strepavidin coated magnetic beads  (New England Biolabs)


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    Streptavidin Magnetic Beads
    Description:
    Streptavidin Magnetic Beads 5 ml
    Catalog Number:
    s1420s
    Price:
    318
    Size:
    5 ml
    Category:
    Magnetic Separation Equipment
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    Structured Review

    New England Biolabs strepavidin coated magnetic beads
    Streptavidin Magnetic Beads
    Streptavidin Magnetic Beads 5 ml
    https://www.bioz.com/result/strepavidin coated magnetic beads/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    strepavidin coated magnetic beads - by Bioz Stars, 2020-09
    99/100 stars

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    Incubation:

    Article Title: Simple and Efficient Room-Temperature Release of Biotinylated Nucleic Acids from Streptavidin and Its Application to Selective Molecular Detection
    Article Snippet: .. For bead capture, 500 ng of the resulting mixture was incubated with 25 μ L of streptavidin beads resuspended in 2× binding/washing buffer, with the rest reserved for solid-state (SS)-nanopore measurements. ..

    Article Title: miR-106b-responsive gene landscape identifies regulation of Kruppel-like factor family
    Article Snippet: .. 90% of cell lysate was incubated with streptavidin magnetic beads (New England Biolabs) for 6 hours at 4°C and 10% of cell lysate was used for input RNA. ..

    Binding Assay:

    Article Title: Simple and Efficient Room-Temperature Release of Biotinylated Nucleic Acids from Streptavidin and Its Application to Selective Molecular Detection
    Article Snippet: .. For bead capture, 500 ng of the resulting mixture was incubated with 25 μ L of streptavidin beads resuspended in 2× binding/washing buffer, with the rest reserved for solid-state (SS)-nanopore measurements. ..

    Magnetic Beads:

    Article Title: Src kinase phosphorylates Notch1 to inhibit MAML binding
    Article Snippet: .. Streptavidin magnetic beads (10 µL, New England BioLabs) were used to precipitate biotinylated species on a magnetic tube rack. .. Specific protein targets were detected using primary antibodies followed by membrane stripping before detection of overall biotinylated proteins.

    Article Title: Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB
    Article Snippet: .. 80 μl of pre-washed streptavidin magnetic beads (NEB) were added, mixed and rotated at room temperature for 10 minutes. ..

    Article Title: The Conserved C-Terminus of the PcrA/UvrD Helicase Interacts Directly with RNA Polymerase
    Article Snippet: .. Pull down experiments Pull down experiments were carried out using streptavidin magnetic beads (New England Biolabs). .. Each addition or washing step was performed at 4 °C by placing Eppendorf tubes containing beads on a rotator device, designed to continually but gently mix the beads with the sample.

    Article Title: miR-106b-responsive gene landscape identifies regulation of Kruppel-like factor family
    Article Snippet: .. 90% of cell lysate was incubated with streptavidin magnetic beads (New England Biolabs) for 6 hours at 4°C and 10% of cell lysate was used for input RNA. ..

    Article Title: Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions
    Article Snippet: .. Bead washing Aliquots of 20 μl of Streptavidin magnetic beads (New England Biolabs, S1420S) were pre-washed three times with 2× BW buffer ( ); resuspended in 50 μl 2× BW; mixed with the 50 μl SPEX primer extension reaction and rotated at room temperature for 30 min to immobilize biotinylated molecules to the beads; then a series of washes with 2× BW, 0.15 M NaOH and 1× Tris/EDTA (TE, pH 7.5) were carried out as described by Chen et al. ( ) to remove everything but biotinylated molecules. .. The beads were resuspended to 14 μl with 0.1× Qiagen buffer EB (10 mM Tris·Cl, pH 8.5).

    Article Title: Aberrant Glycosylation in the Human Trabecular Meshwork
    Article Snippet: .. The precipitate was recovered with 25 μl of 4μg/μl streptavidin coupled magnetic beads (cat# S1420S, New England Biolabs, Ipswitch, MA). ..

