streptavidin coated magnetic beads  (New England Biolabs)


Bioz Verified Symbol New England Biolabs is a verified supplier  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 90
    Name:
    Streptavidin Magnetic Beads
    Description:
    Streptavidin Magnetic Beads 5 ml
    Catalog Number:
    s1420s
    Price:
    303
    Size:
    5 ml
    Category:
    Magnetic Separation Equipment
    Buy from Supplier


    Structured Review

    New England Biolabs streptavidin coated magnetic beads
    Streptavidin Magnetic Beads
    Streptavidin Magnetic Beads 5 ml
    https://www.bioz.com/result/streptavidin coated magnetic beads/product/New England Biolabs
    Average 90 stars, based on 13 article reviews
    Price from $9.99 to $1999.99
    streptavidin coated magnetic beads - by Bioz Stars, 2020-01
    90/100 stars

    Images

    1) Product Images from "Simultaneous and stoichiometric purification of hundreds of oligonucleotides"

    Article Title: Simultaneous and stoichiometric purification of hundreds of oligonucleotides

    Journal: Nature Communications

    doi: 10.1038/s41467-018-04870-w

    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
    Figure Legend 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

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

    2) Product Images from "Selection of Single-Stranded DNA Molecular Recognition Elements against Exotoxin A Using a Novel Decoy-SELEX Method and Sensitive Detection of Exotoxin A in Human Serum"

    Article Title: Selection of Single-Stranded DNA Molecular Recognition Elements against Exotoxin A Using a Novel Decoy-SELEX Method and Sensitive Detection of Exotoxin A in Human Serum

    Journal: BioMed Research International

    doi: 10.1155/2015/417641

    Structures of targets used in the Decoy-SELEX and SPR cross-binding assays. (a) Ribbon structure of the target of interest, Exotoxin A (PDB 1IKQ, 66 kDa) [ 8 ]. (b) Ribbon structure of streptavidin (PDB 4GJS, 60 kDa) used in cross bind assays [ 23 ]. ((c), (d)) Ribbon structures of bovine serum albumin (PDB 4F5S, 66.5 kDa) and Cholera toxin (PDB 2A5D, 84 kDa) used in negative rounds of selection and crossing binding assays [ 24 , 25 ]. (e) Chemical structure of biotin used in negative rounds of selection and cross-binding assays.
    Figure Legend Snippet: Structures of targets used in the Decoy-SELEX and SPR cross-binding assays. (a) Ribbon structure of the target of interest, Exotoxin A (PDB 1IKQ, 66 kDa) [ 8 ]. (b) Ribbon structure of streptavidin (PDB 4GJS, 60 kDa) used in cross bind assays [ 23 ]. ((c), (d)) Ribbon structures of bovine serum albumin (PDB 4F5S, 66.5 kDa) and Cholera toxin (PDB 2A5D, 84 kDa) used in negative rounds of selection and crossing binding assays [ 24 , 25 ]. (e) Chemical structure of biotin used in negative rounds of selection and cross-binding assays.

    Techniques Used: SPR Assay, Binding Assay, Selection

    3) Product Images from "Identification of novel proteins binding the AU-rich element of α-prothymosin mRNA through the selection of open reading frames (RIDome)"

    Article Title: Identification of novel proteins binding the AU-rich element of α-prothymosin mRNA through the selection of open reading frames (RIDome)

    Journal: RNA Biology

    doi: 10.1080/15476286.2015.1107702

    In vitro validation of the selected RNA-binding proteins by ELISA-based assays. ( A) Validation by phage ELISA. The reactivity of 12 top-ranking genes was tested on the ARE PTMA RNA oligonucleotide. To test specificity, a mutated RNA (AREmut PTMA ), an ssDNA oligonucleotide and streptavidin served as controls. Values are indicated as the fold signal vs. the background (uncoated wells). ( B) BLASTP analysis of ORF clones validated by GST ELISA. ELAVL1, RBM38, R3HDM2 and RALY contain at least one conserved RNA-binding domain. ( C) Validation by GST ELISA. Selected ORFs with positive phage ELISA results were subcloned into a compatible pGEX vector and purified as GST fusion proteins. Assays were performed as in A.
    Figure Legend Snippet: In vitro validation of the selected RNA-binding proteins by ELISA-based assays. ( A) Validation by phage ELISA. The reactivity of 12 top-ranking genes was tested on the ARE PTMA RNA oligonucleotide. To test specificity, a mutated RNA (AREmut PTMA ), an ssDNA oligonucleotide and streptavidin served as controls. Values are indicated as the fold signal vs. the background (uncoated wells). ( B) BLASTP analysis of ORF clones validated by GST ELISA. ELAVL1, RBM38, R3HDM2 and RALY contain at least one conserved RNA-binding domain. ( C) Validation by GST ELISA. Selected ORFs with positive phage ELISA results were subcloned into a compatible pGEX vector and purified as GST fusion proteins. Assays were performed as in A.

