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  • 99
    Millipore oligo
    CaRF binds DNA directly. Human CaRF was expressed in bacteria (E. Coli hCaRF) or synthesized in vitro by <t>TNT</t> (hCaRF). Rabbit reticulocyte lysate without CaRF expression was used as control. 2µL of CaRF protein or TNT control was incubated with radiolabeled CaRE1 <t>oligos</t> in the absence (-) or presence of a 50-fold molar excess of competing unlabeled wildtype (W) or mutant (M) CaRE1 probe. Unbound probe is at the bottom of the gel. Arrowhead indicates the complex between CaRF and CaRE1.
    Oligo, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 1854 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/oligo/product/Millipore
    Average 99 stars, based on 1854 article reviews
    Price from $9.99 to $1999.99
    oligo - by Bioz Stars, 2020-07
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    CaRF binds DNA directly. Human CaRF was expressed in bacteria (E. Coli hCaRF) or synthesized in vitro by TNT (hCaRF). Rabbit reticulocyte lysate without CaRF expression was used as control. 2µL of CaRF protein or TNT control was incubated with radiolabeled CaRE1 oligos in the absence (-) or presence of a 50-fold molar excess of competing unlabeled wildtype (W) or mutant (M) CaRE1 probe. Unbound probe is at the bottom of the gel. Arrowhead indicates the complex between CaRF and CaRE1.

    Journal: PLoS ONE

    Article Title: Genome-Wide Identification of Calcium-Response Factor (CaRF) Binding Sites Predicts a Role in Regulation of Neuronal Signaling Pathways

    doi: 10.1371/journal.pone.0010870

    Figure Lengend Snippet: CaRF binds DNA directly. Human CaRF was expressed in bacteria (E. Coli hCaRF) or synthesized in vitro by TNT (hCaRF). Rabbit reticulocyte lysate without CaRF expression was used as control. 2µL of CaRF protein or TNT control was incubated with radiolabeled CaRE1 oligos in the absence (-) or presence of a 50-fold molar excess of competing unlabeled wildtype (W) or mutant (M) CaRE1 probe. Unbound probe is at the bottom of the gel. Arrowhead indicates the complex between CaRF and CaRE1.

    Article Snippet: Oligos were incubated with TNT hCaRF or a control TNT master mix and immunoprecipitated with the M2 anti-FLAG epitope antibody (Sigma, St. Louis, MO).

    Techniques: Synthesized, In Vitro, Expressing, Incubation, Mutagenesis

    Identification of a consensus CaRF binding element. hCaRF synthesized by TNT (hCaRF) or control rabbit reticulocyte without CaRF (control) was used to coprecipitate oligonucleotides from a library of random 16mers. a) After four rounds of enrichment and amplification, the final pulldown from each sample was radiolabeled and mixed with hCaRF for evaluation by EMSA. Equal amounts of radiolabeled oligos are present in each pool (gray arrowhead), however a CaRF binding band is retarded only from the pool that was isolated by coprecipitation with hCaRF (black arrowhead). b) WebLogo ( http://weblogo.berkeley.edu/ ) representation of the cCaRE consensus motif derived from the 62 sequences in Table S3 . The position of the bases is indicated along the bottom from 1–16, and the height of the letters indicates the enrichment of that base at each position. If all four bases were equally likely to be present at any position, no base is indicated. c) Alignment of the cCaRE and CaRE1 motifs. Black indicates bases that are conserved between the elements, and gray shows bases that vary. Y = C/T, S = C/G, and N = any base. d) Comparison of the affinity of CaRF for CaRE1 and cCaRE. A constant amount of hCaRF was bound to radiolabeled CaRE1 (B) or cCaRE (C) probes and the relative affinity of the interactions were assessed by competition EMSA upon the addition of a 150, 100, or 50-fold molar excess of unlabeled CaRE1 probe. The band retarded upon CaRF binding is indicated by the arrowhead.

    Journal: PLoS ONE

    Article Title: Genome-Wide Identification of Calcium-Response Factor (CaRF) Binding Sites Predicts a Role in Regulation of Neuronal Signaling Pathways

