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kpni  (New England Biolabs)


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    Structured Review

    New England Biolabs kpni
    Kpni, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 1703 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/kpni/KpnI-HF/pmc13170675-221-60-62
    Average 97 stars, based on 1703 article reviews
    kpni - by Bioz Stars, 2026-10
    97/100 stars

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    Related Articles

    Blocking Assay:

    Article Title: An inducible CRISPRi system for phenotypic analysis of essential genes in Pseudomonas aeruginosa
    Article Snippet: .. The gene block and pUC18T-miniTn7T-pBAD-dcas9-Gm plasmid were restriction-digested with HindIII and KpnI and ligated together (T4 DNA ligase, New England Biolabs, Ipswich MA) to produce the first-generation CRISPRi A plasmid pUC18T-miniTn7T-pBAD-dcas9-pD-Gm (9,326 bp). sgRNAs were cloned into the CRISPRi A plasmid using standard CRISPRi protocols established in mycobacteria using BsmBI cut sites ( ). ..

    Plasmid Preparation:

    Article Title: An inducible CRISPRi system for phenotypic analysis of essential genes in Pseudomonas aeruginosa
    Article Snippet: .. The gene block and pUC18T-miniTn7T-pBAD-dcas9-Gm plasmid were restriction-digested with HindIII and KpnI and ligated together (T4 DNA ligase, New England Biolabs, Ipswich MA) to produce the first-generation CRISPRi A plasmid pUC18T-miniTn7T-pBAD-dcas9-pD-Gm (9,326 bp). sgRNAs were cloned into the CRISPRi A plasmid using standard CRISPRi protocols established in mycobacteria using BsmBI cut sites ( ). ..

    Article Title: Intrathecal delivery of AAVrh10-mHexa combined with anti-inflammatory treatment reduces neuropathological markers and extends the lifespan of mice with early-onset Tay-Sachs disease
    Article Snippet: Vector verification was performed through restriction enzyme mapping. .. EcoRI (Biolab NEB Cat# 0101 S), KpnI (Biolab NEB Cat# 3142 S), and PstI (Biolab NEB Cat# 3140 S) enzymes were used for the mammalian expression vector. .. In contrast, BamHI (Biolab NEB Cat# 0136 S) was used to confirm the packaging vector pAAV2/rh10 and the helper vector pAdDeltaF6.

    Article Title: Systematic multi-reference vertebrate ACE2 sequence similarity analysis predicts species susceptibility to SARS-related sarbecoviruses
    Article Snippet: Codon-optimized ACE2 ORF sequences were synthesized as gene fragments (mouse, pig, narwhal, reindeer, Coquerel’s sifaka, sinicus bat allele 1443, affinis bat), which contain 5’ KpnI and 3’ MluI restriction sites for downstream cloning into above described the pCMV6-humanACE2-MYC-FLAG backbone, or directly synthesized as complete expression plasmids (hedgehog, ruff, Himalayan frog, sinicus bat allele 3358) by Twist Bioscience. .. ACE2 gene fragments were cloned into KpnI (NEB R3142S) and MluI (R3198S) double-digested pCMV6-MYC-FLAG plasmid backbone using the InFusion cloning kit (Takara 638,948). pCDNA3-SARS-CoV-2-beta-S ( QRN78347.1 ) expression plasmid was provided by Dr. Wilen (Yale University). pCAGGS-SARS-WIV1-S ( KF367457.1 ), pCAGGS-SARS-CoV-Tor2-S ( YP_009825051.1 ), pCAGGS -SARS-CoV-2-WA1-S ( QIQ50192.1 ), pCAGGS-SARS-CoV-2-delta-S ( UBG84005.1 ), pCAGGS- BANAL236-S ( MZ937003 ), and pCAGGS-BANAL52-S ( MZ937000 ) were synthesized as gene blocks by Twist Bioscience and subcloned into XbaI (NEB R0145S) and NotI (NEB R3189S) double-digested pCAGGS plasmids by Gibson Assembly (NEB HiFi M5520). pTwist-SARS-CoV-2-BA1-S ( UFO69279.1 ), pTwist-SARS-CoV-2-BA4-S ( UPP14409.1 ), expression plasmids were directly synthesized by Twist Bioscience. ..