    Techniques Used: In Vitro, RNA Binding Assay, Enzyme-linked Immunosorbent Assay, Clone Assay, Plasmid Preparation, Purification

    4) Product Images from "The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs"

    Article Title: The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs

    Journal: The FASEB Journal

    doi: 10.1096/fj.201901618RR

    ILF3 binds the human FRAM in vitro and upon transfection of hminiSINEUP-GFP. A ) Schematic representation of hminiSINEUP-GFP constructs. The overlapping region with sense GFP mRNA, representing the BD (green), spans 39 nt of GFP 5′UTR (gray). The FRAM is the ED (red) of hSINEUP R12A-AS1 ( 30 ). hminiSINEUP-GFPΔFRAM presents the BD but lacks the FRAM sequence. B ) Analysis by phage ELISA of the binding of dsRBM2 to the human FRAM repeats RNA sequence. ELISA signals were normalized to the invSINEB2 of AS Uchl1 (SINEB2). As negative controls, bindings on streptavidin (strep) and 2 unrelated RNAs {polyuridine [poly(U)] and adenylate-uridylate–rich element (ARE)} were measured ( n = 3). C ) RNA-IP assay on endogenous ILF3 and ectopically expressed hminiSINEUP-GFP or hminiSINEUP-GFPΔFRAM in HEK 293T/17. IgGs were used as ILF3 immunoprecipitation (IP) specificity control. RNA enrichments in ILF3 IP fraction were quantified with real-time quantitative PCR and expressed as (2 Δ Ct ) × 100 ILF3 IP ÷ (2 Δ Ct ) × 100 IgG. Δ C t was calculated on input, and RNA content in IP or IgG was normalized on UBC mRNA. D ) ILF3 IP efficiency was checked by Western blot performed with anti-DRBP76 (ILF3) antibody. Data are representative of 4 independent experiments and indicate means ± sd . NS, not significant. * P
    Figure Legend Snippet: ILF3 binds the human FRAM in vitro and upon transfection of hminiSINEUP-GFP. A ) Schematic representation of hminiSINEUP-GFP constructs. The overlapping region with sense GFP mRNA, representing the BD (green), spans 39 nt of GFP 5′UTR (gray). The FRAM is the ED (red) of hSINEUP R12A-AS1 ( 30 ). hminiSINEUP-GFPΔFRAM presents the BD but lacks the FRAM sequence. B ) Analysis by phage ELISA of the binding of dsRBM2 to the human FRAM repeats RNA sequence. ELISA signals were normalized to the invSINEB2 of AS Uchl1 (SINEB2). As negative controls, bindings on streptavidin (strep) and 2 unrelated RNAs {polyuridine [poly(U)] and adenylate-uridylate–rich element (ARE)} were measured ( n = 3). C ) RNA-IP assay on endogenous ILF3 and ectopically expressed hminiSINEUP-GFP or hminiSINEUP-GFPΔFRAM in HEK 293T/17. IgGs were used as ILF3 immunoprecipitation (IP) specificity control. RNA enrichments in ILF3 IP fraction were quantified with real-time quantitative PCR and expressed as (2 Δ Ct ) × 100 ILF3 IP ÷ (2 Δ Ct ) × 100 IgG. Δ C t was calculated on input, and RNA content in IP or IgG was normalized on UBC mRNA. D ) ILF3 IP efficiency was checked by Western blot performed with anti-DRBP76 (ILF3) antibody. Data are representative of 4 independent experiments and indicate means ± sd . NS, not significant. * P

    Techniques Used: In Vitro, Transfection, Construct, Sequencing, Enzyme-linked Immunosorbent Assay, Binding Assay, Immunoprecipitation, Real-time Polymerase Chain Reaction, Western Blot

    ILF3 is the dominant SINEUP-interacting ORF isolated by phage display selection. A ) Schematic representation of ILF3 domains: NF45-homology domain, nuclear localization signal (NLS), dsRBMs 1 and 2, RGG motif, and GQSY domain. B ) Reads alignment to ILF3 gene showed specific enrichment of dsRBM2 (black arrows) in invSINEB2 library (middle) and AS Uchl1 Δ5′ library (bottom) but not in the NS library (top). Blue bars indicate the gene; green bars correspond to exons. C ) Representative phage ELISA experiment of the binding of the invSINEB2 sequence to ILF3 and the RNA-recognition motif of negative controls (SRSF5 and hnRNPA3). D ) Analysis by phage ELISA of the binding of dsRBM2 to AS Uchl1 Δ5′ and invSINEB2 RNA sequences. E ) Analysis by GST ELISA of the binding specificity of ILF3 dsRBM1 and mouse-human dsRBM2 to AS Uchl1 Δ5′ and invSINEB2 RNA sequences. Domains were produced as GST fusion polypeptides. Strep, streptavidin. Data indicate means ± sd . Data are representative of n = 3 independent replicas.
    Figure Legend Snippet: ILF3 is the dominant SINEUP-interacting ORF isolated by phage display selection. A ) Schematic representation of ILF3 domains: NF45-homology domain, nuclear localization signal (NLS), dsRBMs 1 and 2, RGG motif, and GQSY domain. B ) Reads alignment to ILF3 gene showed specific enrichment of dsRBM2 (black arrows) in invSINEB2 library (middle) and AS Uchl1 Δ5′ library (bottom) but not in the NS library (top). Blue bars indicate the gene; green bars correspond to exons. C ) Representative phage ELISA experiment of the binding of the invSINEB2 sequence to ILF3 and the RNA-recognition motif of negative controls (SRSF5 and hnRNPA3). D ) Analysis by phage ELISA of the binding of dsRBM2 to AS Uchl1 Δ5′ and invSINEB2 RNA sequences. E ) Analysis by GST ELISA of the binding specificity of ILF3 dsRBM1 and mouse-human dsRBM2 to AS Uchl1 Δ5′ and invSINEB2 RNA sequences. Domains were produced as GST fusion polypeptides. Strep, streptavidin. Data indicate means ± sd . Data are representative of n = 3 independent replicas.

