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asisi  (New England Biolabs)


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    Structured Review

    New England Biolabs asisi
    Asisi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 255 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/asisi/AsiSI/pmc12969024-258-21-22
    Average 96 stars, based on 255 article reviews
    asisi - by Bioz Stars, 2026-09
    96/100 stars

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    Related Articles

    Expressing:

    Article Title: Hierarchical TBX6-FOXC Regulatory Logic Controls Human Trunk Mesoderm Diversification
    Article Snippet: .. For Dox-inducible expression of transgenes of interest, the dCas9-KRAB-U6-gRNA cassette was excised with NotI (NEB, R3189) and AsiSI (NEB, R0630) and transgenes were cloned in by In Fusion. .. FOXC1 and TWIST1 transgenes were synthesised by Twist Biosciences. mCherry was synthesised by Vectorbuilder (VB240515-1632gka).

    Article Title: Novel missense variants in COX15 cause oocyte degeneration and female infertility.
    Article Snippet: Purpose To identify novel pathogenic genes and variants responsible for oocyte degeneration and death.. Methods Whole-exome sequencing was conducted in 78 individuals with primary infertility characterized with oocyte degeneration and death, followed by Sanger sequencing of candidate variants.. Pathogenicity of identified COX15 variants was characterized through morphological assessment, AlphaFold3-based structural modeling and functional validation including Western blotting and immunofluorescence.

    Clone Assay:

    Article Title: Hierarchical TBX6-FOXC Regulatory Logic Controls Human Trunk Mesoderm Diversification
    Article Snippet: .. For Dox-inducible expression of transgenes of interest, the dCas9-KRAB-U6-gRNA cassette was excised with NotI (NEB, R3189) and AsiSI (NEB, R0630) and transgenes were cloned in by In Fusion. .. FOXC1 and TWIST1 transgenes were synthesised by Twist Biosciences. mCherry was synthesised by Vectorbuilder (VB240515-1632gka).

    Article Title: Targeted Covalent Inhibition of Plasmodium FK506 Binding Protein 35
    Article Snippet: .. For NanoBRET assays, full length Plasmodium falciparum FKBP35 and human FKBP12 DNA were ordered as gBlocks from IDT and cloned using the Promega Flexi® system (Promega, cat. C8640). into NanoLuc® Luciferase Reporter pFN31 vectors (Promega, cat. N1311) with AsiSI and PmeI restriction endonucleases (NEB) to generate pFN31A-Nluc-CMV-Hygro-Flexi-FKBP12 and pFN31A-Nluc-CMV-Hygro-Flexi-FKBP35 vectors. ..

    other:

    Article Title: Characterization of variants associated with Cerebral Small Vessel Disease identifies a functional SNV in Versican
    Article Snippet: 10μg of pMPRAv3:Δluc:ΔxbaI (Addgene) was digested with SfiI (NEB) at 50C overnight and gel extracted (NucleoSpin Gel & PCR clean-up column, Macherey-Nagel).

    Article Title: Single-cell CRISPR activation screens in primary B cells discover gene regulatory mechanisms for hundreds of autoimmune risk loci
    Article Snippet: To clone the MPRA library into lentiviral vector pLS-mP (a gift from Nadav Ahituv; Addgene #81225), 125 ng of the oligonucleotide pool DNA was amplified in 4 × 50 μL reactions with 0.5 μM MPRAlib_PCR1_FW and MPRAlib_PCR1_RV primers and following conditions: 98°C for 1 min, (98°C for 10 s, 60°C for 15 s, 72°C for 20 s) × 5 cycles, 72°C for 5 min. 150 ng of purified PCR product split into 4 × 50 μL reactions and amplified with 0.5 μM MPRAlib_PCR2_FW and MPRAlib_BC_PCR2_RV primers under following conditions: 98°C for 2 min, (98°C for 15 s, 60°C for 20 s, 72°C for 30 s) × 4 cycles, 72°C for 5 min. At this step, a unique 13 bp molecular barcode (from primer MPRA_PCR2_FW) was added to each CRE.