    doi: 10.1371/journal.pone.0010870

    Figure Lengend Snippet: Identification of a consensus CaRF binding element. hCaRF synthesized by TNT (hCaRF) or control rabbit reticulocyte without CaRF (control) was used to coprecipitate oligonucleotides from a library of random 16mers. a) After four rounds of enrichment and amplification, the final pulldown from each sample was radiolabeled and mixed with hCaRF for evaluation by EMSA. Equal amounts of radiolabeled oligos are present in each pool (gray arrowhead), however a CaRF binding band is retarded only from the pool that was isolated by coprecipitation with hCaRF (black arrowhead). b) WebLogo ( http://weblogo.berkeley.edu/ ) representation of the cCaRE consensus motif derived from the 62 sequences in Table S3 . The position of the bases is indicated along the bottom from 1–16, and the height of the letters indicates the enrichment of that base at each position. If all four bases were equally likely to be present at any position, no base is indicated. c) Alignment of the cCaRE and CaRE1 motifs. Black indicates bases that are conserved between the elements, and gray shows bases that vary. Y = C/T, S = C/G, and N = any base. d) Comparison of the affinity of CaRF for CaRE1 and cCaRE. A constant amount of hCaRF was bound to radiolabeled CaRE1 (B) or cCaRE (C) probes and the relative affinity of the interactions were assessed by competition EMSA upon the addition of a 150, 100, or 50-fold molar excess of unlabeled CaRE1 probe. The band retarded upon CaRF binding is indicated by the arrowhead.

    Article Snippet: Oligos were incubated with TNT hCaRF or a control TNT master mix and immunoprecipitated with the M2 anti-FLAG epitope antibody (Sigma, St. Louis, MO).

    Techniques: Binding Assay, Synthesized, Amplification, Isolation, Derivative Assay

    Hybrid HAC formation in HT1080 cells. (a) Representative FISH images of clones containing a HAC (left) and an array integration in an endogenous chromosome (right). (b, c) Screening of blasticidin-resistant clones by FISH. Diagrams represent the frequency of metaphases with HACs (black bars) and array integrations (gray bars) ( N = 25) in HT1080 cells without (b) and with (c) CENP-A overexpression. (d) Frequency of HAC-containing clones with (CENP-A OE) and without (CENP-A WT) transient CENP-A overexpression during HAC formation. Only clones with a minimum of 10% metaphases containing HACs were considered as positive (10 vs 33%). (e) Representative two-color oligo-FISH images showing different hybrid HACs (clone 20.CA.07-top and 20.CA.24-bottom) containing tetO (red) and lacOgal4 (green) domains. Images were captured at optimized exposure times to clearly distinguish both signals in either clone (for signal intensity comparison between clones, see Figure S2 ). (f) Representative image of an HT1080 cell containing HAC clone 20.CA.24 and expressing both lacI-GFP (green) and tetR-mCherry (red) fusion proteins. Merged image (right panel) represents the overlay of GFP, mCherry, and DAPI channels. (g) Frequency of HAC-containing metaphases in the indicated clones containing HACs in the presence of blasticidin and after 30 days after blasticidin washout. The HAC loss rate is indicated in red. (h) Representative immunofluorescence images on metaphase spreads of HAC clone 20.CA.24 and stained with the indicated antibodies. Scale bars = 10 μm.

    Journal: ACS Synthetic Biology

    Article Title: Generation of a Synthetic Human Chromosome with Two Centromeric Domains for Advanced Epigenetic Engineering Studies

    doi: 10.1021/acssynbio.8b00018

    Figure Lengend Snippet: Hybrid HAC formation in HT1080 cells. (a) Representative FISH images of clones containing a HAC (left) and an array integration in an endogenous chromosome (right). (b, c) Screening of blasticidin-resistant clones by FISH. Diagrams represent the frequency of metaphases with HACs (black bars) and array integrations (gray bars) ( N = 25) in HT1080 cells without (b) and with (c) CENP-A overexpression. (d) Frequency of HAC-containing clones with (CENP-A OE) and without (CENP-A WT) transient CENP-A overexpression during HAC formation. Only clones with a minimum of 10% metaphases containing HACs were considered as positive (10 vs 33%). (e) Representative two-color oligo-FISH images showing different hybrid HACs (clone 20.CA.07-top and 20.CA.24-bottom) containing tetO (red) and lacOgal4 (green) domains. Images were captured at optimized exposure times to clearly distinguish both signals in either clone (for signal intensity comparison between clones, see Figure S2 ). (f) Representative image of an HT1080 cell containing HAC clone 20.CA.24 and expressing both lacI-GFP (green) and tetR-mCherry (red) fusion proteins. Merged image (right panel) represents the overlay of GFP, mCherry, and DAPI channels. (g) Frequency of HAC-containing metaphases in the indicated clones containing HACs in the presence of blasticidin and after 30 days after blasticidin washout. The HAC loss rate is indicated in red. (h) Representative immunofluorescence images on metaphase spreads of HAC clone 20.CA.24 and stained with the indicated antibodies. Scale bars = 10 μm.

