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Biotin 2

Biotin 2 is a vitamin B complex essential for carboxylase enzymes and metabolism.
It plays a crucial role in fatty acid synthesis, gluconeogenesis, and amino acid catabolism.
Biotin 2 supports healthy hair, skin, and nails, and is involved in energy production.
Reasearchers can use PubCompare.ai to optimize biotin 2 studies, easily locating and identifying the best protocols and products from literature, pre-prints, and patents.
This AI-driven tool helps achieve reproducable and acurate results for biotin 2 research.

Most cited protocols related to «Biotin 2»

We constructed the paired-end DNA libraries with insert sizes larger than 2 kb by self-ligation of the DNA fragments and merging the two ends of the DNA fragment. We randomly fragmented the circularized DNA and enriched the fragments crossing the merged boundaries using magnetic beads with biotin and streptavidin. The sequencing process followed the manufacturer’s instructions (Illumina), and the fluorescent images were processed to sequences using the Illumina data processing pipeline (v1.1).
The genome sequence was assembled with short reads using SOAPdenovo software6 (http://soap.genomics.org.cn), which adopts the de Bruijn graph data structure to construct contigs7 (link). The reads were then realigned to the contig sequence, and the paired-end relationship between the reads was transferred to linkage between contigs. We constructed scaffolds starting with short paired-ends and then iterated the scaffolding process, step by step, using longer insert size paired-ends. To fill the intra-scaffold gaps, we used the paired-end information to retrieve read pairs that had one read well-aligned on the contigs and another read located in the gap region, then did a local assembly for the collected reads.
Known transposable elements were identified using RepeatMasker (version 3.2.6)14 against the Repbase31 (link) transposable element library (version 2008-08-01), and highly diverged transposable elements were identified with RepeatProteinMask14 by aligning the genome sequence to the curated transposable-element-related proteins. A de novo panda repeat library was constructed using RepeatModeller14 . Using evidence-based gene prediction, the human and dog genes (Ensembl release 52) were projected onto the panda genome, and the gene loci were defined by using both sequence similarity and whole-genome synteny information. De novo gene prediction was performed using Genscan16 (link) and Augustus17 (link). A reference gene set was created by merging all of the gene sets. The sequencing reads were mapped on the panda genome sequence using SOAPaligner8 (link), and heterozygous SNPs were identified by SOAPsnp9 (link).
Publication 2009
Amino Acid Sequence Biotin DNA Library DNA Transposable Elements Genes Genetic Loci Genome Heterozygote Homo sapiens Ligation Selfish DNA Single Nucleotide Polymorphism Streptavidin Synteny
Both hiPSCs and hESCs (>p20) were split at 1:10 or 1:12 ratios, using EDTA as above and grown for 4 days, at which time they reached ~85% confluence. Medium was changed to CDM3, consisting of RPMI 1640 (11875, Life Technologies), 500 µg/mL Oryza sativa-derived recombinant human albumin (A0237, Sigma-Aldrich, 75 mg/mL stock solution in WFI H2O, stored at −20 °C), and 213 µg/mL L-ascorbic acid 2-phosphate (Sigma-Aldrich, 64 mg/mL stock solution in WFI H2O, stored at −20 °C). Medium was changed every other day (48 h). For d0-d2, medium was supplemented with 6 µM CHIR99021 (LC Laboratories). On d2, medium was changed to CDM3 supplemented with 2 µM Wnt-C59 (Selleck Chemicals). Medium was changed on d4 and every other day for CDM3. Contracting cells were noted from d7.
