioimmunoprecipitation Assay Sodium Ascorbate Sodium Azide Streptavidin Trolox C

Top products related to «Benzonase»

Benzonase by Merck Group

Sourced in United States, Germany, Switzerland, United Kingdom, France, Denmark, Canada, Japan, Macao

Benzonase is a recombinant endonuclease enzyme that can degrade DNA and RNA. It is commonly used in various laboratory applications to remove nucleic acid contaminants from protein samples.

Benzonase nuclease by Merck Group

Sourced in United States, Germany, Macao, Switzerland, United Kingdom, France

Benzonase nuclease is a recombinant endonuclease that catalyzes the hydrolytic cleavage of DNA and RNA. It is effective in removing nucleic acids from protein samples, cell extracts, and other biological preparations.

Protease inhibitor cocktail by Roche

Sourced in United States, Switzerland, Germany, China, United Kingdom, France, Canada, Japan, Italy, Australia, Austria, Sweden, Spain, Cameroon, India, Macao, Belgium, Israel

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.

Protease inhibitor cocktail by Merck Group

Sourced in United States, Germany, China, United Kingdom, Italy, Japan, Sao Tome and Principe, France, Canada, Macao, Switzerland, Spain, Australia, Israel, Hungary, Ireland, Denmark, Brazil, Poland, India, Mexico, Senegal, Netherlands, Singapore

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.

Complete protease inhibitor cocktail by Roche

Sourced in United States, Germany, Switzerland, United Kingdom, China, France, Japan, Canada, Spain, Belgium, Australia, Sweden, Italy, Ireland, Macao

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.

Lysozyme by Merck Group

Sourced in United States, Germany, United Kingdom, Japan, China, Poland, Ireland, Switzerland, Italy, Sao Tome and Principe, India, Canada, France, Belgium, Australia, Netherlands, Singapore, Denmark, Macao, Portugal

Lysozyme is an enzyme that catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan, which is a major component of the cell walls of gram-positive bacteria. This function makes lysozyme an effective antimicrobial agent.

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.

Benzonase endonuclease by Merck Group

Sourced in United States, Germany, France

Benzonase endonuclease is a recombinant DNA/RNA-specific endonuclease enzyme that can degrade DNA and RNA. It non-specifically cleaves the phosphodiester bonds in nucleic acids, resulting in the generation of 5'-phosphomononucleotides. The enzyme is widely used in various biotechnology applications, particularly in the purification of biomolecules, such as proteins, from cellular samples.

Turbo dnase by Thermo Fisher Scientific

Sourced in United States, Germany, United Kingdom, Japan, France, Lithuania, Canada, Australia, Netherlands, Denmark

Turbo DNase is a laboratory equipment product designed for the efficient degradation of DNA molecules. It functions by rapidly and effectively removing any unwanted DNA from samples, ensuring the integrity and purity of subsequent analyses.

Pierce bca protein assay kit by Thermo Fisher Scientific

Sourced in United States, United Kingdom, Germany, China, Australia, Switzerland, France, Italy, Canada, Spain, Japan, Belgium, Sweden, Lithuania, Austria, Denmark, Poland, Ireland, Portugal, Finland, Czechia, Norway, Macao, India, Singapore

The Pierce BCA Protein Assay Kit is a colorimetric-based method for the quantification of total protein in a sample. It utilizes the bicinchoninic acid (BCA) reaction, where proteins reduce Cu2+ to Cu+ in an alkaline environment, and the resulting purple-colored reaction is measured spectrophotometrically.

What is Benzonase and how is it used in research?

Benzonase is a highly efficient endonuclease enzyme that can rapidly and thoroughly digest both DNA and RNA. This makes it a valuable tool in molecular biology and biochemistry research. Researchers commonly use Benzonase to degrade nucleic acids in samples, which facilitates protein purification and other experimental procedures. Benzonase's ability to rapidly and thoroughly digest nucleic acids has made it indispensable for a wide range of applications, including cell lysis, sample clarification, and nucleic acid removal.

What are some common challenges in using Benzonase effectively?

One of the main challenges in using Benzonase is ensuring optimal conditions for its activity and effectiveness. Factors like enzyme concentration, incubation time, and reaction conditions can all impact Benzonase's performance. Researchers need to carefully optimize these parameters to achieve thorough nucleic acid digestion without compromising other experimental components.

Are there different variations or types of Benzonase available?

Yes, there are several variations of Benzonase available. In addition to the standard formulation, there are also nuclease-free versions, as well as Benzonase that has been engineered for enhanced activity or specificity. Researchers should carefully evaluate the different Benzonase products to determine which one best suits their particular experimental needs and protocols.

What are some of the key applications of Benzonase in research?

Benzonase has a wide range of applications in research, including: 1. Cell lysis and sample clarification: Benzonase can be used to degrade nucleic acids during cell lysis, helping to reduce sample viscosity and facilitate downstream processing. 2. Protein purification: Benzonase is often used in protein purification workflows to remove contaminating nucleic acids, improving the purity and quality of the final protein product. 3. Nucleic acid removal: Benzonase is a valuable tool for removing unwanted DNA or RNA from various samples, such as viral preparations, cell culture supernatants, and biopharmaceutical products.

How can PubCompare.ai help optimize the use of Benzonase in research?

PubCompare.ai can be a valuable resource for researchers looking to optimize their use of Benzonase. The platform allows you to efficiently screen the literature for relevant Benzonase protocols, leveraging AI to pinpoint critical insights that can help identify the most effective and reproducible methods. By comparing different Benzonase protocols side-by-side, the platform can highlight key differences in effectiveness, enabling you to choose the best approach for your specific research goals and enhance the reproducibility and accuracy of your Benzonase experiments.

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