    Techniques Used: Isolation, Selection, Enzyme-linked Immunosorbent Assay, Binding Assay, Sequencing, Produced

    5) Product Images from "Selection of Single-Stranded DNA Molecular Recognition Elements against Exotoxin A Using a Novel Decoy-SELEX Method and Sensitive Detection of Exotoxin A in Human Serum"

    Article Title: Selection of Single-Stranded DNA Molecular Recognition Elements against Exotoxin A Using a Novel Decoy-SELEX Method and Sensitive Detection of Exotoxin A in Human Serum

    Journal: BioMed Research International

    doi: 10.1155/2015/417641

    Structures of targets used in the Decoy-SELEX and SPR cross-binding assays. (a) Ribbon structure of the target of interest, Exotoxin A (PDB 1IKQ, 66 kDa) [ 8 ]. (b) Ribbon structure of streptavidin (PDB 4GJS, 60 kDa) used in cross bind assays [ 23 ]. ((c), (d)) Ribbon structures of bovine serum albumin (PDB 4F5S, 66.5 kDa) and Cholera toxin (PDB 2A5D, 84 kDa) used in negative rounds of selection and crossing binding assays [ 24 , 25 ]. (e) Chemical structure of biotin used in negative rounds of selection and cross-binding assays.
    Figure Legend Snippet: Structures of targets used in the Decoy-SELEX and SPR cross-binding assays. (a) Ribbon structure of the target of interest, Exotoxin A (PDB 1IKQ, 66 kDa) [ 8 ]. (b) Ribbon structure of streptavidin (PDB 4GJS, 60 kDa) used in cross bind assays [ 23 ]. ((c), (d)) Ribbon structures of bovine serum albumin (PDB 4F5S, 66.5 kDa) and Cholera toxin (PDB 2A5D, 84 kDa) used in negative rounds of selection and crossing binding assays [ 24 , 25 ]. (e) Chemical structure of biotin used in negative rounds of selection and cross-binding assays.

    Techniques Used: SPR Assay, Binding Assay, Selection

    6) Product Images from "A Novel mRNA Level Subtraction Method for Quick Identification of Target-Orientated Uniquely Expressed Genes Between Peanut Immature Pod and Leaf"

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

    Journal: Biological Procedures Online

    doi: 10.1007/s12575-009-9022-z

    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.
    Figure Legend 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.

    Techniques Used:

    7) Product Images from "La-related protein 1 (LARP1) repression of TOP mRNA translation is mediated through its cap-binding domain and controlled by an adjacent regulatory region"

    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

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkx1237

    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.
    Figure Legend 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.

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

    8) Product Images from "mTORC1 Balances Cellular Amino Acid Supply with Demand for Protein Synthesis through Post-transcriptional Control of ATF4"

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

    Journal: Cell reports

    doi: 10.1016/j.celrep.2017.04.042

    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.
    Figure Legend 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.

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

    9) Product Images from "A Novel mRNA Level Subtraction Method for Quick Identification of Target-Orientated Uniquely Expressed Genes Between Peanut Immature Pod and Leaf"

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

    Journal: Biological Procedures Online

    doi: 10.1007/s12575-009-9022-z

    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.
    Figure Legend 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.

    Techniques Used:

    10) Product Images from "La-related protein 1 (LARP1) repression of TOP mRNA translation is mediated through its cap-binding domain and controlled by an adjacent regulatory region"

    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

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkx1237

    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.
    Figure Legend 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.

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

    11) Product Images from "A Novel mRNA Level Subtraction Method for Quick Identification of Target-Orientated Uniquely Expressed Genes Between Peanut Immature Pod and Leaf"

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

    Journal: Biological Procedures Online

    doi: 10.1007/s12575-009-9022-z

    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.
    Figure Legend 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.

    Techniques Used:

    Related Articles

    Centrifugation:

    Article Title: Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1
    Article Snippet: Cell lysates were cleared by centrifugation at 40,000 rpm in Beckman L-80 ultracentrifuge at room temperature for 30 minutes using Ti 70.1 rotor. .. The pH of the eluate was neutralized and loaded onto streptavidin magnetic beads (New England Biolabs).

    Article Title: Age dependency of vasopressin pulmonary vasodilatory effect in rats
    Article Snippet: The digest was then passed through 70 μm cell strainer to remove tissue fragments, pelleted by centrifugation at 200 G for 10 min and resuspended with 2% fetal bovine serum (FBS, Gibco) in phosphate buffered solution containing 5μl biotinylated rat anti-mouse CD31 antibody (BD, PharMingen, San Diego, CA). .. After incubation on ice for 1h, the endothelial cells were immobilized with streptavidin magnetic beads (New England Biolabs, Ipswich, MA) on ice.

    Amplification:

    Article Title: Selection of an improved RNA polymerase ribozyme with superior extension and fidelity
    Article Snippet: The pool was applied to streptavidin magnetic beads (NEB) and washed three times with SSC 0.5× buffer. .. This DNA was then PCR amplified, BtgI digested, and ligated to the selection DNA/RNA primer before starting the subsequent round of selection.

    Expressing:

    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. .. Relative expression of IL8, KLF2 and α Tubulin1A was analyzed by qRT-PCR.

    Article Title: Age dependency of vasopressin pulmonary vasodilatory effect in rats
    Article Snippet: Western blotting Primary endothelial and smooth muscle cells retrieved from intrapulmonary and mesenteric arteries, as well as the whole tissue extracts were utilized to measured vasopressin V1a and V2 receptors expression. .. After incubation on ice for 1h, the endothelial cells were immobilized with streptavidin magnetic beads (New England Biolabs, Ipswich, MA) on ice.

    Neutralization:

    Article Title: Nitric oxide alleviates cell death through protein S-nitrosylation and transcriptional regulation during the ageing of elm seeds
    Article Snippet: Finally, the pellet was analysed using either immunoblotting with anti-biotin antibody (Cayman) or affinity purification using streptavidin magnetic beads (NEB). .. The pellet was re-suspended in neutralization buffer (25 mM HEPES-NaOH, 100 mM NaCl, 1 mM EDTA, and 0.5% Triton X-100, pH 7.5) and transferred to bind with streptavidin beads.