Other additions to cardiac differentiation media tested were 10.7 µg/mL recombinant human transferrin, 14 µg/mL sodium selenite, 1 µg/mL linoleic acid, 1 µg/mL linolenic acid, 2 ng/mL triiodo-l-thyronine, 2 µg/mL L-carnitine, 1 µg/mL D,L-alpha-tocopherol acetate, 100 ng/mL retinol acetate, 1 µg/mL ethanolamine, 20 ng/mL corticosterone, 9 ng/mL progesterone, 47 ng/mL lipoic acid, 100 ng/mL retinol, 1 µg/mL D,L-alpha-tocopherol, 100 ng/mL biotin, 2.5 ug/mL catalase, 2.5 µg/mL glutathione, 2.5 µg/mL superoxide dismutase, 2 µg/mL L-carnitine, 15 µg/mL D(+)-galactose, 16.1 µg/mL putrescine, 450 µM 1-thioglycerol, 55 µM 2-mercaptoethanol, and 64 µg/mL L-ascorbic acid 2-phosphate (all from Sigma-Aldrich).
Basal media assessed were DMEM (catalogue #11965), DMEM/F12 (11330), IMDM (12440), IMDM/F12 (12440/11765), RPMI 1640 (11875), McCoy’s 5A (16600), M199 (with Earle’s Salts, 11150), MEMα (with Earle’s Salts, no nucleosides, 12561), and MEM (with Earle’s Salts, 11095) (all from Life Technologies). RPMI 1640 media assessed were RPMI 1640 with L-glutamine (catalogue number 11875), RPMI 1640 with L-glutamine and HEPES (22400), RPMI 1640 with GlutaMAX (61870), and RPMI with GlutaMAX and HEPES (72400) (all from Life Technologies).
Albumin sources assessed were human serum albumin (A1653, Sigma-Aldrich), Oryza sativa-derived recombinant human albumin (A0237, Sigma-Aldrich), Saccharomyces cerevisiae-derived recombinant Albucult (Novozymes Biopahrma/A6608, Sigma Aldrich), Oryza sativa-derived recombinant Cellastim (Invitria/A9731, Sigma Aldrich), and embryo-grade bovine serum albumin (A3311, Sigma Aldrich).
Wnt inhibitors assessed were IWP-2, IWR-1 (both Sigma-Aldrich), XAV-939, ICG-001 (Selleck Chemicals), IWP-4 (Stemgent), and Wnt-C59 (Selleck Chemicals). GSK3B inhibitors assessed were CHIR99021 (LC Laboratories), BIO, TWS119 (Selleck Chemicals), 1-azenkenpaullone, TDZD-8, ARA014418, and 3F8 (all Sigma-Aldrich). Inhibitors used for pathway analysis were PD173074, SB203580, LDN193189, SB431542 (all Selleck Chemicals), SU5402, Dorsomorphin, A83-01 (all Tocris), ALK5 inhibitor (Stemgent), and ITD-1 (Xcessbio). All small molecules were resuspended to 10 mM in dimethyl sulfoxide (DMSO) and used at 5 µM except for Wnt-C59 which was used at 2 µM.
For control treatments (0 µM) 0.1% DMSO was used. Comparisons of differentiation media were made to RPMI+B27-ins consisting of RPMI 1640 (11875) supplemented with 2% B27 without insulin (0050129SA, Life Technologies), and StemPro-34 (Life Technologies) supplemented as shown in Supplementary Table 1. LI-APEL low insulin medium and Xeno-free Differentiation Medium were made as described2 (link), 9 (link), 48 (link). For optimization of cardiac differentiation conditions, cells were differentiated in 12-well plates and samples were analyzed at day 15 of differentiation after dissociation with TrypLE Express for 10 min at 37 °C.
Publication 2014
Our approach, termed isoTOP-ABPP (isotopic Tandem Orthogonal Proteolysis – Activity-Based Protein Profiling), has four features to enable quantitative analysis of native cysteine reactivity (Fig. 1a): [1] an electrophilic iodoacetamide (IA) probe to label cysteine residues in proteins that also has [2] an alkyne handle for “click chemistry” conjugation of probe-labeled proteins19 (link) to [3] an azide-functionalized TEV-protease recognition peptide containing a biotin group for streptavidin-enrichment of probe-labeled proteins20 (link) and [4] an isotopically-labeled valine for quantitative mass spectrometry (MS) measurements of IA-labeled peptides across multiple proteomes (Supplementary Fig. 1). Following tandem on-bead proteolytic digestions with trypsin and TEV protease15 (link),20 (link), probe-labeled peptides attached to isotopic tags are released and analyzed by liquid chromatography-high-resolution MS to identify IA-modified cysteines and quantify their extent of labeling based on MS2 and MS1 profiles, respectively. An isoTOP-ABPP ratio, R, is generated for each identified cysteine that reflects the difference in signal intensity between light and heavy tag-conjugated proteomes.