    Article Title: Compositions and methods for targeted delivery of CRISPR-Cas effector polypeptides and transgenes
    Article Snippet: In-Fusion (Takara Bio) cloning was used to clone Gag-Cas9 and Env into the pCAGGS expression vector. pCF221 (Addgene plasmid #121669) was modified to express mNeonGreen (Allele Biotechnology) or the α-CD19-4-1BBζ-P2A-mCherry (CAR-P2A-mCherry) construct (Hill et al., 2018; Muller et al., 2020) in place of mCherry and was used as the sgRNA-expressing lentiviral transfer plasmid. .. For generation of hybrid Cas9-VLPs, the guide RNA expression cassette was removed from the CAR-P2A-mCherry lentiviral plasmid via digestion with EcoRI and KpnI (NEB). .. The following primers (IDT) were phosphorylated, annealed, and ligated into the digested vector: 5′-cATCGATCTTAAGTCGCGACTCGAg (SEQ ID NO:164) and 5′-aattcTCGAGTCGCGACTTAAGATCGATggtac (SEQ ID NO:165).

    Article Title: Intrathecal delivery of AAVrh10-mHexa combined with anti-inflammatory treatment reduces neuropathological markers and extends the lifespan of mice with early-onset Tay-Sachs disease.
    Article Snippet: Vector verification was performed through restriction enzyme mapping. .. EcoRI (Biolab NEB Cat# 0101 S), KpnI (Biolab NEB Cat# 3142 S), and PstI (Biolab NEB Cat# 3140 S) enzymes were used for the mammalian expression vector. .. In contrast, BamHI (Biolab NEB Cat# 0136 S) was used to confirm the packaging vector pAAV2/rh10 and the helper vector pAdDeltaF6.

    Clone Assay:

    Article Title: An inducible CRISPRi system for phenotypic analysis of essential genes in Pseudomonas aeruginosa
    Article Snippet: .. The gene block and pUC18T-miniTn7T-pBAD-dcas9-Gm plasmid were restriction-digested with HindIII and KpnI and ligated together (T4 DNA ligase, New England Biolabs, Ipswich MA) to produce the first-generation CRISPRi A plasmid pUC18T-miniTn7T-pBAD-dcas9-pD-Gm (9,326 bp). sgRNAs were cloned into the CRISPRi A plasmid using standard CRISPRi protocols established in mycobacteria using BsmBI cut sites ( ). ..

    Article Title: Systematic multi-reference vertebrate ACE2 sequence similarity analysis predicts species susceptibility to SARS-related sarbecoviruses
    Article Snippet: Codon-optimized ACE2 ORF sequences were synthesized as gene fragments (mouse, pig, narwhal, reindeer, Coquerel’s sifaka, sinicus bat allele 1443, affinis bat), which contain 5’ KpnI and 3’ MluI restriction sites for downstream cloning into above described the pCMV6-humanACE2-MYC-FLAG backbone, or directly synthesized as complete expression plasmids (hedgehog, ruff, Himalayan frog, sinicus bat allele 3358) by Twist Bioscience. .. ACE2 gene fragments were cloned into KpnI (NEB R3142S) and MluI (R3198S) double-digested pCMV6-MYC-FLAG plasmid backbone using the InFusion cloning kit (Takara 638,948). pCDNA3-SARS-CoV-2-beta-S ( QRN78347.1 ) expression plasmid was provided by Dr. Wilen (Yale University). pCAGGS-SARS-WIV1-S ( KF367457.1 ), pCAGGS-SARS-CoV-Tor2-S ( YP_009825051.1 ), pCAGGS -SARS-CoV-2-WA1-S ( QIQ50192.1 ), pCAGGS-SARS-CoV-2-delta-S ( UBG84005.1 ), pCAGGS- BANAL236-S ( MZ937003 ), and pCAGGS-BANAL52-S ( MZ937000 ) were synthesized as gene blocks by Twist Bioscience and subcloned into XbaI (NEB R0145S) and NotI (NEB R3189S) double-digested pCAGGS plasmids by Gibson Assembly (NEB HiFi M5520). pTwist-SARS-CoV-2-BA1-S ( UFO69279.1 ), pTwist-SARS-CoV-2-BA4-S ( UPP14409.1 ), expression plasmids were directly synthesized by Twist Bioscience. ..