    Article Snippet: For oligo-FISH experiments, oligonucleotides recognizing the tetO sequence (5′- ACTAGCAGCAGAGCTCTCCCTATCAGTGATAGAGACTAG-3′) labeled with Digoxigenin, and oligonucleotides recognizing both lacO (5′- CATGTGGAATTGTGAGCGGATAACAATTTGTGG-3′) and Gal4 (5′- TCGACGGAGGACAGTCCTCCG-3′) sequences labeled with Biotin were synthesized (Sigma).

    Techniques: HAC Assay, Fluorescence In Situ Hybridization, Clone Assay, Over Expression, Expressing, Immunofluorescence, Staining

    Schematic image illustrating the Golden gate cloning of multiple gRNAs into the concatemer vector containing 3 gRNA expression cassettes . Annealed oligos (gRNA targets), DNA ligase and the Bbs I restriction enzyme are mixed with the gRNA concatemer vector in a single reaction. Repeated temperature cycles facilitate repeated digestion (21 °C) and ligation (37 °C). Bbs I digestion generates the custom-designed overhangs unique for each cassette. During the ligation, gRNAs are integrated into the vector by cassette-specific integration, determined by the matching overhangs of the gRNA and the vector. If the original fragment containing the two Bbs I restriction sites is ligated back into the vector it will again be removed in the following round of digestion. In contrast, upon ligation of a gRNA the Bbs I restriction site is disrupted and hence the gRNA cannot be removed during the following rounds of digestion. Blue – Bbs I enzyme, pink – T7 DNA ligase, U6 – U6 promoter, gRNA1.1–1.3 represent different gRNAs for the same gene (e.g. gRNA1.1 – gRNA1 for gene 1).

    Journal: Developmental Biology

    Article Title: Simultaneous paralogue knockout using a CRISPR-concatemer in mouse small intestinal organoids

    doi: 10.1016/j.ydbio.2016.10.016

    Figure Lengend Snippet: Schematic image illustrating the Golden gate cloning of multiple gRNAs into the concatemer vector containing 3 gRNA expression cassettes . Annealed oligos (gRNA targets), DNA ligase and the Bbs I restriction enzyme are mixed with the gRNA concatemer vector in a single reaction. Repeated temperature cycles facilitate repeated digestion (21 °C) and ligation (37 °C). Bbs I digestion generates the custom-designed overhangs unique for each cassette. During the ligation, gRNAs are integrated into the vector by cassette-specific integration, determined by the matching overhangs of the gRNA and the vector. If the original fragment containing the two Bbs I restriction sites is ligated back into the vector it will again be removed in the following round of digestion. In contrast, upon ligation of a gRNA the Bbs I restriction site is disrupted and hence the gRNA cannot be removed during the following rounds of digestion. Blue – Bbs I enzyme, pink – T7 DNA ligase, U6 – U6 promoter, gRNA1.1–1.3 represent different gRNAs for the same gene (e.g. gRNA1.1 – gRNA1 for gene 1).

    Article Snippet: 2.1.2 Multiple gRNA cloning gRNAs were ordered as oligonucleotides (oligos) from Sigma Aldrich.

    Techniques: Clone Assay, Plasmid Preparation, Expressing, Ligation

    K Ca 3.1 inhibition modulates oxygen consumption profile in a subset of PDAC cell lines. (A) Seahorse XF Mito Stress test was performed to measure mitochondrial function upon various concentrations of rac-16 treatment of Mia PaCa-2, (B) , Panc-1, (C) BxPC-3, and (D) Capan-1 cells. n = 3. Oligo is oligomycin A, FCCP is carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone, A/R is a mix of antimycin A and rotenone. n = 6.

    Journal: PLoS ONE

    Article Title: Identification of KCa3.1 Channel as a Novel Regulator of Oxidative Phosphorylation in a Subset of Pancreatic Carcinoma Cell Lines

    doi: 10.1371/journal.pone.0160658

    Figure Lengend Snippet: K Ca 3.1 inhibition modulates oxygen consumption profile in a subset of PDAC cell lines. (A) Seahorse XF Mito Stress test was performed to measure mitochondrial function upon various concentrations of rac-16 treatment of Mia PaCa-2, (B) , Panc-1, (C) BxPC-3, and (D) Capan-1 cells. n = 3. Oligo is oligomycin A, FCCP is carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone, A/R is a mix of antimycin A and rotenone. n = 6.

    Article Snippet: Oligomycin (Oligo), FCCP (carbonyl cyanide-4 (trifluoromethoxy) phenylhydrazone), rotenone (R) and antimycin A (A) were obtained from Sigma-Aldrich (St. Louis, MO, USA), diluted in DMSO to 10 mM stock solutions and stored in -20°C.

    Techniques: Inhibition