We first verified the accuracy of isoTOP-ABPP by labeling varying amounts of a mouse liver proteome (1X, 2X, 4X) with the IA-probe followed by click chemistry conjugation with either the heavy- or light-variants of the azide-TEV-biotin tag. The observed signals for labeled cysteines closely matched the expected proteome ratios (R1:1 ≈ 1, R2:1 ≈ 2, or R4:1 ≈ 4, respectively; Supplementary Fig. 2). A representative MS/MS profile of an IA-labeled peptide from our proteomic experiments is provided in Supplementary Fig. 3.
In contrast to traditional cysteine-alkylating protocols for proteomics that use millimolar concentrations of IA to stoichiometrically modify all cysteines in denatured proteins21 (link), we hypothesized that, by applying low (micromolar) concentrations of the IA-probe to native proteomes, differences in the extent of alkylation would reflect differences in cysteine reactivity, rather than abundance. This hypothesis predicts that the reactivity of cysteines can be measured on a proteome-wide scale in isoTOP-ABPP experiments that compare low versus high concentrations of IA-probe, where hyperreactive cysteines would be expected to label to completion at low probe concentrations (generating isoTOP-ABPP ratios with R[high]:[low] ≈ 1) and less reactive cysteines should show concentration-dependent increases in IA-probe labeling (generating isoTOP-ABPP ratios with R[high]:[low] >> 1) (Supplementary Fig. 4). We tested this idea by performing four parallel isoTOP-ABPP experiments with the soluble proteome of the human breast cancer cell line MCF7 using pair-wise IA-probe concentrations of 10:10 μM, 20:10 μM, 50:10 μM and 100:10 μM (light:heavy). More than 800 probe-labeled cysteines were identified on 522 proteins, the vast majority of which exhibited escalating isoTOP-ABPP ratios (Fig. 1b) expected for reactions that did not reach completion over the tested probe concentration range. In contrast, a small subset of cysteines (< 10%) showed nearly identical ratios at all probe concentrations tested (R1:1 ≈ R2:1 ≈ R5:1 ≈ R10:1 ≈ 1, Fig. 1b, shaded blue box). An expanded analysis of multiple human cancer line (Supplementary Fig. 5 and Supplementary Table 1) and mouse tissue (Supplementary Fig. 6 and Supplementary Table 2) proteomes treated with low (10 μM) and high (100 μM) IA-probe concentrations revealed consistent isoTOP-ABPP ratios for individual cysteine residues, indicating that the propensity of a cysteine to display high IA reactivity is an intrinsic property of the residue (and presumably its local protein environment), and not, in general, contingent on features specific to a particular cell or tissue. Additionally, isoTOP-ABPP ratios showed no correlation with either protein abundance or peptide ion intensity (Supplementary Fig. 7), indicating that they were independent of potential MS-based ionization sources for saturation. Finally, we confirmed that similar isoTOP-ABPP ratios were obtained for cysteines in reactions where time rather than the concentration of probe was varied (Supplementary Fig. 8 and Supplementary Table 3), confirming that low isoTOP-ABPP ratios reflect rapid reaction kinetics (hyperreactivity), rather than saturable binding interactions (see Supplementary Discussion).
Publication 2010
Cells were incubated for 24 h in complete media supplemented with 1 µg/ml doxycycline and 50 µM biotin. After three PBS washes, cells (for small-scale analysis, <107; for large scale analysis, 4 × 107) were lysed at 25°C in 1 ml lysis buffer (50 mM Tris, pH 7.4, 500 mM NaCl, 0.4% SDS, 5 mM EDTA, 1 mM DTT, and 1x Complete protease inhibitor [Roche]) and sonicated. Triton X-100 was added to 2% final concentration. After further sonication, an equal volume of 4°C 50 mM Tris (pH 7.4) was added before additional sonication (subsequent steps at 4°C) and centrifugation at 16,000 relative centrifugal force. Supernatants were incubated with 600 µl Dynabeads (MyOne Steptavadin C1; Invitrogen) overnight. Beads were collected and washed twice for 8 min at 25°C (all subsequent steps at 25°C) in 1 ml wash buffer 1 (2% SDS in dH2O). This was repeated once with wash buffer 2 (0.1% deoxycholate, 1% Triton X-100, 500 mM NaCl, 1 mM EDTA, and 50 mM Hepes, pH 7.5), once with wash buffer 3 (250 mM LiCl, 0.5% NP-40, 0.5% deoxycholate, 1 mM EDTA, and 10 mM Tris, pH 8.1) and twice with wash buffer 4 (50 mM Tris, pH 7.4, and 50 mM NaCl). 