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    New England Biolabs streptavidin coated magnetic beads
    General scheme applied for identifying peanut immature pod-specific genes (tracer mRNA (1)) after a single round subtraction . B biotin, S <t>streptavidin,</t> M magnetic bead.
    Streptavidin Coated Magnetic Beads, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/streptavidin coated magnetic beads/product/New England Biolabs
    Average 99 stars, based on 13 article reviews
    Price from $9.99 to $1999.99
    streptavidin coated magnetic beads - by Bioz Stars, 2020-09
    99/100 stars
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    General scheme applied for identifying peanut immature pod-specific genes (tracer mRNA (1)) after a single round subtraction . B biotin, S streptavidin, M magnetic bead.

    Journal: Biological Procedures Online

    Article Title: A Novel mRNA Level Subtraction Method for Quick Identification of Target-Orientated Uniquely Expressed Genes Between Peanut Immature Pod and Leaf

    doi: 10.1007/s12575-009-9022-z

    Figure Lengend Snippet: General scheme applied for identifying peanut immature pod-specific genes (tracer mRNA (1)) after a single round subtraction . B biotin, S streptavidin, M magnetic bead.

    Article Snippet: Streptavidin-coated magnetic beads (1.1 mg/ml) were applied again to purify synthesized double-stranded cDNAs with three times washes.

    Techniques:

    The C-terminal half of LARP1 selectively binds TOP sequences and the adjacent cap structure. ( A ) LARP1 497–1019 selectively recognizes oligopyrimidine RNA sequences and the 5′ cap structure. Extracts were prepared from LARP1-null HEK-293T cells expressing either FLAG-tagged LARP1 497-1019 or an N-terminal fragment (1–496) and treated with vehicle (DMSO) or 250 nM Torin 1 for 2 h. Extracts were then incubated with TOP or non-TOP (nTOP) 10 nt RNAs that were either capped or uncapped and containing a 3′ biotin. RNAs were then isolated using streptavidin-coated beads and analyzed by western blotting for the indicated proteins. ( B ) Endogenous LARP1 selectively recognizes capped oligopyrimidine RNA sequences. Extracts were prepared from WT HEK-293T cells treated with DMSO or 250 nM Torin 1 for 2 h, and then incubated with TOP or non-TOP (nTOP) 10 nt RNA probes that were either capped or uncapped and contained a 3′ biotin. RNA probes were isolated as in (A) and analyzed by western blotting for the indicated proteins. ( C ) LARP1 497–1019 fails to interact with PABP. Extracts were prepared from LARP1-null HEK-293T cells expressing either FLAG-tagged LARP1 497-1019 or an N-terminal fragment (1–496) and treated with vehicle (DMSO) or 250 nM Torin 1 for 2 h. FLAG-tagged proteins were then isolated by FLAG-affinity purification in the presence of RNase A, and analyzed by western blotting for the indicated proteins. ( D ) LARP1 mutation that disrupts cap binding prevents TOP mRNA regulation. LARP1-null HEK-293T cells were transfected with the indicated LARP1 cDNAs, along with TOP and non-TOP (nTOP) reporters as in Figure 1D , treated with vehicle (DMSO) or 250 nM Torin 1 for 6 h, and then analyzed for levels of Renilla and firefly luciferase. Data are Renilla/firefly, normalized to vehicle-treated nTOP levels for each LARP1 construct ( n = 3, error bars are SD). ( E ) Expression levels of LARP1 497–1019 WT and Y883A fragments. Cell extracts from cells treated as in (D) were analyzed by western blotting for the indicated proteins.

