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pcat 3 basic vector  (New England Biolabs)


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    New England Biolabs pcat 3 basic vector
    Pcat 3 Basic Vector, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2897 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/pcat+3+basic+vector/BglII/pmc03889558-102-18-28
    Average 99 stars, based on 2897 article reviews
    pcat 3 basic vector - by Bioz Stars, 2026-10
    99/100 stars

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    Related Articles

    Cloning:

    Article Title: Chitosan nanogel-stabilized fusion dsRNA enables pathway-directed RNAi suppression of Bemisia tabaci
    Article Snippet: RNA interference offers a sequence-specific alternative to broad-spectrum insecticides, but spray delivery is constrained by extracellular dsRNA degradation, inefficient oral uptake, poor plant retention, and compensatory buffering in essential signaling pathways.. We developed a chitosan nanogel-stabilized fusion dsRNA targeting three insulin/insulin-like signaling genes in Bemisia tabaci.. A tri-component insulin-like peptide (ILP)-insulin receptor (InR)-insulin receptor substrate (IRS) cassette was cloned, expressed in Escherichia coli HT115 (DE3), purified, and complexed in a polymer-reinforced chitosan nanogel (PNG).

    Article Title: Promiscuous fungal peroxygenase from Chaetomium globosum by directed evolution
    Article Snippet: The PTM1 Trace salts solution was sterilized by filtration and consisted .. REAGENT or RESOURCE SOURCE IDENTIFIER BglII New England Biolabs (USA) R0144 PmeI New England Biolabs (USA) R0560 BamHI New England Biolabs (USA) R0136 XhoI New England Biolabs (USA) R0146 Gibson Assembly Master Mix New England Biolabs (USA) E2611 iProof High-Fidelity DNA Polymerase Bio-Rad (USA) 1725301 Yeast Transformation Kit Merck Life Science (USA) YEAST1 NucleoSpin plasmid kit Macherey-Nagel (Germany) 740588.50 PCR Clean-up kit Macherey-Nagel (Germany) 740609.50 Zymoprep yeast plasmid miniprep kit Zymo Research (USA) D2004 Oligonucleotides Primers (see Cloning section) Integrated DNA Technologies (USA) N/A Recombinant DNA pJRoC30 California Institute of Technology (USA) N/A pBSY5Z Bisy (Austria) N/A Deposited data DNA sequences Supplemental information N/A GC/MS data Supplemental information N/A Software and algorithms Prism 10 GraphPad (USA) N/A AlphaFold 2 Open source N/A Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ N/A PROPKA 3.1 Schrodinger N/A AMBER (ff03.r1) https://ambermd.org N/A BIOVIA Discovery Studio Visualizer https://www.3ds.com/products/biovia/discovery-studio/ visualization N/A NAMD 3.0 https://www.ks.uiuc.edu/Research/namd/ N/A Zenodo MD deposit https://doi.org/10.5281/zenodo.19047657 N/A iScience 29, 117534, October 16, 2026 13 of the following ingredients: 6 g/L CuSO4 5H2O, NaI 0.08 g/L, 3 g/L MnSO4 ⋅ H2O, 0.2 g/L Na2MoO4, 0.02 g/L H3BO3, 0.5 g/L CoCl2, 20 g/L ZnCl2, 65 g/L FeSO4 ⋅ 7H2O, 0.2 Biotin, 5 mL/L sulfuric acid. .. Cloning of CglUPO in S. cerevisiae The gene encoding for the main CglUPO (GenBank accession no.: CHGG_00319, NCBI reference sequence: XM_001219539.1) from Chaetomium globosum (Mycobank no.: 172545, strain CBS 148.51) was used to synthesize several fusion genes attaching the signal peptides of peroxygenases from Marasmius rotula,36 Chaetomium globosum,9 Agrocybe aegerita wildtype and evolved secretion leader (PaDa-I)18 and Caldariomyces fumago.37 CglUPO fusions were cloned under the control of the GAL1 promoter of the pJRoC30 expression shuttle vector, using BamHI and XhoI restriction enzymes.

    Expressing:

    Article Title: Chitosan nanogel-stabilized fusion dsRNA enables pathway-directed RNAi suppression of Bemisia tabaci
    Article Snippet: RNA interference offers a sequence-specific alternative to broad-spectrum insecticides, but spray delivery is constrained by extracellular dsRNA degradation, inefficient oral uptake, poor plant retention, and compensatory buffering in essential signaling pathways.. We developed a chitosan nanogel-stabilized fusion dsRNA targeting three insulin/insulin-like signaling genes in Bemisia tabaci.. A tri-component insulin-like peptide (ILP)-insulin receptor (InR)-insulin receptor substrate (IRS) cassette was cloned, expressed in Escherichia coli HT115 (DE3), purified, and complexed in a polymer-reinforced chitosan nanogel (PNG).

    Article Title: A cis -encoded RNA interaction controls sub-operonic spoVG expression in Staphylococcus aureus
    Article Snippet: .. The yabJ - spoVG transcript was amplified from VISA JKD6008 using Phusion DNA polymerase (NEB) and cloned into the pCN33 vector [ ] at the BglII/EcoRV enzyme sites to allow translational read-through to gfp under constitutive expression of the P tufA promoter ( Supplementary Table 2C ). .. The yabJ 5’UTR sequence was amplified from VISA JKD6008 using Phusion DNA polymerase (NEB) and cloned into the pICS3 vector [ ] at the PstI/EcoRI enzyme sites, allowing co-constitutive expression with pCN33 as previously described [ ].