10% of the sample was reserved for Western blot analysis. Bound proteins were removed from the magnetic beads with 50 µl of Laemmli SDS-sample buffer saturated with biotin at 98°C. For the larger scale preparation, 90% of the sample to be analyzed by mass spectrometry was washed twice in 50 mM NH4HCO3.
Publication 2012
Biotin Buffers Cells Centrifugation Deoxycholate Doxycycline Edetic Acid HEPES Laemmli buffer Mass Spectrometry Nonidet P-40 Protease Inhibitors Proteins Sodium Chloride Triton X-100 Tromethamine Western Blot
Fluorescence in situ hybridization (FISH) was performed to map repeated DNAs on the mitotic and meiotic chromosomes of H. obliquidens. Five DNA probes containing sequences of different classes of repeated DNA were used for chromosome hybridization. (i) 5S rDNA probe: complete repeat units of 5S rDNA of H. obliquidens were obtained by the polymerase chain reaction (PCR) with the primers 5SA (5'-TAC GCC CGA TCT CGT CCG ATC - 3') and 5SB (5' - CAG GCT GGT ATG GCC GTA AGC-3') designed from the rainbow trout 5S rRNA sequence [63 (link)] and successfully applied for the amplification of 5S rDNA of other cichlids [64 (link),65 (link)]. (ii) 18S rDNA probe: a segment of 1,400 base pairs (bp) of the 18S rRNA gene of H. obliquidens was obtained by PCR with the primers 18Sf 5'CCG CTT TGG TGA CTC TTG AT and18Sr 5'CCG AGG ACC TCA CTA AAC CA. The 18S primers were designed from the catfish Ictalurus punctatus (GenBank accession number AF021880) and have been successfully used to amplify 18S rRNA genes of different fish species [65 (link),66 (link)]. (iii) SATA satellite: repeated satellite DNA isolated and cloned from O. niloticus [29 (link)]; (iv) Telomeric DNA sequences: in vitro synthesized oligomers of telomeric repeats (GGGTTA)7/(TAACCC)7; (v) Clones BAC-C4E09 and BAC-C5E01: Bacterial artificial chromosomes containing several classes of repeated elements from the O. niloticus genome [29 (link)].
Probes were labeled by nick translation with biotin 14-dATP (Bionick labeling system-Invitrogen). After denaturation of chromosomal DNA in 70% formamide/2× SSC for 40 seconds at 70°C, hybridization mixtures containing 100 ng of denatured probe, 10 mg/ml dextran sulfate, 2× SSC and 50% formamide, in a final volume of 30 μl, were dropped on the slides and the hybridization was performed overnight at 37°C in a 2× SSC moist chamber. Post-hybridization washes were carried out at 45°C in 2× SSC/50% formamide for 15 min, followed by a second wash in 2× SSC for 15 min, and a final wash at room temperature in 4× SSC for 15 min. Detection of hybridized probes was carried out with 0.07% avidin FITC conjugate (Sigma) in C buffer (0.1 M NaHCO3 /0.15 M NaCl) for 1 h, followed by two rounds of signal amplification using 2.5% anti-avidin biotin conjugate (Sigma) in blocking buffer (1.26% NaHCO3, 0.018% sodium citrate, 0.0386% Triton X-100 an 1% non-fat dried milk) for 30 min. Each treatment with anti-avidin biotin conjugate was followed by a treatment with avidin-FITC. The treatments with avidin-FITC and anti-avidin-biotin were conducted in a 2× SSC moist chamber at 37°C. After each amplification step, the slides were washed three times for 5 min each in blocking buffer at 42°C. Chromosomes were counterstained with propidium iodide diluted in antifade (Vectashield Mounting Medium, Vector). Hybridized chromosomes were visualized using an Olympus BX 61 microscope, and images were captured with a digital camera Olympus DP71 with the software Image-Pro MC 6.0. Karyotypes and metaphases were arranged with Adobe Photoshop 7.0 software.
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Publication 2010