    Control:

    Article Title: Intravenous oncolytic vaccinia expressing transgenes for enhanced safety, inhibition of shedding, imaging, and systemic cancer immunotherapy
    Article Snippet: Codon-optimized transgene sequences of WT HSV-TK and HSV-TK variants TK.007, SR39, and dm30 were synthetized with the P-SE/L synthetic early-late promoter and homologous flanking regions for the ΔJ2R insertion site (GenScript, Piscataway, NJ) and liberated from the pUC57 plasmid via PCR amplification. .. Viral genomic DNA from the control virus was purified and digested with the restriction enzymes AscI (NEB, Ipswich, MA, R0558) and AsiSI (NEB R0630), targeting cut sites engineered into regions flanking the ΔJ2R insertion site. .. To construct the HSV-TK variants, viral genomic DNA from TK.WT containing WT HSV-TK was used as a template and cut using CRISPR-Cas guide RNAs (IDT) targeting DNA sequences in the WT HSV-TK gene.

    Article Title: Intravenous Oncolytic Vaccinia Expressing Transgenes for Enhanced Safety, Inhibition of Shedding and Systemic Cancer Immunotherapy
    Article Snippet: 393 All the modifications in the viruses described in Table 1 were generated using the same 394 procedure by recombination and reactivation of vaccinia virus DNA.39 Codon optimized 395 transgene sequences of wild type (WT) HSV-TK and HSV-TK variants TK.007, SR39, and 396 dm30 were synthetized with the P-SE/L synthetic early-late promoter and homologous flanking 397 regions for the ΔJ2R insertion site (GenScript, Piscataway, NJ) and liberated from the pUC57 398 plasmid via PCR amplification. .. Viral genomic DNA from the control virus was purified40 and 399 digested with restriction enzymes AscI (NEB, Ipswich, MA, R0558) and AsiSI (NEB R0630) 400 targeting cut sites engineered into regions flanking the ΔJ2R insertion site. .. To construct the 401 HSV-TK variants, viral genomic DNA from TK.WT containing WT HSV-TK was used as 402 template and cut using CRISPR/Cas guide RNAs (IDT) targeting DNA sequences in the WT 403 HSV-TK gene.

    Article Title: Novel missense variants in COX15 cause oocyte degeneration and female infertility.
    Article Snippet: Purpose To identify novel pathogenic genes and variants responsible for oocyte degeneration and death.. Methods Whole-exome sequencing was conducted in 78 individuals with primary infertility characterized with oocyte degeneration and death, followed by Sanger sequencing of candidate variants.. Pathogenicity of identified COX15 variants was characterized through morphological assessment, AlphaFold3-based structural modeling and functional validation including Western blotting and immunofluorescence.

    Virus:

    Article Title: Intravenous oncolytic vaccinia expressing transgenes for enhanced safety, inhibition of shedding, imaging, and systemic cancer immunotherapy
    Article Snippet: Codon-optimized transgene sequences of WT HSV-TK and HSV-TK variants TK.007, SR39, and dm30 were synthetized with the P-SE/L synthetic early-late promoter and homologous flanking regions for the ΔJ2R insertion site (GenScript, Piscataway, NJ) and liberated from the pUC57 plasmid via PCR amplification. .. Viral genomic DNA from the control virus was purified and digested with the restriction enzymes AscI (NEB, Ipswich, MA, R0558) and AsiSI (NEB R0630), targeting cut sites engineered into regions flanking the ΔJ2R insertion site. .. To construct the HSV-TK variants, viral genomic DNA from TK.WT containing WT HSV-TK was used as a template and cut using CRISPR-Cas guide RNAs (IDT) targeting DNA sequences in the WT HSV-TK gene.