    Construct:

    Article Title: Chitosan nanogel-stabilized fusion dsRNA enables pathway-directed RNAi suppression of Bemisia tabaci
    Article Snippet: RNA interference offers a sequence-specific alternative to broad-spectrum insecticides, but spray delivery is constrained by extracellular dsRNA degradation, inefficient oral uptake, poor plant retention, and compensatory buffering in essential signaling pathways.. We developed a chitosan nanogel-stabilized fusion dsRNA targeting three insulin/insulin-like signaling genes in Bemisia tabaci.. A tri-component insulin-like peptide (ILP)-insulin receptor (InR)-insulin receptor substrate (IRS) cassette was cloned, expressed in Escherichia coli HT115 (DE3), purified, and complexed in a polymer-reinforced chitosan nanogel (PNG).

    Article Title: Emergence and evolution of chimeric pseudogenes (φgenes) contribute to genetic and functional diversity of the human genome.
    Article Snippet: .. For the full-length and constructs ( 1 and 2) in pUAST, KpnI-HF (NEB, #R3142S) and NotI (NEB, #R0189S) were employed; UP (upstream region) was achieved using NdeI (NEB, #R0111S) and BglII (NEB, #R0144S); TATA promoter using SbfI-HF (NEB, #R3642S) and BglII. .. For insertion of RMND5A and ANAPC1 sequences into the pGL3 vector, digestion was performed using KpnI and HindIII (NEB, #R0104S).

    Article Title: Emergence and evolution of chimeric pseudogenes (φgenes) contribute to genetic and functional diversity of the human genome
    Article Snippet: .. For the full-length and Δ constructs (Δ1 and Δ2) in pUAST, KpnI-HF (NEB, #R3142S) and NotI (NEB, #R0189S) were employed; Δ UP (upstream region) was achieved using NdeI (NEB, #R0111S) and BglII (NEB, #R0144S); Δ TATA promoter using SbfI-HF (NEB, #R3642S) and BglII. .. For insertion of RMND5A and ANAPC1 sequences into the pGL3 vector, digestion was performed using KpnI and HindIII (NEB, #R0104S).

    Clone Assay:

    Article Title: Chitosan nanogel-stabilized fusion dsRNA enables pathway-directed RNAi suppression of Bemisia tabaci
    Article Snippet: RNA interference offers a sequence-specific alternative to broad-spectrum insecticides, but spray delivery is constrained by extracellular dsRNA degradation, inefficient oral uptake, poor plant retention, and compensatory buffering in essential signaling pathways.. We developed a chitosan nanogel-stabilized fusion dsRNA targeting three insulin/insulin-like signaling genes in Bemisia tabaci.. A tri-component insulin-like peptide (ILP)-insulin receptor (InR)-insulin receptor substrate (IRS) cassette was cloned, expressed in Escherichia coli HT115 (DE3), purified, and complexed in a polymer-reinforced chitosan nanogel (PNG).

    Article Title: A cis -encoded RNA interaction controls sub-operonic spoVG expression in Staphylococcus aureus
    Article Snippet: .. The yabJ - spoVG transcript was amplified from VISA JKD6008 using Phusion DNA polymerase (NEB) and cloned into the pCN33 vector [ ] at the BglII/EcoRV enzyme sites to allow translational read-through to gfp under constitutive expression of the P tufA promoter ( Supplementary Table 2C ). .. The yabJ 5’UTR sequence was amplified from VISA JKD6008 using Phusion DNA polymerase (NEB) and cloned into the pICS3 vector [ ] at the PstI/EcoRI enzyme sites, allowing co-constitutive expression with pCN33 as previously described [ ].

    Ligation:

    Article Title: Chitosan nanogel-stabilized fusion dsRNA enables pathway-directed RNAi suppression of Bemisia tabaci
    Article Snippet: RNA interference offers a sequence-specific alternative to broad-spectrum insecticides, but spray delivery is constrained by extracellular dsRNA degradation, inefficient oral uptake, poor plant retention, and compensatory buffering in essential signaling pathways.. We developed a chitosan nanogel-stabilized fusion dsRNA targeting three insulin/insulin-like signaling genes in Bemisia tabaci.. A tri-component insulin-like peptide (ILP)-insulin receptor (InR)-insulin receptor substrate (IRS) cassette was cloned, expressed in Escherichia coli HT115 (DE3), purified, and complexed in a polymer-reinforced chitosan nanogel (PNG).

    Yeast:

    Article Title: Promiscuous fungal peroxygenase from Chaetomium globosum by directed evolution
    Article Snippet: The PTM1 Trace salts solution was sterilized by filtration and consisted .. REAGENT or RESOURCE SOURCE IDENTIFIER BglII New England Biolabs (USA) R0144 PmeI New England Biolabs (USA) R0560 BamHI New England Biolabs (USA) R0136 XhoI New England Biolabs (USA) R0146 Gibson Assembly Master Mix New England Biolabs (USA) E2611 iProof High-Fidelity DNA Polymerase Bio-Rad (USA) 1725301 Yeast Transformation Kit Merck Life Science (USA) YEAST1 NucleoSpin plasmid kit Macherey-Nagel (Germany) 740588.50 PCR Clean-up kit Macherey-Nagel (Germany) 740609.50 Zymoprep yeast plasmid miniprep kit Zymo Research (USA) D2004 Oligonucleotides Primers (see Cloning section) Integrated DNA Technologies (USA) N/A Recombinant DNA pJRoC30 California Institute of Technology (USA) N/A pBSY5Z Bisy (Austria) N/A Deposited data DNA sequences Supplemental information N/A GC/MS data Supplemental information N/A Software and algorithms Prism 10 GraphPad (USA) N/A AlphaFold 2 Open source N/A Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ N/A PROPKA 3.1 Schrodinger N/A AMBER (ff03.r1) https://ambermd.org N/A BIOVIA Discovery Studio Visualizer https://www.3ds.com/products/biovia/discovery-studio/ visualization N/A NAMD 3.0 https://www.ks.uiuc.edu/Research/namd/ N/A Zenodo MD deposit https://doi.org/10.5281/zenodo.19047657 N/A iScience 29, 117534, October 16, 2026 13 of the following ingredients: 6 g/L CuSO4 5H2O, NaI 0.08 g/L, 3 g/L MnSO4 ⋅ H2O, 0.2 g/L Na2MoO4, 0.02 g/L H3BO3, 0.5 g/L CoCl2, 20 g/L ZnCl2, 65 g/L FeSO4 ⋅ 7H2O, 0.2 Biotin, 5 mL/L sulfuric acid. .. Cloning of CglUPO in S. cerevisiae The gene encoding for the main CglUPO (GenBank accession no.: CHGG_00319, NCBI reference sequence: XM_001219539.1) from Chaetomium globosum (Mycobank no.: 172545, strain CBS 148.51) was used to synthesize several fusion genes attaching the signal peptides of peroxygenases from Marasmius rotula,36 Chaetomium globosum,9 Agrocybe aegerita wildtype and evolved secretion leader (PaDa-I)18 and Caldariomyces fumago.37 CglUPO fusions were cloned under the control of the GAL1 promoter of the pJRoC30 expression shuttle vector, using BamHI and XhoI restriction enzymes.

    Transformation Assay:

    Article Title: Promiscuous fungal peroxygenase from Chaetomium globosum by directed evolution
    Article Snippet: The PTM1 Trace salts solution was sterilized by filtration and consisted .. REAGENT or RESOURCE SOURCE IDENTIFIER BglII New England Biolabs (USA) R0144 PmeI New England Biolabs (USA) R0560 BamHI New England Biolabs (USA) R0136 XhoI New England Biolabs (USA) R0146 Gibson Assembly Master Mix New England Biolabs (USA) E2611 iProof High-Fidelity DNA Polymerase Bio-Rad (USA) 1725301 Yeast Transformation Kit Merck Life Science (USA) YEAST1 NucleoSpin plasmid kit Macherey-Nagel (Germany) 740588.50 PCR Clean-up kit Macherey-Nagel (Germany) 740609.50 Zymoprep yeast plasmid miniprep kit Zymo Research (USA) D2004 Oligonucleotides Primers (see Cloning section) Integrated DNA Technologies (USA) N/A Recombinant DNA pJRoC30 California Institute of Technology (USA) N/A pBSY5Z Bisy (Austria) N/A Deposited data DNA sequences Supplemental information N/A GC/MS data Supplemental information N/A Software and algorithms Prism 10 GraphPad (USA) N/A AlphaFold 2 Open source N/A Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ N/A PROPKA 3.1 Schrodinger N/A AMBER (ff03.r1) https://ambermd.org N/A BIOVIA Discovery Studio Visualizer https://www.3ds.com/products/biovia/discovery-studio/ visualization N/A NAMD 3.0 https://www.ks.uiuc.edu/Research/namd/ N/A Zenodo MD deposit https://doi.org/10.5281/zenodo.19047657 N/A iScience 29, 117534, October 16, 2026 13 of the following ingredients: 6 g/L CuSO4 5H2O, NaI 0.08 g/L, 3 g/L MnSO4 ⋅ H2O, 0.2 g/L Na2MoO4, 0.02 g/L H3BO3, 0.5 g/L CoCl2, 20 g/L ZnCl2, 65 g/L FeSO4 ⋅ 7H2O, 0.2 Biotin, 5 mL/L sulfuric acid. .. Cloning of CglUPO in S. cerevisiae The gene encoding for the main CglUPO (GenBank accession no.: CHGG_00319, NCBI reference sequence: XM_001219539.1) from Chaetomium globosum (Mycobank no.: 172545, strain CBS 148.51) was used to synthesize several fusion genes attaching the signal peptides of peroxygenases from Marasmius rotula,36 Chaetomium globosum,9 Agrocybe aegerita wildtype and evolved secretion leader (PaDa-I)18 and Caldariomyces fumago.37 CglUPO fusions were cloned under the control of the GAL1 promoter of the pJRoC30 expression shuttle vector, using BamHI and XhoI restriction enzymes.

    Plasmid Preparation:

    Article Title: Promiscuous fungal peroxygenase from Chaetomium globosum by directed evolution
    Article Snippet: The PTM1 Trace salts solution was sterilized by filtration and consisted .. REAGENT or RESOURCE SOURCE IDENTIFIER BglII New England Biolabs (USA) R0144 PmeI New England Biolabs (USA) R0560 BamHI New England Biolabs (USA) R0136 XhoI New England Biolabs (USA) R0146 Gibson Assembly Master Mix New England Biolabs (USA) E2611 iProof High-Fidelity DNA Polymerase Bio-Rad (USA) 1725301 Yeast Transformation Kit Merck Life Science (USA) YEAST1 NucleoSpin plasmid kit Macherey-Nagel (Germany) 740588.50 PCR Clean-up kit Macherey-Nagel (Germany) 740609.50 Zymoprep yeast plasmid miniprep kit Zymo Research (USA) D2004 Oligonucleotides Primers (see Cloning section) Integrated DNA Technologies (USA) N/A Recombinant DNA pJRoC30 California Institute of Technology (USA) N/A pBSY5Z Bisy (Austria) N/A Deposited data DNA sequences Supplemental information N/A GC/MS data Supplemental information N/A Software and algorithms Prism 10 GraphPad (USA) N/A AlphaFold 2 Open source N/A Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ N/A PROPKA 3.1 Schrodinger N/A AMBER (ff03.r1) https://ambermd.org N/A BIOVIA Discovery Studio Visualizer https://www.3ds.com/products/biovia/discovery-studio/ visualization N/A NAMD 3.0 https://www.ks.uiuc.edu/Research/namd/ N/A Zenodo MD deposit https://doi.org/10.5281/zenodo.19047657 N/A iScience 29, 117534, October 16, 2026 13 of the following ingredients: 6 g/L CuSO4 5H2O, NaI 0.08 g/L, 3 g/L MnSO4 ⋅ H2O, 0.2 g/L Na2MoO4, 0.02 g/L H3BO3, 0.5 g/L CoCl2, 20 g/L ZnCl2, 65 g/L FeSO4 ⋅ 7H2O, 0.2 Biotin, 5 mL/L sulfuric acid. .. Cloning of CglUPO in S. cerevisiae The gene encoding for the main CglUPO (GenBank accession no.: CHGG_00319, NCBI reference sequence: XM_001219539.1) from Chaetomium globosum (Mycobank no.: 172545, strain CBS 148.51) was used to synthesize several fusion genes attaching the signal peptides of peroxygenases from Marasmius rotula,36 Chaetomium globosum,9 Agrocybe aegerita wildtype and evolved secretion leader (PaDa-I)18 and Caldariomyces fumago.37 CglUPO fusions were cloned under the control of the GAL1 promoter of the pJRoC30 expression shuttle vector, using BamHI and XhoI restriction enzymes.

    Article Title: Human respiratory syncytial virus regulates the expression of interferon-stimulated genes through modulation of fibrillarin.
    Article Snippet: .. Both the plasmid and the PCR-amplified insert were digested with the restriction enzymes BglII (New England Biolabs, #R0144S) and HindIII (New England Biolabs, #R0104S). .. Following digestion, the plasmid vector was dephosphorylated using alkaline phosphatase (Thermo Fisher Scientific, #EF0652).

    Article Title: A cis -encoded RNA interaction controls sub-operonic spoVG expression in Staphylococcus aureus
    Article Snippet: .. The yabJ - spoVG transcript was amplified from VISA JKD6008 using Phusion DNA polymerase (NEB) and cloned into the pCN33 vector [ ] at the BglII/EcoRV enzyme sites to allow translational read-through to gfp under constitutive expression of the P tufA promoter ( Supplementary Table 2C ). .. The yabJ 5’UTR sequence was amplified from VISA JKD6008 using Phusion DNA polymerase (NEB) and cloned into the pICS3 vector [ ] at the PstI/EcoRI enzyme sites, allowing co-constitutive expression with pCN33 as previously described [ ].

    Article Title: Long-read RNA sequencing identifies non-coding isoform switching as a regulator of cell fate
    Article Snippet: Snhg26 PCR-amplified cDNA transcript sequence was validated by Sanger sequencing and cloned into the PB-TetO-AIO destination vector using GatewayTM cloning (ThermoFisher Scientific #11789020 & #11791020) strategy according to the manufacturer’s instructions. .. For Snhg26 transcript 216 (Ensmust00000268635 or “Snhg26.216”), the Snhg26.217 containing plasmid was digested with BglII (NEB #R0144) and XcmI (NEB #R0533) to remove a part of exon 4. ..

    Polymerase Chain Reaction:

    Article Title: Promiscuous fungal peroxygenase from Chaetomium globosum by directed evolution
    Article Snippet: The PTM1 Trace salts solution was sterilized by filtration and consisted .. REAGENT or RESOURCE SOURCE IDENTIFIER BglII New England Biolabs (USA) R0144 PmeI New England Biolabs (USA) R0560 BamHI New England Biolabs (USA) R0136 XhoI New England Biolabs (USA) R0146 Gibson Assembly Master Mix New England Biolabs (USA) E2611 iProof High-Fidelity DNA Polymerase Bio-Rad (USA) 1725301 Yeast Transformation Kit Merck Life Science (USA) YEAST1 NucleoSpin plasmid kit Macherey-Nagel (Germany) 740588.50 PCR Clean-up kit Macherey-Nagel (Germany) 740609.50 Zymoprep yeast plasmid miniprep kit Zymo Research (USA) D2004 Oligonucleotides Primers (see Cloning section) Integrated DNA Technologies (USA) N/A Recombinant DNA pJRoC30 California Institute of Technology (USA) N/A pBSY5Z Bisy (Austria) N/A Deposited data DNA sequences Supplemental information N/A GC/MS data Supplemental information N/A Software and algorithms Prism 10 GraphPad (USA) N/A AlphaFold 2 Open source N/A Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ N/A PROPKA 3.1 Schrodinger N/A AMBER (ff03.r1) https://ambermd.org N/A BIOVIA Discovery Studio Visualizer https://www.3ds.com/products/biovia/discovery-studio/ visualization N/A NAMD 3.0 https://www.ks.uiuc.edu/Research/namd/ N/A Zenodo MD deposit https://doi.org/10.5281/zenodo.19047657 N/A iScience 29, 117534, October 16, 2026 13 of the following ingredients: 6 g/L CuSO4 5H2O, NaI 0.08 g/L, 3 g/L MnSO4 ⋅ H2O, 0.2 g/L Na2MoO4, 0.02 g/L H3BO3, 0.5 g/L CoCl2, 20 g/L ZnCl2, 65 g/L FeSO4 ⋅ 7H2O, 0.2 Biotin, 5 mL/L sulfuric acid. .. Cloning of CglUPO in S. cerevisiae The gene encoding for the main CglUPO (GenBank accession no.: CHGG_00319, NCBI reference sequence: XM_001219539.1) from Chaetomium globosum (Mycobank no.: 172545, strain CBS 148.51) was used to synthesize several fusion genes attaching the signal peptides of peroxygenases from Marasmius rotula,36 Chaetomium globosum,9 Agrocybe aegerita wildtype and evolved secretion leader (PaDa-I)18 and Caldariomyces fumago.37 CglUPO fusions were cloned under the control of the GAL1 promoter of the pJRoC30 expression shuttle vector, using BamHI and XhoI restriction enzymes.