    Construct:

    Article Title: Src kinase phosphorylates Notch1 to inhibit MAML binding
    Article Snippet: 293 T cells were Trans IT®-LT1 (Mirus) lipid transfected with either 2058–2161::BirA or N1ICD::BirA fusion constructs. .. Streptavidin magnetic beads (10 µL, New England BioLabs) were used to precipitate biotinylated species on a magnetic tube rack.

    DNA Binding Assay:

    Article Title: The Huntington's disease mutation impairs Huntingtin's role in the transport of NF-\u03baB from the synapse to the nucleus
    Article Snippet: Paragraph title: NF-κB DNA-binding assay ... Five hundred micrograms of streptavidin magnetic beads (New England BioLabs) were washed with 1 ml of buffer A (20 m m Tris–HCl, pH 7.5, 0.5 m sodium chloride, 1 m m EDTA) using a magnetic separation rack (New England BioLabs).

    Incubation:

    Article Title: Dopamine Neuron Stimulating Actions of a GDNF Propeptide
    Article Snippet: DNSP-11 Pull-down Assay with Rat Substantia Nigra Homogenate Fischer 344 rat substantia nigra was homogenized in homogenization buffer (modified from with 20 mM HEPES, pH 7.4) and cytosolic fraction (supernatant) collected after 30 minutes at 100,000 g. 50 µg of bDNSP-11 was incubated with fraction for 15 minutes on ice. .. Sample was added to streptavidin magnetic beads (New England Biolabs), pelleted, and washed four times in homogenization buffer.

    Article Title: Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1
    Article Snippet: Cleared lysates were incubated with Ni-NTA agarose (QIAGEN, 500 µl slurry pre-equilibrated in buffer-1) for 3 hours at room temperature. .. The pH of the eluate was neutralized and loaded onto streptavidin magnetic beads (New England Biolabs).

    Article Title: The Huntington's disease mutation impairs Huntingtin's role in the transport of NF-\u03baB from the synapse to the nucleus
    Article Snippet: Five hundred micrograms of streptavidin magnetic beads (New England BioLabs) were washed with 1 ml of buffer A (20 m m Tris–HCl, pH 7.5, 0.5 m sodium chloride, 1 m m EDTA) using a magnetic separation rack (New England BioLabs). .. After washing, the beads were resuspended in 50 µl of buffer A supplemented with 250 pmol of biotinylated double-stranded DNA oligonucleotides (Integrated DNA Technologies) containing a wild-type κB site [5′-AGTTGAGGGGACTTTCCCAGGC-3′], and incubated for 10 min at room temperature to allow for binding of the biotinylated oligonucleotides to the streptavidin beads.

    Article Title: Kinetic mechanism for viral dsRNA length discrimination by MDA5 filaments
    Article Snippet: .. The binding reaction was quenched with 60 μg/mL heparin and 2 mM ADP⋅AlF4 and was incubated with streptavidin magnetic beads (New England BioLabs). ..

    Article Title: Comparison of Protein Gut Samples from Rhipicephalus spp. Using a Crude and an Innovative Preparation Method for Proteome Analysis
    Article Snippet: Cell lysis was performed by adding 100 µL of 1× PBS, 1% Triton X-100, 10% glycerol, 100 µm oxidized glutathione and PIC to the biotinylated cells, incubated for an hour on ice, with gentle agitation every 10 min. Biotinylated cells were centrifuged at 20,000× g at 4 °C for 20 min, with the supernatant containing the cytoplasmic and biotinylated surface proteins collected. .. Streptavidin magnetic beads (New England Biolabs, Arundel, QLD, Australia) were used to purify the biotinylated surface proteins from the cytoplasmic proteins as per the manufacturer’s instructions.

    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: Selection of an improved RNA polymerase ribozyme with superior extension and fidelity
    Article Snippet: The emulsion was incubated for ∼18 h at room temperature after heat inactivating the T7 RNAP. .. The pool was applied to streptavidin magnetic beads (NEB) and washed three times with SSC 0.5× buffer.

    Article Title: Age dependency of vasopressin pulmonary vasodilatory effect in rats
    Article Snippet: .. After incubation on ice for 1h, the endothelial cells were immobilized with streptavidin magnetic beads (New England Biolabs, Ipswich, MA) on ice. .. The endothelial cells were then placed on the EasySep magnet (Stemcell technologies, Vancouver, BC, Canada) for 5 min and unbound cells were removed.

    Stripping Membranes:

    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.

    Activity Assay:

    Article Title: The Huntington's disease mutation impairs Huntingtin's role in the transport of NF-\u03baB from the synapse to the nucleus
    Article Snippet: The DNA-binding activity of NF-κB in the nuclear extract was analyzed by DNA pull-down assay as follows. .. Five hundred micrograms of streptavidin magnetic beads (New England BioLabs) were washed with 1 ml of buffer A (20 m m Tris–HCl, pH 7.5, 0.5 m sodium chloride, 1 m m EDTA) using a magnetic separation rack (New England BioLabs).

    Mass Spectrometry:

    Article Title: Dopamine Neuron Stimulating Actions of a GDNF Propeptide
    Article Snippet: Sample was added to streptavidin magnetic beads (New England Biolabs), pelleted, and washed four times in homogenization buffer. .. MS data were compared to the Uniprot database utilizing the Paragon™ algorithm in ProteinPilot Version 2.0 (Applied Bioscience).

    Modification:

    Article Title: Dopamine Neuron Stimulating Actions of a GDNF Propeptide
    Article Snippet: DNSP-11 Pull-down Assay with Rat Substantia Nigra Homogenate Fischer 344 rat substantia nigra was homogenized in homogenization buffer (modified from with 20 mM HEPES, pH 7.4) and cytosolic fraction (supernatant) collected after 30 minutes at 100,000 g. 50 µg of bDNSP-11 was incubated with fraction for 15 minutes on ice. .. Sample was added to streptavidin magnetic beads (New England Biolabs), pelleted, and washed four times in homogenization buffer.