    Article Title: Intravenous Oncolytic Vaccinia Expressing Transgenes for Enhanced Safety, Inhibition of Shedding and Systemic Cancer Immunotherapy
    Article Snippet: 393 All the modifications in the viruses described in Table 1 were generated using the same 394 procedure by recombination and reactivation of vaccinia virus DNA.39 Codon optimized 395 transgene sequences of wild type (WT) HSV-TK and HSV-TK variants TK.007, SR39, and 396 dm30 were synthetized with the P-SE/L synthetic early-late promoter and homologous flanking 397 regions for the ΔJ2R insertion site (GenScript, Piscataway, NJ) and liberated from the pUC57 398 plasmid via PCR amplification. .. Viral genomic DNA from the control virus was purified40 and 399 digested with restriction enzymes AscI (NEB, Ipswich, MA, R0558) and AsiSI (NEB R0630) 400 targeting cut sites engineered into regions flanking the ΔJ2R insertion site. .. To construct the 401 HSV-TK variants, viral genomic DNA from TK.WT containing WT HSV-TK was used as 402 template and cut using CRISPR/Cas guide RNAs (IDT) targeting DNA sequences in the WT 403 HSV-TK gene.

    Purification:

    Article Title: Intravenous oncolytic vaccinia expressing transgenes for enhanced safety, inhibition of shedding, imaging, and systemic cancer immunotherapy
    Article Snippet: Codon-optimized transgene sequences of WT HSV-TK and HSV-TK variants TK.007, SR39, and dm30 were synthetized with the P-SE/L synthetic early-late promoter and homologous flanking regions for the ΔJ2R insertion site (GenScript, Piscataway, NJ) and liberated from the pUC57 plasmid via PCR amplification. .. Viral genomic DNA from the control virus was purified and digested with the restriction enzymes AscI (NEB, Ipswich, MA, R0558) and AsiSI (NEB R0630), targeting cut sites engineered into regions flanking the ΔJ2R insertion site. .. To construct the HSV-TK variants, viral genomic DNA from TK.WT containing WT HSV-TK was used as a template and cut using CRISPR-Cas guide RNAs (IDT) targeting DNA sequences in the WT HSV-TK gene.

    Plasmid Preparation:

    Article Title: The role of the lysine histone methylase KMT2D in chronic myeloid leukemia
    Article Snippet: The KMT2D -encoding plasmid was provided by Promega (Cat# FHC12732, Madison, Wisconsin, United States) and the plasmid harboring the KMT2D p. (Trp191Arg) variant was obtained by mutagenesis at GenScript (Rijswijk, Netherlands). .. The empty pFN21A vector was obtained through restriction enzyme cloning with AsiSI and Pme1 (both New England Biolabs). .. Plasmid DNA was isolated using PureYield Plasmid Multiprep System (Promega) or NucleoBond Xtra Midi Kit (Macherey Nagel GmbH).

    Cloning:

    Article Title: The role of the lysine histone methylase KMT2D in chronic myeloid leukemia
    Article Snippet: The KMT2D -encoding plasmid was provided by Promega (Cat# FHC12732, Madison, Wisconsin, United States) and the plasmid harboring the KMT2D p. (Trp191Arg) variant was obtained by mutagenesis at GenScript (Rijswijk, Netherlands). .. The empty pFN21A vector was obtained through restriction enzyme cloning with AsiSI and Pme1 (both New England Biolabs). .. Plasmid DNA was isolated using PureYield Plasmid Multiprep System (Promega) or NucleoBond Xtra Midi Kit (Macherey Nagel GmbH).

    Sequencing:

    Article Title: Novel missense variants in COX15 cause oocyte degeneration and female infertility.
    Article Snippet: Purpose To identify novel pathogenic genes and variants responsible for oocyte degeneration and death.. Methods Whole-exome sequencing was conducted in 78 individuals with primary infertility characterized with oocyte degeneration and death, followed by Sanger sequencing of candidate variants.. Pathogenicity of identified COX15 variants was characterized through morphological assessment, AlphaFold3-based structural modeling and functional validation including Western blotting and immunofluorescence.

    Polymerase Chain Reaction:

    Article Title: Novel missense variants in COX15 cause oocyte degeneration and female infertility.
    Article Snippet: Purpose To identify novel pathogenic genes and variants responsible for oocyte degeneration and death.. Methods Whole-exome sequencing was conducted in 78 individuals with primary infertility characterized with oocyte degeneration and death, followed by Sanger sequencing of candidate variants.. Pathogenicity of identified COX15 variants was characterized through morphological assessment, AlphaFold3-based structural modeling and functional validation including Western blotting and immunofluorescence.