    Article Title: Human respiratory syncytial virus regulates the expression of interferon-stimulated genes through modulation of fibrillarin.
    Article Snippet: .. Both the plasmid and the PCR-amplified insert were digested with the restriction enzymes BglII (New England Biolabs, #R0144S) and HindIII (New England Biolabs, #R0104S). .. Following digestion, the plasmid vector was dephosphorylated using alkaline phosphatase (Thermo Fisher Scientific, #EF0652).

    Recombinant:

    Article Title: Promiscuous fungal peroxygenase from Chaetomium globosum by directed evolution
    Article Snippet: The PTM1 Trace salts solution was sterilized by filtration and consisted .. REAGENT or RESOURCE SOURCE IDENTIFIER BglII New England Biolabs (USA) R0144 PmeI New England Biolabs (USA) R0560 BamHI New England Biolabs (USA) R0136 XhoI New England Biolabs (USA) R0146 Gibson Assembly Master Mix New England Biolabs (USA) E2611 iProof High-Fidelity DNA Polymerase Bio-Rad (USA) 1725301 Yeast Transformation Kit Merck Life Science (USA) YEAST1 NucleoSpin plasmid kit Macherey-Nagel (Germany) 740588.50 PCR Clean-up kit Macherey-Nagel (Germany) 740609.50 Zymoprep yeast plasmid miniprep kit Zymo Research (USA) D2004 Oligonucleotides Primers (see Cloning section) Integrated DNA Technologies (USA) N/A Recombinant DNA pJRoC30 California Institute of Technology (USA) N/A pBSY5Z Bisy (Austria) N/A Deposited data DNA sequences Supplemental information N/A GC/MS data Supplemental information N/A Software and algorithms Prism 10 GraphPad (USA) N/A AlphaFold 2 Open source N/A Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ N/A PROPKA 3.1 Schrodinger N/A AMBER (ff03.r1) https://ambermd.org N/A BIOVIA Discovery Studio Visualizer https://www.3ds.com/products/biovia/discovery-studio/ visualization N/A NAMD 3.0 https://www.ks.uiuc.edu/Research/namd/ N/A Zenodo MD deposit https://doi.org/10.5281/zenodo.19047657 N/A iScience 29, 117534, October 16, 2026 13 of the following ingredients: 6 g/L CuSO4 5H2O, NaI 0.08 g/L, 3 g/L MnSO4 ⋅ H2O, 0.2 g/L Na2MoO4, 0.02 g/L H3BO3, 0.5 g/L CoCl2, 20 g/L ZnCl2, 65 g/L FeSO4 ⋅ 7H2O, 0.2 Biotin, 5 mL/L sulfuric acid. .. Cloning of CglUPO in S. cerevisiae The gene encoding for the main CglUPO (GenBank accession no.: CHGG_00319, NCBI reference sequence: XM_001219539.1) from Chaetomium globosum (Mycobank no.: 172545, strain CBS 148.51) was used to synthesize several fusion genes attaching the signal peptides of peroxygenases from Marasmius rotula,36 Chaetomium globosum,9 Agrocybe aegerita wildtype and evolved secretion leader (PaDa-I)18 and Caldariomyces fumago.37 CglUPO fusions were cloned under the control of the GAL1 promoter of the pJRoC30 expression shuttle vector, using BamHI and XhoI restriction enzymes.

    Pyrolysis Gas Chromatography:

    Article Title: Promiscuous fungal peroxygenase from Chaetomium globosum by directed evolution
    Article Snippet: The PTM1 Trace salts solution was sterilized by filtration and consisted .. REAGENT or RESOURCE SOURCE IDENTIFIER BglII New England Biolabs (USA) R0144 PmeI New England Biolabs (USA) R0560 BamHI New England Biolabs (USA) R0136 XhoI New England Biolabs (USA) R0146 Gibson Assembly Master Mix New England Biolabs (USA) E2611 iProof High-Fidelity DNA Polymerase Bio-Rad (USA) 1725301 Yeast Transformation Kit Merck Life Science (USA) YEAST1 NucleoSpin plasmid kit Macherey-Nagel (Germany) 740588.50 PCR Clean-up kit Macherey-Nagel (Germany) 740609.50 Zymoprep yeast plasmid miniprep kit Zymo Research (USA) D2004 Oligonucleotides Primers (see Cloning section) Integrated DNA Technologies (USA) N/A Recombinant DNA pJRoC30 California Institute of Technology (USA) N/A pBSY5Z Bisy (Austria) N/A Deposited data DNA sequences Supplemental information N/A GC/MS data Supplemental information N/A Software and algorithms Prism 10 GraphPad (USA) N/A AlphaFold 2 Open source N/A Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ N/A PROPKA 3.1 Schrodinger N/A AMBER (ff03.r1) https://ambermd.org N/A BIOVIA Discovery Studio Visualizer https://www.3ds.com/products/biovia/discovery-studio/ visualization N/A NAMD 3.0 https://www.ks.uiuc.edu/Research/namd/ N/A Zenodo MD deposit https://doi.org/10.5281/zenodo.19047657 N/A iScience 29, 117534, October 16, 2026 13 of the following ingredients: 6 g/L CuSO4 5H2O, NaI 0.08 g/L, 3 g/L MnSO4 ⋅ H2O, 0.2 g/L Na2MoO4, 0.02 g/L H3BO3, 0.5 g/L CoCl2, 20 g/L ZnCl2, 65 g/L FeSO4 ⋅ 7H2O, 0.2 Biotin, 5 mL/L sulfuric acid. .. Cloning of CglUPO in S. cerevisiae The gene encoding for the main CglUPO (GenBank accession no.: CHGG_00319, NCBI reference sequence: XM_001219539.1) from Chaetomium globosum (Mycobank no.: 172545, strain CBS 148.51) was used to synthesize several fusion genes attaching the signal peptides of peroxygenases from Marasmius rotula,36 Chaetomium globosum,9 Agrocybe aegerita wildtype and evolved secretion leader (PaDa-I)18 and Caldariomyces fumago.37 CglUPO fusions were cloned under the control of the GAL1 promoter of the pJRoC30 expression shuttle vector, using BamHI and XhoI restriction enzymes.

    Software:

    Article Title: Promiscuous fungal peroxygenase from Chaetomium globosum by directed evolution
    Article Snippet: The PTM1 Trace salts solution was sterilized by filtration and consisted .. REAGENT or RESOURCE SOURCE IDENTIFIER BglII New England Biolabs (USA) R0144 PmeI New England Biolabs (USA) R0560 BamHI New England Biolabs (USA) R0136 XhoI New England Biolabs (USA) R0146 Gibson Assembly Master Mix New England Biolabs (USA) E2611 iProof High-Fidelity DNA Polymerase Bio-Rad (USA) 1725301 Yeast Transformation Kit Merck Life Science (USA) YEAST1 NucleoSpin plasmid kit Macherey-Nagel (Germany) 740588.50 PCR Clean-up kit Macherey-Nagel (Germany) 740609.50 Zymoprep yeast plasmid miniprep kit Zymo Research (USA) D2004 Oligonucleotides Primers (see Cloning section) Integrated DNA Technologies (USA) N/A Recombinant DNA pJRoC30 California Institute of Technology (USA) N/A pBSY5Z Bisy (Austria) N/A Deposited data DNA sequences Supplemental information N/A GC/MS data Supplemental information N/A Software and algorithms Prism 10 GraphPad (USA) N/A AlphaFold 2 Open source N/A Dali server http://ekhidna2.biocenter.helsinki.fi/dali/ N/A PROPKA 3.1 Schrodinger N/A AMBER (ff03.r1) https://ambermd.org N/A BIOVIA Discovery Studio Visualizer https://www.3ds.com/products/biovia/discovery-studio/ visualization N/A NAMD 3.0 https://www.ks.uiuc.edu/Research/namd/ N/A Zenodo MD deposit https://doi.org/10.5281/zenodo.19047657 N/A iScience 29, 117534, October 16, 2026 13 of the following ingredients: 6 g/L CuSO4 5H2O, NaI 0.08 g/L, 3 g/L MnSO4 ⋅ H2O, 0.2 g/L Na2MoO4, 0.02 g/L H3BO3, 0.5 g/L CoCl2, 20 g/L ZnCl2, 65 g/L FeSO4 ⋅ 7H2O, 0.2 Biotin, 5 mL/L sulfuric acid. .. Cloning of CglUPO in S. cerevisiae The gene encoding for the main CglUPO (GenBank accession no.: CHGG_00319, NCBI reference sequence: XM_001219539.1) from Chaetomium globosum (Mycobank no.: 172545, strain CBS 148.51) was used to synthesize several fusion genes attaching the signal peptides of peroxygenases from Marasmius rotula,36 Chaetomium globosum,9 Agrocybe aegerita wildtype and evolved secretion leader (PaDa-I)18 and Caldariomyces fumago.37 CglUPO fusions were cloned under the control of the GAL1 promoter of the pJRoC30 expression shuttle vector, using BamHI and XhoI restriction enzymes.

    Amplification:

    Article Title: A cis -encoded RNA interaction controls sub-operonic spoVG expression in Staphylococcus aureus
    Article Snippet: .. The yabJ - spoVG transcript was amplified from VISA JKD6008 using Phusion DNA polymerase (NEB) and cloned into the pCN33 vector [ ] at the BglII/EcoRV enzyme sites to allow translational read-through to gfp under constitutive expression of the P tufA promoter ( Supplementary Table 2C ). .. The yabJ 5’UTR sequence was amplified from VISA JKD6008 using Phusion DNA polymerase (NEB) and cloned into the pICS3 vector [ ] at the PstI/EcoRI enzyme sites, allowing co-constitutive expression with pCN33 as previously described [ ].