    Western Blot:

    Article Title: Age dependency of vasopressin pulmonary vasodilatory effect in rats
    Article Snippet: Paragraph title: Western blotting ... After incubation on ice for 1h, the endothelial cells were immobilized with streptavidin magnetic beads (New England Biolabs, Ipswich, MA) on ice.

    Conjugation Assay:

    Article Title: Comparison of Protein Gut Samples from Rhipicephalus spp. Using a Crude and an Innovative Preparation Method for Proteome Analysis
    Article Snippet: Isolated epithelial cells were biotinylated using a Biotin (Type A) conjugation kit (ABCAM, Wetherill Park, NSW, Australia), at a molar ratio 1:1 surface protein to conjugate as per the manufacturer’s instructions. .. Streptavidin magnetic beads (New England Biolabs, Arundel, QLD, Australia) were used to purify the biotinylated surface proteins from the cytoplasmic proteins as per the manufacturer’s instructions.

    Transfection:

    Article Title: miR-106b-responsive gene landscape identifies regulation of Kruppel-like factor family
    Article Snippet: Pull down of biotinylated RNA : Mz-ChA-1 cells were transfected with 50 nM of biotinylated microRNA using Lipofectamine RNAiMAX in triplicate. .. 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.

    Ligation:

    Article Title: Src kinase phosphorylates Notch1 to inhibit MAML binding
    Article Snippet: Paragraph title: Proximity biotin ligation assays ... Streptavidin magnetic beads (10 µL, New England BioLabs) were used to precipitate biotinylated species on a magnetic tube rack.

    Protease Inhibitor:

    Article Title: Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1
    Article Snippet: Proteins were eluted in 8 ml of buffer-2 (8 M urea, 200 mM NaCl, 2% SDS, 50 mM sodium phosphate, 10 mM EDTA, 100 mM Tris-HCl, pH 4.3, and EDTA-free protease inhibitor mix for His-Tag sequences (RPI)). .. The pH of the eluate was neutralized and loaded onto streptavidin magnetic beads (New England Biolabs).

    Article Title: The Huntington's disease mutation impairs Huntingtin's role in the transport of NF-\u03baB from the synapse to the nucleus
    Article Snippet: One mouse forebrain was homogenized in 2.4 ml of ice-cold homogenization buffer [HB;20 m m Tricine–KOH, pH 7.8, 0.25 m sucrose, 25 m m potassium chloride, 5 m m magnesium chloride, 1× protease inhibitor cocktail (Roche, Complete EDTA-free)]. .. Five hundred micrograms of streptavidin magnetic beads (New England BioLabs) were washed with 1 ml of buffer A (20 m m Tris–HCl, pH 7.5, 0.5 m sodium chloride, 1 m m EDTA) using a magnetic separation rack (New England BioLabs).

    Article Title: miR-106b-responsive gene landscape identifies regulation of Kruppel-like factor family
    Article Snippet: After 24 hours, cells were lysed (20 mM Tris, pH 7.5, 100 mM KCl, 5 mM MgCl2, 0.3% NP40, 50 U of RNase OUT and complete protease inhibitor) and incubated on ice for 10 minutes. .. 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.

    Protein Concentration:

    Article Title: The Huntington's disease mutation impairs Huntingtin's role in the transport of NF-\u03baB from the synapse to the nucleus
    Article Snippet: Five hundred micrograms of streptavidin magnetic beads (New England BioLabs) were washed with 1 ml of buffer A (20 m m Tris–HCl, pH 7.5, 0.5 m sodium chloride, 1 m m EDTA) using a magnetic separation rack (New England BioLabs). .. The DNA-coated beads were then washed three times with 1 ml of buffer A and incubated for 30 min at room temperature in 400 µl of buffer B [20 m m Tris–HCl, pH 7.5, 20 m m sodium chloride, 1 m m dithiothreitol] supplemented with 50 ng/µl poly(dI-dC) and 100 µl of nuclear extract (1 mg/ml total protein concentration).

    Sequencing:

    Article Title: Metabolite Profiling of the Antisense Oligonucleotide Eluforsen Using Liquid Chromatography-Mass Spectrometry
    Article Snippet: Its sequence was 5′-AUC AUA GGA AAC ACC AAA GAU GAU AUU UUC UUU-3′. .. RNase A was acquired from Thermo Fisher Scientific (Waltham, MA, USA), and Exo T, the reaction buffer (10× NE buffer 4), and streptavidin magnetic beads were purchased from New England Biolabs (Ipswich, MA, USA).

    Sonication:

    Article Title: Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1
    Article Snippet: Lysates were thawed at room temperature, resuspended in 5 ml of buffer-1 then sonicated using a 1/8″ microprobe tip of Branson sonifer cell disruptor Model 250/450. .. The pH of the eluate was neutralized and loaded onto streptavidin magnetic beads (New England Biolabs).

    Affinity Purification:

    Article Title: Nitric oxide alleviates cell death through protein S-nitrosylation and transcriptional regulation during the ageing of elm seeds
    Article Snippet: .. Finally, the pellet was analysed using either immunoblotting with anti-biotin antibody (Cayman) or affinity purification using streptavidin magnetic beads (NEB). .. The pellet was re-suspended in neutralization buffer (25 mM HEPES-NaOH, 100 mM NaCl, 1 mM EDTA, and 0.5% Triton X-100, pH 7.5) and transferred to bind with streptavidin beads.