Most recents protocols related to «Biotin 2»

Timing: 1 day

In this step, biotin tag is added to the newly available free thiol sites which were previously palmitoylated for affinity enrichment. The palmitoylated proteins can be detected using antibody against the protein of interest or if the protein was co-expressed with a tag on it.

Dissolve the protein pellet in 200 μL of flex buffer supplemented with 20 mM Biotin-HPDP.

Incubate the samples at 22°C–24°C with end-over-end rotation for 1 h.

Perform protein precipitation one final time as described in steps 19–24.

Dissolve the protein in 100 μL of flex buffer.

Estimate protein concentration by mini-BCA assay (Figure 1C) using a 10 μL protein sample.

Normalize protein concentration for any variability across samples.

Remove a 20 μL aliquot from each sample to load as an input control. Mix the sample with 20 μL of 2x SDS-PAGE Laemmli buffer and store at −20°C until ready to load.

Dilute the remaining 70 μL sample 10 times by adding 630 μL of core buffer. This dilutes the SDS concentration to 0.1%.

Add 30 μL of pre-washed streptavidin agarose beads directly to each sample and vortex for ∼10 s to mix the contents.

To first wash and prepare the streptavidin-agarose beads, add 30 μL agarose beads per sample to 500 μL of core buffer.

Spin at 10,000 g for 2 min at room temperature.

Wash the agarose beads for a total of 3 times taking 500 μL core buffer each time. After the final wash step, resuspend the beads in 30 μL of core buffer per sample.

Incubate the samples with end-over-end rotation at 4°C for 18 h–24 h.

The following day, wash the samples with 500 μL of core buffer supplemented with 0.1% SDS and 0.1% NP-40.

Repeat washes for a total of 3 times, spinning the samples at 12,000 g for 5 min between each of the washes.

To the pellet (Figure 1D), add 75 μL of 1x Laemmli buffer and store at −20°C until ready for SDS-PAGE.

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Publication 2024
Not available on PMC !
The cells were cultured in 100 mm dishes under standard culture conditions, maintaining a temperature of 37°C with 5% CO 2 and appropriate humidity, following the guidelines recommended by ATCC. For the PMP biotinylation, the cells were washed three times with PBS to eliminate FBS (Fetal Bovine Serum) and other medium additives. The cells were then covered with growth medium containing 0.25 µM of either TurboID or TurboID-START, along with 1 mM ATP, 3 mM MgCl2, and 500 µM biotin. The biotinylation reaction was allowed to proceed for 30 minutes at 37°C. To stop the biotinylation reaction, the cells were transferred onto ice and washed ve times with PBS. The chemical biotinylation of PMPs was achieved using a commercially available EZ-link Sulfo-NHS-LC-Biotinylation kit (Thermo Scienti c, USA), following the instructions. CHO cells that were not biotinylated by TurboID, TurboID-START, or the chemical method were used as the negative control.
Publication 2024
Not available on PMC !
Biotin-labeled wild-type (wt) miR-629-3p (Biotin-miR-629-3p-wt), mutated (mut) miR-629-3p (Biotin-miR-629-3p-mut) or antagonistic miR-629-3p probe (Biotin-NC) were incubated with cell lysates, followed by incubation with M-280 streptavidin magnetic beads (Sigma) for 2 h at 4°C. Pulldown RNAs were analyzed using qRT-PCR.
Publication 2024
The biotin-labeled lncRNA probe (PSMA3-AS1, 5’- TACAAAATCCATCTGCT GACCCCTG-biotin-TEG-3′; MIR22HG, 5′-TCTCTACCACTGTCCCACACGCATC-biotin-TEG-3′; biotin-TEG, biotin with 15 atom triethylene glycol spacer) was synthesized by Hangzhou Youkang Biotechnology Inc. The lncRNA-biotin probe was incubated with streptavidin magnetic beads (Beyotime) in 1 × Binding & washing buffer (10 mM Tris–HCl, 1 mM EDTA, 2 M NaCl, 0.01–0.1% Tween-20, pH 7.5) for 30 min at room temperature. Then the lysate of cells were incubated with washed beads in for 2 h at 4 °C. Subsequently, miRNAs or proteins were extracted from the beads. The miRNA extraction was performed using mirVana miRNA Isolation Kit (Thermo Fisher Scientific) and analyzed by qPCR. The proteins were eluted using 0.1% SDS, followed by SDS-PAGE. Mass spectrometry was used for identification of binding proteins.
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Publication 2024