    Journal: Nucleic Acids Research

    Article Title: La-related protein 1 (LARP1) repression of TOP mRNA translation is mediated through its cap-binding domain and controlled by an adjacent regulatory region

    doi: 10.1093/nar/gkx1237

    Figure Lengend Snippet: The C-terminal half of LARP1 selectively binds TOP sequences and the adjacent cap structure. ( A ) LARP1 497–1019 selectively recognizes oligopyrimidine RNA sequences and the 5′ cap structure. Extracts were prepared from LARP1-null HEK-293T cells expressing either FLAG-tagged LARP1 497-1019 or an N-terminal fragment (1–496) and treated with vehicle (DMSO) or 250 nM Torin 1 for 2 h. Extracts were then incubated with TOP or non-TOP (nTOP) 10 nt RNAs that were either capped or uncapped and containing a 3′ biotin. RNAs were then isolated using streptavidin-coated beads and analyzed by western blotting for the indicated proteins. ( B ) Endogenous LARP1 selectively recognizes capped oligopyrimidine RNA sequences. Extracts were prepared from WT HEK-293T cells treated with DMSO or 250 nM Torin 1 for 2 h, and then incubated with TOP or non-TOP (nTOP) 10 nt RNA probes that were either capped or uncapped and contained a 3′ biotin. RNA probes were isolated as in (A) and analyzed by western blotting for the indicated proteins. ( C ) LARP1 497–1019 fails to interact with PABP. Extracts were prepared from LARP1-null HEK-293T cells expressing either FLAG-tagged LARP1 497-1019 or an N-terminal fragment (1–496) and treated with vehicle (DMSO) or 250 nM Torin 1 for 2 h. FLAG-tagged proteins were then isolated by FLAG-affinity purification in the presence of RNase A, and analyzed by western blotting for the indicated proteins. ( D ) LARP1 mutation that disrupts cap binding prevents TOP mRNA regulation. LARP1-null HEK-293T cells were transfected with the indicated LARP1 cDNAs, along with TOP and non-TOP (nTOP) reporters as in Figure 1D , treated with vehicle (DMSO) or 250 nM Torin 1 for 6 h, and then analyzed for levels of Renilla and firefly luciferase. Data are Renilla/firefly, normalized to vehicle-treated nTOP levels for each LARP1 construct ( n = 3, error bars are SD). ( E ) Expression levels of LARP1 497–1019 WT and Y883A fragments. Cell extracts from cells treated as in (D) were analyzed by western blotting for the indicated proteins.

    Article Snippet: Materials Reagents were obtained from the following sources: antibodies for S6K, phospho-T389-S6K, eIF2α, phospho-Ser51-eIF2α, Raptor, mTOR, 4EBP1, LARP1, NCBP1, eIF4E, eIF4G and PABP from Cell Signaling Technology; primary antibodies for eIF3b and HRP-labeled secondary antibodies from Santa Cruz Biotechnology; IRDye secondary antibodies from LI-COR; Dulbecco’s modified Eagle’s medium (DMEM) from Life Technologies; heat-inactivated Fetal Bovine Serum (IFS) and 7mGDP from Sigma Aldrich; DNase I, T4 DNA ligase 1, T4 RNA Ligase I, T7 RNA polymerase, polynucleotide kinase, Protoscript II reverse transcriptase, Vaccinia Capping System, Oligo d(T)25 Magnetic beads and streptavidin-coated magnetic beads from New England Biolabs; iTaq Universal SYBR Green Supermix and Bradford Protein Assay from Bio-rad; RNeasy Plus Mini Kit from Qiagen; Dual Luciferase Assay from Promega; and X-tremeGENE 9 transfection reagent from Roche.

    Techniques: Expressing, Incubation, Isolation, Western Blot, Affinity Purification, Mutagenesis, Binding Assay, Transfection, Luciferase, Construct