    Binding Assay:

    Article Title: The Huntington's disease mutation impairs Huntingtin's role in the transport of NF-\u03baB from the synapse to the nucleus
    Article Snippet: Five hundred micrograms of streptavidin magnetic beads (New England BioLabs) were washed with 1 ml of buffer A (20 m m Tris–HCl, pH 7.5, 0.5 m sodium chloride, 1 m m EDTA) using a magnetic separation rack (New England BioLabs). .. After washing, the beads were resuspended in 50 µl of buffer A supplemented with 250 pmol of biotinylated double-stranded DNA oligonucleotides (Integrated DNA Technologies) containing a wild-type κB site [5′-AGTTGAGGGGACTTTCCCAGGC-3′], and incubated for 10 min at room temperature to allow for binding of the biotinylated oligonucleotides to the streptavidin beads.

    Article Title: Kinetic mechanism for viral dsRNA length discrimination by MDA5 filaments
    Article Snippet: .. The binding reaction was quenched with 60 μg/mL heparin and 2 mM ADP⋅AlF4 and was incubated with streptavidin magnetic beads (New England BioLabs). ..

    Article Title: Identification of novel PANDAR protein interaction partners involved in splicing regulation
    Article Snippet: .. To rule out unspecific binding of proteins to streptavidin magnetic beads, beads without RNA were used. .. The supernatants of cell lysates (as described before) were incubated with either PANDAR coated or empty beads for 2 h at 4 °C on a rotating wheel.

    Pull Down Assay:

    Article Title: Dopamine Neuron Stimulating Actions of a GDNF Propeptide
    Article Snippet: Paragraph title: DNSP-11 Pull-down Assay with Rat Substantia Nigra Homogenate ... Sample was added to streptavidin magnetic beads (New England Biolabs), pelleted, and washed four times in homogenization buffer.

    Article Title: The Huntington's disease mutation impairs Huntingtin's role in the transport of NF-\u03baB from the synapse to the nucleus
    Article Snippet: The DNA-binding activity of NF-κB in the nuclear extract was analyzed by DNA pull-down assay as follows. .. Five hundred micrograms of streptavidin magnetic beads (New England BioLabs) were washed with 1 ml of buffer A (20 m m Tris–HCl, pH 7.5, 0.5 m sodium chloride, 1 m m EDTA) using a magnetic separation rack (New England BioLabs).

    Magnetic Beads:

    Article Title: Dopamine Neuron Stimulating Actions of a GDNF Propeptide
    Article Snippet: .. Sample was added to streptavidin magnetic beads (New England Biolabs), pelleted, and washed four times in homogenization buffer. .. Bound proteins were eluted by Solubilization/Rehydration Solution (7 M Urea, 2 M Thiourea, 50 mM DTT, 4% CHAPS, 1% NP-40, 0.2% Carrier ampholytes, 0.0002% Bromophenol blue), and analyzed by 2D-PAGE (BioRad) and later identified by MALDI-TOF MS/MS.

    Article Title: Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1
    Article Snippet: .. The pH of the eluate was neutralized and loaded onto streptavidin magnetic beads (New England Biolabs). .. A 200 µl slurry of beads was pre-equilibrated in buffer-3 (8 M urea, 200 mM NaCl, 0.2% SDS, 100 mM Tris-HCl, pH 8.0, and EDTA-free protease inhibitor mix for His-Tag sequences).

    Article Title: The Huntington's disease mutation impairs Huntingtin's role in the transport of NF-\u03baB from the synapse to the nucleus
    Article Snippet: .. Five hundred micrograms of streptavidin magnetic beads (New England BioLabs) were washed with 1 ml of buffer A (20 m m Tris–HCl, pH 7.5, 0.5 m sodium chloride, 1 m m EDTA) using a magnetic separation rack (New England BioLabs). .. After washing, the beads were resuspended in 50 µl of buffer A supplemented with 250 pmol of biotinylated double-stranded DNA oligonucleotides (Integrated DNA Technologies) containing a wild-type κB site [5′-AGTTGAGGGGACTTTCCCAGGC-3′], and incubated for 10 min at room temperature to allow for binding of the biotinylated oligonucleotides to the streptavidin beads.

    Article Title: Nitric oxide alleviates cell death through protein S-nitrosylation and transcriptional regulation during the ageing of elm seeds
    Article Snippet: .. Finally, the pellet was analysed using either immunoblotting with anti-biotin antibody (Cayman) or affinity purification using streptavidin magnetic beads (NEB). .. The pellet was re-suspended in neutralization buffer (25 mM HEPES-NaOH, 100 mM NaCl, 1 mM EDTA, and 0.5% Triton X-100, pH 7.5) and transferred to bind with streptavidin 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: Kinetic mechanism for viral dsRNA length discrimination by MDA5 filaments
    Article Snippet: .. The binding reaction was quenched with 60 μg/mL heparin and 2 mM ADP⋅AlF4 and was incubated with streptavidin magnetic beads (New England BioLabs). ..

    Article Title: Comparison of Protein Gut Samples from Rhipicephalus spp. Using a Crude and an Innovative Preparation Method for Proteome Analysis
    Article Snippet: .. Streptavidin magnetic beads (New England Biolabs, Arundel, QLD, Australia) were used to purify the biotinylated surface proteins from the cytoplasmic proteins as per the manufacturer’s instructions. ..

    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: Metabolite Profiling of the Antisense Oligonucleotide Eluforsen Using Liquid Chromatography-Mass Spectrometry
    Article Snippet: .. RNase A was acquired from Thermo Fisher Scientific (Waltham, MA, USA), and Exo T, the reaction buffer (10× NE buffer 4), and streptavidin magnetic beads were purchased from New England Biolabs (Ipswich, MA, USA). .. Magnesium acetate, EDTA, DTT, guanidine hydrochloride, Triton X-100, tetrahydrofuran (THF), ammonium bicarbonate (NH4 HCO3 ), tris (2-carboxyethyl) phosphine (TCEP), and sodium chloride (NaCl) were obtained from Sigma Aldrich (St. Louis, MO, USA) as well.