    FLAG-tag:

    Article Title: Novel missense variants in COX15 cause oocyte degeneration and female infertility.
    Article Snippet: Purpose To identify novel pathogenic genes and variants responsible for oocyte degeneration and death.. Methods Whole-exome sequencing was conducted in 78 individuals with primary infertility characterized with oocyte degeneration and death, followed by Sanger sequencing of candidate variants.. Pathogenicity of identified COX15 variants was characterized through morphological assessment, AlphaFold3-based structural modeling and functional validation including Western blotting and immunofluorescence.

    Construct:

    Article Title: Novel missense variants in COX15 cause oocyte degeneration and female infertility.
    Article Snippet: Purpose To identify novel pathogenic genes and variants responsible for oocyte degeneration and death.. Methods Whole-exome sequencing was conducted in 78 individuals with primary infertility characterized with oocyte degeneration and death, followed by Sanger sequencing of candidate variants.. Pathogenicity of identified COX15 variants was characterized through morphological assessment, AlphaFold3-based structural modeling and functional validation including Western blotting and immunofluorescence.

    Luciferase:

    Article Title: Targeted Covalent Inhibition of Plasmodium FK506 Binding Protein 35
    Article Snippet: .. For NanoBRET assays, full length Plasmodium falciparum FKBP35 and human FKBP12 DNA were ordered as gBlocks from IDT and cloned using the Promega Flexi® system (Promega, cat. C8640). into NanoLuc® Luciferase Reporter pFN31 vectors (Promega, cat. N1311) with AsiSI and PmeI restriction endonucleases (NEB) to generate pFN31A-Nluc-CMV-Hygro-Flexi-FKBP12 and pFN31A-Nluc-CMV-Hygro-Flexi-FKBP35 vectors. ..



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    Image Search Results


    A) Schematic of the MPRA synthetic oligonucleotide including a forward primer (F), 102 bp of flanking sequence before, and 102 bp of flanking sequence after, the variant followed by a miniPromotor (miniP)- GFP construct, a 10 bp barcode and reverse primer (R). The oligo library was cloned into the pMPRAv3:Δluc:ΔxbaI vector and transfected into HEK293 cells. DNA and RNA was isolated separately and sequenced using MiSeq. B) Bioinformatic workflow for the MPRA analysis showing how allele-specific enhancers were identified. C) Fold change in expression for alelle specific enhancers in the indicated genes. Blue bars show significant allele-specific activity.

    Journal: bioRxiv

    Article Title: Characterization of variants associated with Cerebral Small Vessel Disease identifies a functional SNV in Versican

    doi: 10.64898/2026.03.16.712010

    Figure Lengend Snippet: A) Schematic of the MPRA synthetic oligonucleotide including a forward primer (F), 102 bp of flanking sequence before, and 102 bp of flanking sequence after, the variant followed by a miniPromotor (miniP)- GFP construct, a 10 bp barcode and reverse primer (R). The oligo library was cloned into the pMPRAv3:Δluc:ΔxbaI vector and transfected into HEK293 cells. DNA and RNA was isolated separately and sequenced using MiSeq. B) Bioinformatic workflow for the MPRA analysis showing how allele-specific enhancers were identified. C) Fold change in expression for alelle specific enhancers in the indicated genes. Blue bars show significant allele-specific activity.

    Article Snippet: The MPRA library incorporating GFP was created using 2μg of MiniGFP amplicon and 1μg of AsiSI linearized MPRA oligo library and assembled using NEBuilder HiFi DNA Assembly at 50C for 90 min, then purified with NucleoSpin PCR clean-up column, eluted and digested to remove remaining uncut vector by incubation with 25U AsiSI, and 5U RecBCD Plasmidsafe nuclease (NEB), 10μg BSA, 1 mM ATP in a 100μl reaction at 37 C overnight followed by NucleoSpin PCR clean-up column.