    Stoichiometrically normalizing oligonucleotide purification (SNOP) concept and workflow. a The input reagents for SNOP are chemically synthesized oligonucleotide precursors P 1 through P N that contain imperfect synthesis products with 5′ truncations and/or internal deletions, and with potentially very different concentrations. SNOP produces a pool of oligonucleotide products O 1 through O N that has high fractions of oligos with perfect sequence, and with all products at roughly equal concentration. SNOP uses a single biotinylated capture probe oligonucleotide synthesized with a degenerate “SWSWSW” randomer subsequence. Each instance of the randomer is complementary to one precursor tag sequence. The different instances of the capture probe are all at roughly equal concentration, due to split-pool oligo synthesis. Precursors with perfect tag sequences hybridize to the probe and are captured by streptavidin-coated magnetic beads. Subsequent cleavage at the deoxyuracil (dU) site using the USER enzyme mix ( https://www.neb.com/products/m5505-user-enzyme ) releases the oligo products into solution. Setting the capture probe to be the limiting reagent allows all SNOP products to be all at roughly equal concentrations. b SNOP enriches the fraction of perfect oligos because synthesis errors are correlated; molecules with no truncations or deletions in the tag sequences are also more likely to not have any deletions in the oligo product sequence. Shown in this panel are NGS sequence analysis results of a pool of N = 64 precursor oligonucleotides; error bars show standard deviation across different oligos (see Methods for library preparation details). c SNOP is very sensitive to small sequence changes in the tag; even single-nucleotide variations result in significantly reduced binding yield (see also Supplementary Note). This property allows SNOP products to be both highly pure and stoichiometrically normalized

    Journal: Nature Communications

    Article Title: Simultaneous and stoichiometric purification of hundreds of oligonucleotides

    doi: 10.1038/s41467-018-04870-w

    Figure Lengend Snippet: Stoichiometrically normalizing oligonucleotide purification (SNOP) concept and workflow. a The input reagents for SNOP are chemically synthesized oligonucleotide precursors P 1 through P N that contain imperfect synthesis products with 5′ truncations and/or internal deletions, and with potentially very different concentrations. SNOP produces a pool of oligonucleotide products O 1 through O N that has high fractions of oligos with perfect sequence, and with all products at roughly equal concentration. SNOP uses a single biotinylated capture probe oligonucleotide synthesized with a degenerate “SWSWSW” randomer subsequence. Each instance of the randomer is complementary to one precursor tag sequence. The different instances of the capture probe are all at roughly equal concentration, due to split-pool oligo synthesis. Precursors with perfect tag sequences hybridize to the probe and are captured by streptavidin-coated magnetic beads. Subsequent cleavage at the deoxyuracil (dU) site using the USER enzyme mix ( https://www.neb.com/products/m5505-user-enzyme ) releases the oligo products into solution. Setting the capture probe to be the limiting reagent allows all SNOP products to be all at roughly equal concentrations. b SNOP enriches the fraction of perfect oligos because synthesis errors are correlated; molecules with no truncations or deletions in the tag sequences are also more likely to not have any deletions in the oligo product sequence. Shown in this panel are NGS sequence analysis results of a pool of N = 64 precursor oligonucleotides; error bars show standard deviation across different oligos (see Methods for library preparation details). c SNOP is very sensitive to small sequence changes in the tag; even single-nucleotide variations result in significantly reduced binding yield (see also Supplementary Note). This property allows SNOP products to be both highly pure and stoichiometrically normalized

    Article Snippet: Subsequent solid-phase separation using streptavidin-coated magnetic beads removes unbound precursors, and applying USER enzyme mix (New England Biolabs) cleaves the oligo products from the tags at the dU site.

    Techniques: Purification, Synthesized, Sequencing, Concentration Assay, Oligo Synthesis, Magnetic Beads, Next-Generation Sequencing, Standard Deviation, Binding Assay