    Article Title: Selection of an improved RNA polymerase ribozyme with superior extension and fidelity
    Article Snippet: .. The pool was applied to streptavidin magnetic beads (NEB) and washed three times with SSC 0.5× buffer. ..

    Article Title: Dopamine Neuron Stimulating Actions of a GDNF Propeptide
    Article Snippet: .. In the presence (top) and absence (bottom) of bDNSP-11 with streptavidin magnetic beads. .. F344 substantia nigra was homogenized in homogenization buffer and cytosolic fraction (supernatant) collected after 30 minutes at 100,000 g. 50 µg of bDNSP-11 was incubated with fraction for 15 minutes on ice.

    Article Title: Age dependency of vasopressin pulmonary vasodilatory effect in rats
    Article Snippet: .. After incubation on ice for 1h, the endothelial cells were immobilized with streptavidin magnetic beads (New England Biolabs, Ipswich, MA) on ice. .. The endothelial cells were then placed on the EasySep magnet (Stemcell technologies, Vancouver, BC, Canada) for 5 min and unbound cells were removed.

    Mutagenesis:

    Article Title: The Huntington's disease mutation impairs Huntingtin's role in the transport of NF-\u03baB from the synapse to the nucleus
    Article Snippet: Five hundred micrograms of streptavidin magnetic beads (New England BioLabs) were washed with 1 ml of buffer A (20 m m Tris–HCl, pH 7.5, 0.5 m sodium chloride, 1 m m EDTA) using a magnetic separation rack (New England BioLabs). .. An equal amount of biotinylated oligonucleotides containing a mutant κB site [5′-AGTTGAGGCGACTTTCCCAGGC-3′] was used as negative control.

    Isolation:

    Article Title: Comparison of Protein Gut Samples from Rhipicephalus spp. Using a Crude and an Innovative Preparation Method for Proteome Analysis
    Article Snippet: Paragraph title: 2.2. Isolation of Single Epithelial Cells and Purification of Surface Proteins ... Streptavidin magnetic beads (New England Biolabs, Arundel, QLD, Australia) were used to purify the biotinylated surface proteins from the cytoplasmic proteins as per the manufacturer’s instructions.

    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. .. After pull down, RNA was isolated using mir Vana kit.

    Article Title: Age dependency of vasopressin pulmonary vasodilatory effect in rats
    Article Snippet: For vascular endothelial cells isolation the tissue digested with 1 mg/ml of collagenase type II (Sigma-Aldrich, Oakville, Ontario, Canada) for 2h at 37°C. .. After incubation on ice for 1h, the endothelial cells were immobilized with streptavidin magnetic beads (New England Biolabs, Ipswich, MA) on ice.

    Tandem Mass Spectroscopy:

    Article Title: Dopamine Neuron Stimulating Actions of a GDNF Propeptide
    Article Snippet: Sample was added to streptavidin magnetic beads (New England Biolabs), pelleted, and washed four times in homogenization buffer. .. Bound proteins were eluted by Solubilization/Rehydration Solution (7 M Urea, 2 M Thiourea, 50 mM DTT, 4% CHAPS, 1% NP-40, 0.2% Carrier ampholytes, 0.0002% Bromophenol blue), and analyzed by 2D-PAGE (BioRad) and later identified by MALDI-TOF MS/MS.

    Labeling:

    Article Title: Kinetic mechanism for viral dsRNA length discrimination by MDA5 filaments
    Article Snippet: For binding kinetics, labeled MDA5 (0.3 μM) was incubated with 3′-biotinylated dsRNA (0.6 μg/mL) at 37 °C in buffer A with 2 mM ADPCP for the indicated time periods. .. The binding reaction was quenched with 60 μg/mL heparin and 2 mM ADP⋅AlF4 and was incubated with streptavidin magnetic beads (New England BioLabs).

    Purification:

    Article Title: Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1
    Article Snippet: Paragraph title: Protein–RNA purification ... The pH of the eluate was neutralized and loaded onto streptavidin magnetic beads (New England Biolabs).

    Article Title: Comparison of Protein Gut Samples from Rhipicephalus spp. Using a Crude and an Innovative Preparation Method for Proteome Analysis
    Article Snippet: Paragraph title: 2.2. Isolation of Single Epithelial Cells and Purification of Surface Proteins ... Streptavidin magnetic beads (New England Biolabs, Arundel, QLD, Australia) were used to purify the biotinylated surface proteins from the cytoplasmic proteins as per the manufacturer’s instructions.

    Dot Blot:

    Article Title: miR-106b-responsive gene landscape identifies regulation of Kruppel-like factor family
    Article Snippet: Biotinylated RNA was quantified by dot blot on hybond N+. .. 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.

    Polymerase Chain Reaction:

    Article Title: Selection of an improved RNA polymerase ribozyme with superior extension and fidelity
    Article Snippet: The pool was applied to streptavidin magnetic beads (NEB) and washed three times with SSC 0.5× buffer. .. This DNA was then PCR amplified, BtgI digested, and ligated to the selection DNA/RNA primer before starting the subsequent round of selection.

    Quantitative RT-PCR:

    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. .. Relative expression of IL8, KLF2 and α Tubulin1A was analyzed by qRT-PCR.