    Techniques: Sequencing, Variant Assay, Construct, Clone Assay, Plasmid Preparation, Transfection, Isolation, Expressing, Activity Assay

    A) Intergenic region between FOXQ1 and FOXF2 showing location of variants that are significant allele-specific enhancers from the MPRA. B) Table showing the log fold change and adjusted p value for the expression difference between major and minor alleles (allele-specific enhancers).

    Journal: bioRxiv

    Article Title: Characterization of variants associated with Cerebral Small Vessel Disease identifies a functional SNV in Versican

    doi: 10.64898/2026.03.16.712010

    Figure Lengend Snippet: A) Intergenic region between FOXQ1 and FOXF2 showing location of variants that are significant allele-specific enhancers from the MPRA. B) Table showing the log fold change and adjusted p value for the expression difference between major and minor alleles (allele-specific enhancers).

    Article Snippet: The MPRA library incorporating GFP was created using 2μg of MiniGFP amplicon and 1μg of AsiSI linearized MPRA oligo library and assembled using NEBuilder HiFi DNA Assembly at 50C for 90 min, then purified with NucleoSpin PCR clean-up column, eluted and digested to remove remaining uncut vector by incubation with 25U AsiSI, and 5U RecBCD Plasmidsafe nuclease (NEB), 10μg BSA, 1 mM ATP in a 100μl reaction at 37 C overnight followed by NucleoSpin PCR clean-up column.

    Techniques: Expressing

    A) Schematic of where a 2 kb intronic enhancer region was deleted using two CRISPRs. B) Sequences of independent clones with the 2 kb region deleted. C) qPCR of endogenous VCAN in the deleted clones showing that VCAN V3 is significantly downregulated when the enhancer is deleted but there are no significant changes in V0, V1 and V2. D) Schematic of constructs with the major and minor alleles of rs13176921 in a 300bp oligo. E) Luciferase activity is decreased when the minor allele is present, relative to the major allele. N=3 biological replicates, with 3 technical replicates. F) Position weight matrix for NKX3.1 from JASPAR showing location of rs13176921 SNV. G) ChIP for NKX3.1 in the region of rs13176921, a positive control genomic region known to bind NKX3.1 (Chr 19) and a negative control region (Sat2). Statistics used a One Way ANOVA with Dunnett’s multiple comparison test, or the Student’s t-test.

    Journal: bioRxiv

    Article Title: Characterization of variants associated with Cerebral Small Vessel Disease identifies a functional SNV in Versican

    doi: 10.64898/2026.03.16.712010

    Figure Lengend Snippet: A) Schematic of where a 2 kb intronic enhancer region was deleted using two CRISPRs. B) Sequences of independent clones with the 2 kb region deleted. C) qPCR of endogenous VCAN in the deleted clones showing that VCAN V3 is significantly downregulated when the enhancer is deleted but there are no significant changes in V0, V1 and V2. D) Schematic of constructs with the major and minor alleles of rs13176921 in a 300bp oligo. E) Luciferase activity is decreased when the minor allele is present, relative to the major allele. N=3 biological replicates, with 3 technical replicates. F) Position weight matrix for NKX3.1 from JASPAR showing location of rs13176921 SNV. G) ChIP for NKX3.1 in the region of rs13176921, a positive control genomic region known to bind NKX3.1 (Chr 19) and a negative control region (Sat2). Statistics used a One Way ANOVA with Dunnett’s multiple comparison test, or the Student’s t-test.

    Article Snippet: The MPRA library incorporating GFP was created using 2μg of MiniGFP amplicon and 1μg of AsiSI linearized MPRA oligo library and assembled using NEBuilder HiFi DNA Assembly at 50C for 90 min, then purified with NucleoSpin PCR clean-up column, eluted and digested to remove remaining uncut vector by incubation with 25U AsiSI, and 5U RecBCD Plasmidsafe nuclease (NEB), 10μg BSA, 1 mM ATP in a 100μl reaction at 37 C overnight followed by NucleoSpin PCR clean-up column.

    Techniques: Clone Assay, Construct, Luciferase, Activity Assay, Positive Control, Negative Control, Comparison