    mTOR Controls ATF4 Translation and mRNA Stability (A) mTOR reduces ATF4 mRNA levels. RNA was isolated from cells treated with vehicle (DMSO) or 250 nM Torin 1 for the indicated times and analyzed by qPCR. RNA levels were normalized to GAPDH (n = 3, error bars are SD). (B) mTOR activity has little effect on ATF4 transcription. HEK293T cells were treated with vehicle or 250 nM Torin 1 for 4 hr and then pulsed for 15 and 30 min with 100 μM 4sU. RNA was reacted with MTS-biotin, isolated by streptavidin-affinity purification, and analyzed by qPCR. Synthesis rates were determined by comparing 4sU labeling at 15 and 30 min and compared to changes in steady-state mRNA levels (n = 3, error bars are SD). (C) mTOR inhibition decreases the half-life of ATF4 mRNA. ATF4 −/− HEK293T cells simultaneously expressing doxycycline-repressible constructs encoding ATF4 and GFP were pre-treated with vehicle or 250 nM Torin 1 for 30 min, and then 1 μg/mL doxycycline. mRNA was collected at 0 and 6 hr post-doxycycline addition and analyzed by qPCR. mRNA levels were normalized to GAPDH (n = 3, error bars are SD, but are too small to be visible). (D) ATF4 protein stability is unaffected by mTOR inhibition. Extracts were prepared from HEK293T cells pre-treated with 100 μg/mL cycloheximide for 5 min and then with vehicle (DMSO) or 250 nM Torin 1 for the indicated times, and they were analyzed for the indicated proteins by immunoblotting (left panel) and quantified by normalizing levels of ATF4 to EIF3B (right panel) (n = 3, error bars are SD). (E) mTOR inhibition preferentially decreases translation of the ATF4-coding ORF. Top panel: ribosome profiling data from HEK293T cells treated for 24 hr with vehicle (DMSO) or 250 nM Torin 1 are shown. Bar heights are reads per million (RPM) for each position in the spliced ATF4 transcript, and they are the combined values of two replicate libraries. Bottom panel: organization of ORFs in the ATF4 mRNA is shown. (F) mTOR-regulated change in the translation efficiency of ATF4 ORFs. Translation efficiencies of ATF4 uORF3 and main ORF (mORF) were calculated by normalizing ribosome-protected fragment (RPF) reads from (E) from non-overlapping segments of uORF3 or mORF to RNA levels in DMSO- and Torin 1-treated conditions (n = 2, error bars are SD, significance calculated by t test). (G) Top panel: reporter design. 5′ UTRs are from wild-type human ATF4 (WT), ATF4 with start codon of uORF3 mutated to TAC (DuORF3), or ACTB. Bottom panel: cells were treated with 10 μM TMP to stabilize YFP concurrently with vehicle (DMSO) or 250 nM Torin 1, and they were monitored for fluorescence at the indicated times (n = 9, error bars are SEM). (H) uORF3 is required for mTOR control of full-length ATF4. ATF4 −/− HEK293T cells stably expressing dox-inducible WT or DuORF3 ATF4 were treated with 1.0 μg/mL (WT) or 0.5 μg/mL (ΔuORF3) doxycycline for 40 hr, and then with vehicle (DMSO) or 250 nM Torin 1 for 1 hr. Cell extracts were prepared and analyzed by immunoblotting for the indicated proteins. (I) Gcn2 is required for mTOR control of eIF2α phosphorylation, but not ATF4 translation. Extracts were prepared from Gcn2 +/+ or Gcn2 −/− MEFs treated with vehicle (DMSO) or 250 nM Torin 1 for 4 hr, and they were analyzed by immunoblotting for the indicated proteins.

    Journal: Cell reports

    Article Title: mTORC1 Balances Cellular Amino Acid Supply with Demand for Protein Synthesis through Post-transcriptional Control of ATF4