    Negative Control:

    Article Title: The Huntington's disease mutation impairs Huntingtin's role in the transport of NF-\u03baB from the synapse to the nucleus
    Article Snippet: Five hundred micrograms of streptavidin magnetic beads (New England BioLabs) were washed with 1 ml of buffer A (20 m m Tris–HCl, pH 7.5, 0.5 m sodium chloride, 1 m m EDTA) using a magnetic separation rack (New England BioLabs). .. An equal amount of biotinylated oligonucleotides containing a mutant κB site [5′-AGTTGAGGCGACTTTCCCAGGC-3′] was used as negative control.

    Selection:

    Article Title: Selection of an improved RNA polymerase ribozyme with superior extension and fidelity
    Article Snippet: Paragraph title: Selection ... The pool was applied to streptavidin magnetic beads (NEB) and washed three times with SSC 0.5× buffer.

    Homogenization:

    Article Title: Dopamine Neuron Stimulating Actions of a GDNF Propeptide
    Article Snippet: .. Sample was added to streptavidin magnetic beads (New England Biolabs), pelleted, and washed four times in homogenization buffer. .. Bound proteins were eluted by Solubilization/Rehydration Solution (7 M Urea, 2 M Thiourea, 50 mM DTT, 4% CHAPS, 1% NP-40, 0.2% Carrier ampholytes, 0.0002% Bromophenol blue), and analyzed by 2D-PAGE (BioRad) and later identified by MALDI-TOF MS/MS.

    Article Title: The Huntington's disease mutation impairs Huntingtin's role in the transport of NF-\u03baB from the synapse to the nucleus
    Article Snippet: One mouse forebrain was homogenized in 2.4 ml of ice-cold homogenization buffer [HB;20 m m Tricine–KOH, pH 7.8, 0.25 m sucrose, 25 m m potassium chloride, 5 m m magnesium chloride, 1× protease inhibitor cocktail (Roche, Complete EDTA-free)]. .. Five hundred micrograms of streptavidin magnetic beads (New England BioLabs) were washed with 1 ml of buffer A (20 m m Tris–HCl, pH 7.5, 0.5 m sodium chloride, 1 m m EDTA) using a magnetic separation rack (New England BioLabs).

    Concentration Assay:

    Article Title: Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-Poly(A) Termination Pathway: Nrd1, Nab3, and Sen1
    Article Snippet: The pH of the eluate was neutralized and loaded onto streptavidin magnetic beads (New England Biolabs). .. The streptavidin magnetic beads were resuspended in 0.5 ml of T1 buffer before RNase T1 (Fermentas) was added to obtain a final concentration of 40 U/ml and the bead suspension was incubated at room temperature for 15 minutes.

    Article Title: Selection of an improved RNA polymerase ribozyme with superior extension and fidelity
    Article Snippet: The recovered nucleic acid was denatured by adding KOH to a final concentration of 50 mM. .. The pool was applied to streptavidin magnetic beads (NEB) and washed three times with SSC 0.5× buffer.

    Liquid Chromatography with Mass Spectroscopy:

    Article Title: Metabolite Profiling of the Antisense Oligonucleotide Eluforsen Using Liquid Chromatography-Mass Spectrometry
    Article Snippet: All alkylamines, including DMCHA and DIEA, as well as 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) and LC-MS grade methanol, acetonitrile, and water were purchased from Sigma Aldrich (St. Louis, MO, USA). .. RNase A was acquired from Thermo Fisher Scientific (Waltham, MA, USA), and Exo T, the reaction buffer (10× NE buffer 4), and streptavidin magnetic beads were purchased from New England Biolabs (Ipswich, MA, USA).

    Lysis:

    Article Title: Comparison of Protein Gut Samples from Rhipicephalus spp. Using a Crude and an Innovative Preparation Method for Proteome Analysis
    Article Snippet: Cell lysis was performed by adding 100 µL of 1× PBS, 1% Triton X-100, 10% glycerol, 100 µm oxidized glutathione and PIC to the biotinylated cells, incubated for an hour on ice, with gentle agitation every 10 min. Biotinylated cells were centrifuged at 20,000× g at 4 °C for 20 min, with the supernatant containing the cytoplasmic and biotinylated surface proteins collected. .. Streptavidin magnetic beads (New England Biolabs, Arundel, QLD, Australia) were used to purify the biotinylated surface proteins from the cytoplasmic proteins as per the manufacturer’s instructions.

    Article Title: Age dependency of vasopressin pulmonary vasodilatory effect in rats
    Article Snippet: After incubation on ice for 1h, the endothelial cells were immobilized with streptavidin magnetic beads (New England Biolabs, Ipswich, MA) on ice. .. Bound endothelial cells were lysed in 10 mmol/l Tris–HCl pH 7.4 lysis buffer-containing 1% Triton X-100 and protease/phosphatase inhibitors (Roche Diagnostics Canada, Laval, Quebec, Canada) and centrifuged at 13000g for 30 min. For smooth muscle isolation, the arteries were digested with 1mg/ml collagenase type II for 2h, pelleted at 200G for 10 min, and washed with growth medium composed of DMEM (Wisent, Montreal, Quebec, Canada) supplemented with 10% FBS (Wisent, Montreal, Quebec, Canada) and 2.5% penicillin/streptomycin/fungizone.

    Kinetic Assay:

    Article Title: Kinetic mechanism for viral dsRNA length discrimination by MDA5 filaments
    Article Snippet: Paragraph title: Pull-Down Kinetic Assay. ... The binding reaction was quenched with 60 μg/mL heparin and 2 mM ADP⋅AlF4 and was incubated with streptavidin magnetic beads (New England BioLabs).

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 90
    New England Biolabs streptavidin coated magnetic beads
    Streptavidin Coated Magnetic Beads, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 12 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 90 stars, based on 12 article reviews
    Price from $9.99 to $1999.99
    streptavidin coated magnetic beads - by Bioz Stars, 2020-01
    90/100 stars
      Buy from Supplier

    Image Search Results