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    Transcriptional activity of DHS-S1. (A) Structure and activity of constructs containing DHS-S1 cloned upstream of the CAT gene. The whole DHS-S1 was excised as an SmaI-SmaI fragment (nt 18 to 353 of AAVS1) from plasmid pRVK and cloned in both orientations (indicated by the direction of the arrows) upstream of the intron and the CAT gene into the SmaI site of pCAT 3-basic vector (Promega). Black boxes represent the SV40 promoter. The promoterless plasmid is the pCAT 3-basic vector (Promega), and the control plasmid containing the SV40 promoter is the pCAT 3-promoter vector (Promega). Regions FR1 (nt 1313 to 1616 of AAVS1) and FR3 (nt 2633 to 2927 of AAVS1) were amplified by PCR with plasmid pRVK as a substrate and oligonucleotides carrying SmaI sites at either end. The resulting fragments were digested with restriction enzyme SmaI and cloned into the SmaI site of the pCAT 3-basic vector. Region FR2 (nt 2077 to 2371 of AAVS1) was excised from plasmid pRVK as a BamHI-flanked fragment, filled in by treatment with Klenow enzyme, and inserted into the SmaI site of pCAT 3-basic vector. Ten micrograms of each plasmid was transfected as described previously by calcium phosphate precipitation into 293 and HeLa cells (1). At 15 h posttransfection, the medium was changed: after an additional 24 h, cells were collected and CAT activity in cell extracts was measured by using the Quan-T-CAT assay system (Amersham, Pharmacia). CAT activities were normalized against the luciferase activity derived from a cotransfected cytomegalovirus-luciferase plasmid (1). Results are expressed as milliunits of CAT enzyme present in 10 μg of cell extracts and as fold induction with respect to the promoterless pCAT 3-basic vector. The data are means ± standard deviations of two independent experiments in which two separate plasmid preparations were used. (B) Enhancer activity of DHS-S1 in 293 and HeLa cells. DHS-S1 was cloned in both orientations (represented by the direction of the arrows) into the pCAT 3-promoter vector either into the SmaI site upstream of the SV40 promoter or into the BamHI site downstream of the CAT gene. Similarly, FR1, FR2, and FR3 were cloned in one orientation either into the SmaI site or into the BamHI site of pCAT 3-vector. Transfections were performed, and CAT activities were measured and normalized as described in the legend to Fig. ​Fig.4A.4A. Results are expressed as milliunits of CAT enzyme in 10 μg of cell extracts; fold induction was calculated with respect to that of the pCAT 3-promoter vector. The data are means ± standard deviations of three independent experiments in which at least two different plasmid preparations were used.
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    Transcriptional activity of DHS-S1. (A) Structure and activity of constructs containing DHS-S1 cloned upstream of the CAT gene. The whole DHS-S1 was excised as an SmaI-SmaI fragment (nt 18 to 353 of AAVS1) from plasmid pRVK and cloned in both orientations (indicated by the direction of the arrows) upstream of the intron and the CAT gene into the SmaI site of pCAT 3-basic vector (Promega). Black boxes represent the SV40 promoter. The promoterless plasmid is the pCAT 3-basic vector (Promega), and the control plasmid containing the SV40 promoter is the pCAT 3-promoter vector (Promega). Regions FR1 (nt 1313 to 1616 of AAVS1) and FR3 (nt 2633 to 2927 of AAVS1) were amplified by PCR with plasmid pRVK as a substrate and oligonucleotides carrying SmaI sites at either end. The resulting fragments were digested with restriction enzyme SmaI and cloned into the SmaI site of the pCAT 3-basic vector. Region FR2 (nt 2077 to 2371 of AAVS1) was excised from plasmid pRVK as a BamHI-flanked fragment, filled in by treatment with Klenow enzyme, and inserted into the SmaI site of pCAT 3-basic vector. Ten micrograms of each plasmid was transfected as described previously by calcium phosphate precipitation into 293 and HeLa cells (1). At 15 h posttransfection, the medium was changed: after an additional 24 h, cells were collected and CAT activity in cell extracts was measured by using the Quan-T-CAT assay system (Amersham, Pharmacia). CAT activities were normalized against the luciferase activity derived from a cotransfected cytomegalovirus-luciferase plasmid (1). Results are expressed as milliunits of CAT enzyme present in 10 μg of cell extracts and as fold induction with respect to the promoterless pCAT 3-basic vector. The data are means ± standard deviations of two independent experiments in which two separate plasmid preparations were used. (B) Enhancer activity of DHS-S1 in 293 and HeLa cells. DHS-S1 was cloned in both orientations (represented by the direction of the arrows) into the pCAT 3-promoter vector either into the SmaI site upstream of the SV40 promoter or into the BamHI site downstream of the CAT gene. Similarly, FR1, FR2, and FR3 were cloned in one orientation either into the SmaI site or into the BamHI site of pCAT 3-vector. Transfections were performed, and CAT activities were measured and normalized as described in the legend to Fig. ​Fig.4A.4A. Results are expressed as milliunits of CAT enzyme in 10 μg of cell extracts; fold induction was calculated with respect to that of the pCAT 3-promoter vector. The data are means ± standard deviations of three independent experiments in which at least two different plasmid preparations were used.