    doi: 10.1016/j.celrep.2017.04.042

    Figure Lengend Snippet: mTOR Controls ATF4 Translation and mRNA Stability (A) mTOR reduces ATF4 mRNA levels. RNA was isolated from cells treated with vehicle (DMSO) or 250 nM Torin 1 for the indicated times and analyzed by qPCR. RNA levels were normalized to GAPDH (n = 3, error bars are SD). (B) mTOR activity has little effect on ATF4 transcription. HEK293T cells were treated with vehicle or 250 nM Torin 1 for 4 hr and then pulsed for 15 and 30 min with 100 μM 4sU. RNA was reacted with MTS-biotin, isolated by streptavidin-affinity purification, and analyzed by qPCR. Synthesis rates were determined by comparing 4sU labeling at 15 and 30 min and compared to changes in steady-state mRNA levels (n = 3, error bars are SD). (C) mTOR inhibition decreases the half-life of ATF4 mRNA. ATF4 −/− HEK293T cells simultaneously expressing doxycycline-repressible constructs encoding ATF4 and GFP were pre-treated with vehicle or 250 nM Torin 1 for 30 min, and then 1 μg/mL doxycycline. mRNA was collected at 0 and 6 hr post-doxycycline addition and analyzed by qPCR. mRNA levels were normalized to GAPDH (n = 3, error bars are SD, but are too small to be visible). (D) ATF4 protein stability is unaffected by mTOR inhibition. Extracts were prepared from HEK293T cells pre-treated with 100 μg/mL cycloheximide for 5 min and then with vehicle (DMSO) or 250 nM Torin 1 for the indicated times, and they were analyzed for the indicated proteins by immunoblotting (left panel) and quantified by normalizing levels of ATF4 to EIF3B (right panel) (n = 3, error bars are SD). (E) mTOR inhibition preferentially decreases translation of the ATF4-coding ORF. Top panel: ribosome profiling data from HEK293T cells treated for 24 hr with vehicle (DMSO) or 250 nM Torin 1 are shown. Bar heights are reads per million (RPM) for each position in the spliced ATF4 transcript, and they are the combined values of two replicate libraries. Bottom panel: organization of ORFs in the ATF4 mRNA is shown. (F) mTOR-regulated change in the translation efficiency of ATF4 ORFs. Translation efficiencies of ATF4 uORF3 and main ORF (mORF) were calculated by normalizing ribosome-protected fragment (RPF) reads from (E) from non-overlapping segments of uORF3 or mORF to RNA levels in DMSO- and Torin 1-treated conditions (n = 2, error bars are SD, significance calculated by t test). (G) Top panel: reporter design. 5′ UTRs are from wild-type human ATF4 (WT), ATF4 with start codon of uORF3 mutated to TAC (DuORF3), or ACTB. Bottom panel: cells were treated with 10 μM TMP to stabilize YFP concurrently with vehicle (DMSO) or 250 nM Torin 1, and they were monitored for fluorescence at the indicated times (n = 9, error bars are SEM). (H) uORF3 is required for mTOR control of full-length ATF4. ATF4 −/− HEK293T cells stably expressing dox-inducible WT or DuORF3 ATF4 were treated with 1.0 μg/mL (WT) or 0.5 μg/mL (ΔuORF3) doxycycline for 40 hr, and then with vehicle (DMSO) or 250 nM Torin 1 for 1 hr. Cell extracts were prepared and analyzed by immunoblotting for the indicated proteins. (I) Gcn2 is required for mTOR control of eIF2α phosphorylation, but not ATF4 translation. Extracts were prepared from Gcn2 +/+ or Gcn2 −/− MEFs treated with vehicle (DMSO) or 250 nM Torin 1 for 4 hr, and they were analyzed by immunoblotting for the indicated proteins.

    Article Snippet: Materials Reagents were obtained from the following sources: antibodies for ATF4, S6K, phospho-T389-S6K, eIF2α, phospho-Ser51-eIF2α, 4E-BP1, GCN2, and UPF1 from Cell Signaling Technology; primary antibodies for eIF3b and horseradish peroxidase (HRP)-labeled secondary antibodies from Santa Cruz Biotechnology; IRDye secondary antibodies from LI-COR Biosciences; 14 C-labeled AA mixture (011014750) from MP Biomedicals; Trizol and DMEM from Life Technologies; heat-inactivated fetal bovine serum (FBS), recombinant 4E-BP1, and 7mGDP from Sigma-Aldrich; RNase If, polynucleotide kinase, Proto-script II reverse transcriptase, and streptavidin-coated magnetic beads from New England Biolabs; iTaq Universal SYBR Green Supermix and Bradford Protein Assay from Bio-Rad; MTSEA biotin-XX from Pierce/Thermo Fisher Scientific; RNeasy Plus Mini Kit from QIAGEN; and XtremeGENE 9 transfection reagent from Roche.

    Techniques: Isolation, Real-time Polymerase Chain Reaction, Activity Assay, Affinity Purification, Labeling, Inhibition, Expressing, Construct, Fluorescence, Stable Transfection