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Publication 2024

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The LightShift Chemiluminescent EMSA Kit is a laboratory tool designed to detect and analyze protein-DNA interactions. It uses chemiluminescent detection to visualize and quantify the binding of proteins to specific DNA sequences.
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Bovine serum albumin (BSA) is a common laboratory reagent derived from bovine blood plasma. It is a protein that serves as a stabilizer and blocking agent in various biochemical and immunological applications. BSA is widely used to maintain the activity and solubility of enzymes, proteins, and other biomolecules in experimental settings.
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The Vectastain Elite ABC kit is a specialized laboratory equipment used for the detection and visualization of target proteins or antigens in biological samples. It utilizes an avidin-biotin complex (ABC) system to amplify the signal, enabling researchers to achieve high sensitivity and consistent results in their immunohistochemical or immunocytochemical analyses.
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EZ-Link Sulfo-NHS-LC-Biotin is a water-soluble, amine-reactive biotinylation reagent. It is used to label proteins and other macromolecules with biotin, enabling detection and purification.
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Anti-biotin microbeads are a type of magnetic particle designed for the isolation and enrichment of biotin-labeled cells, proteins, or other biomolecules. These microbeads are coated with an anti-biotin antibody, which binds to the biotin label, allowing the target molecule to be separated from the rest of the sample using a magnetic field.
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The Vectastain ABC kit is a product by Vector Laboratories that is used for the detection of specific target antigens in tissue or cell samples. The kit includes reagents necessary for the avidin-biotin complex (ABC) method of immunohistochemistry. The core function of the Vectastain ABC kit is to provide a reliable and sensitive tool for the visualization of target molecules within a sample.
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Streptavidin agarose beads are a type of affinity chromatography resin. They consist of streptavidin, a protein that binds to biotin, immobilized on agarose beads. These beads are commonly used for the purification and immobilization of biotinylated molecules.

More about "Biotin 2"

Biotin, also known as vitamin B7 or vitamin H, is a water-soluble vitamin that plays a crucial role in the body's metabolism and energy production.
It is an essential cofactor for several carboxylase enzymes, which are involved in processes like fatty acid synthesis, gluconeogenesis, and amino acid catabolism.
Biotin supports the health and function of various body systems, including the hair, skin, and nails.
It is involved in the production of keratin, a protein that is essential for the structural integrity of these tissues.
Biotin deficiency can lead to symptoms like hair loss, skin rashes, and brittle nails.
In addition to its role in metabolism and tissue health, biotin is also important for energy production.
It helps convert food into usable energy, making it an important nutrient for maintaining overall health and well-being.
Researchers can use tools like PubCompare.ai to optimize their biotin studies.
This AI-driven platform helps researchers easily locate and identify the best protocols and products from the literature, preprints, and patents, allowing them to achieve reproducible and accurate results.
When studying biotin, researchers may also utilize other laboratory tools and reagents, such as the LightShift Chemiluminescent EMSA Kit for DNA-protein binding assays, Bovine serum albumin as a blocking agent, the Vectastain Elite ABC kit for immunohistochemistry, the RNeasy Mini Kit for RNA extraction, EZ-Link Sulfo-NHS-LC-Biotin for protein labeling, Anti-biotin microbeads for biotin detection, Dynabeads M-280 Streptavidin for biotin purification, the Vectastain ABC kit for signal amplification, and Streptavidin agarose beads for biotin pulldown experiments.
These tools can help researchers effectively investigate the roles and functions of biotin in various biological systems.