    Journal:

    Article Title: Characteristics of the Adeno-Associated Virus Preintegration Site in Human Chromosome 19: Open Chromatin Conformation and Transcription-Competent Environment

    doi:

    Figure Lengend Snippet: Transcriptional activity of DHS-S1. (A) Structure and activity of constructs containing DHS-S1 cloned upstream of the CAT gene. The whole DHS-S1 was excised as an SmaI-SmaI fragment (nt 18 to 353 of AAVS1) from plasmid pRVK and cloned in both orientations (indicated by the direction of the arrows) upstream of the intron and the CAT gene into the SmaI site of pCAT 3-basic vector (Promega). Black boxes represent the SV40 promoter. The promoterless plasmid is the pCAT 3-basic vector (Promega), and the control plasmid containing the SV40 promoter is the pCAT 3-promoter vector (Promega). Regions FR1 (nt 1313 to 1616 of AAVS1) and FR3 (nt 2633 to 2927 of AAVS1) were amplified by PCR with plasmid pRVK as a substrate and oligonucleotides carrying SmaI sites at either end. The resulting fragments were digested with restriction enzyme SmaI and cloned into the SmaI site of the pCAT 3-basic vector. Region FR2 (nt 2077 to 2371 of AAVS1) was excised from plasmid pRVK as a BamHI-flanked fragment, filled in by treatment with Klenow enzyme, and inserted into the SmaI site of pCAT 3-basic vector. Ten micrograms of each plasmid was transfected as described previously by calcium phosphate precipitation into 293 and HeLa cells (1). At 15 h posttransfection, the medium was changed: after an additional 24 h, cells were collected and CAT activity in cell extracts was measured by using the Quan-T-CAT assay system (Amersham, Pharmacia). CAT activities were normalized against the luciferase activity derived from a cotransfected cytomegalovirus-luciferase plasmid (1). Results are expressed as milliunits of CAT enzyme present in 10 μg of cell extracts and as fold induction with respect to the promoterless pCAT 3-basic vector. The data are means ± standard deviations of two independent experiments in which two separate plasmid preparations were used. (B) Enhancer activity of DHS-S1 in 293 and HeLa cells. DHS-S1 was cloned in both orientations (represented by the direction of the arrows) into the pCAT 3-promoter vector either into the SmaI site upstream of the SV40 promoter or into the BamHI site downstream of the CAT gene. Similarly, FR1, FR2, and FR3 were cloned in one orientation either into the SmaI site or into the BamHI site of pCAT 3-vector. Transfections were performed, and CAT activities were measured and normalized as described in the legend to Fig. ​Fig.4A.4A. Results are expressed as milliunits of CAT enzyme in 10 μg of cell extracts; fold induction was calculated with respect to that of the pCAT 3-promoter vector. The data are means ± standard deviations of three independent experiments in which at least two different plasmid preparations were used.

    Article Snippet: The whole DHS-S1 was excised as an Sma I- Sma I fragment (nt 18 to 353 of AAVS1) from plasmid pRVK and cloned in both orientations (indicated by the direction of the arrows) upstream of the intron and the CAT gene into the Sma I site of pCAT 3-basic vector (Promega).

    Techniques: Activity Assay, Construct, Clone Assay, Plasmid Preparation, Amplification, Transfection, Luciferase, Derivative Assay

    Enhancer activity of DHS-S1 is mainly located in the 181 to 353 region. (A) Graphic representation of the two DHS-S1 subregions, E1-S1 (nt 18 to 181) and E2-S1 (nt 181 to 353), whose transcriptional activity was tested in transient transfection assays. (B) Enhancer activity of E1-S1 and E2-S1 in 293 and HeLa cells. E1-S1 and E2-S1 were obtained as PCR fragments by using plasmid pRVK (see legend to Fig. ​Fig.1)1) as a template, and cloned in both orientations (indicated by the direction of the arrows) into plasmid pCAT 3-promoter either upstream of the SV40 promoter or downstream of the CAT gene (see the legend to Fig. ​Fig.4).4). Transfections, CAT assays, and normalization of the results were performed as described in the legend to Fig. ​Fig.4.4. Results are expressed as milliunits of CAT per 10 μg of cell extracts and as fold induction with respect to the pCAT 3-promoter vector. The data are means ± standard deviations of four independent experiments in which two different plasmid preparations were used.

    Journal:

    Article Title: Characteristics of the Adeno-Associated Virus Preintegration Site in Human Chromosome 19: Open Chromatin Conformation and Transcription-Competent Environment

    doi:

    Figure Lengend Snippet: Enhancer activity of DHS-S1 is mainly located in the 181 to 353 region. (A) Graphic representation of the two DHS-S1 subregions, E1-S1 (nt 18 to 181) and E2-S1 (nt 181 to 353), whose transcriptional activity was tested in transient transfection assays. (B) Enhancer activity of E1-S1 and E2-S1 in 293 and HeLa cells. E1-S1 and E2-S1 were obtained as PCR fragments by using plasmid pRVK (see legend to Fig. ​Fig.1)1) as a template, and cloned in both orientations (indicated by the direction of the arrows) into plasmid pCAT 3-promoter either upstream of the SV40 promoter or downstream of the CAT gene (see the legend to Fig. ​Fig.4).4). Transfections, CAT assays, and normalization of the results were performed as described in the legend to Fig. ​Fig.4.4. Results are expressed as milliunits of CAT per 10 μg of cell extracts and as fold induction with respect to the pCAT 3-promoter vector. The data are means ± standard deviations of four independent experiments in which two different plasmid preparations were used.

    Article Snippet: The whole DHS-S1 was excised as an Sma I- Sma I fragment (nt 18 to 353 of AAVS1) from plasmid pRVK and cloned in both orientations (indicated by the direction of the arrows) upstream of the intron and the CAT gene into the Sma I site of pCAT 3-basic vector (Promega).

    Techniques: Activity Assay, Transfection, Plasmid Preparation, Clone Assay