    Amplification:

    Article Title: A Wnt-induced conformational phospho-switch in DVL3 controls association with Frizzled receptors and Wnt/β-catenin signaling
    Article Snippet: .. hDVL3 segments of interest (IDR2, amino acids 335 to 396; DEP, amino acids 398 to 496; PDZ, amino acids 243 to 351; and PDZ-IDR2-DEP, amino acids 243 to 496) were amplified by polymerase chain reaction (PCR) and inserted into a pETM11 or pET-Z (IDR2) expression vectors via restriction digestion between the 5′-NcoI and 3′-KpnI sites, using BspHI (R0517, NEB) and KpnI (R3142S, NEB) restriction enzymes. .. The DNA segment encoding CK1δ or ε was amplified by PCR and inserted into pETM11 expression vector via restriction digestion between the 5′-NcoI and 3′-EcoRI sites, using NcoI (R0193L, NEB) and EcoRI (R3101S, NEB) restriction enzymes.

    Polymerase Chain Reaction:

    Article Title: A Wnt-induced conformational phospho-switch in DVL3 controls association with Frizzled receptors and Wnt/β-catenin signaling
    Article Snippet: .. hDVL3 segments of interest (IDR2, amino acids 335 to 396; DEP, amino acids 398 to 496; PDZ, amino acids 243 to 351; and PDZ-IDR2-DEP, amino acids 243 to 496) were amplified by polymerase chain reaction (PCR) and inserted into a pETM11 or pET-Z (IDR2) expression vectors via restriction digestion between the 5′-NcoI and 3′-KpnI sites, using BspHI (R0517, NEB) and KpnI (R3142S, NEB) restriction enzymes. .. The DNA segment encoding CK1δ or ε was amplified by PCR and inserted into pETM11 expression vector via restriction digestion between the 5′-NcoI and 3′-EcoRI sites, using NcoI (R0193L, NEB) and EcoRI (R3101S, NEB) restriction enzymes.

    Expressing:

    Article Title: A Wnt-induced conformational phospho-switch in DVL3 controls association with Frizzled receptors and Wnt/β-catenin signaling
    Article Snippet: .. hDVL3 segments of interest (IDR2, amino acids 335 to 396; DEP, amino acids 398 to 496; PDZ, amino acids 243 to 351; and PDZ-IDR2-DEP, amino acids 243 to 496) were amplified by polymerase chain reaction (PCR) and inserted into a pETM11 or pET-Z (IDR2) expression vectors via restriction digestion between the 5′-NcoI and 3′-KpnI sites, using BspHI (R0517, NEB) and KpnI (R3142S, NEB) restriction enzymes. .. The DNA segment encoding CK1δ or ε was amplified by PCR and inserted into pETM11 expression vector via restriction digestion between the 5′-NcoI and 3′-EcoRI sites, using NcoI (R0193L, NEB) and EcoRI (R3101S, NEB) restriction enzymes.

    Article Title: Intrathecal delivery of AAVrh10-mHexa combined with anti-inflammatory treatment reduces neuropathological markers and extends the lifespan of mice with early-onset Tay-Sachs disease
    Article Snippet: Vector verification was performed through restriction enzyme mapping. .. EcoRI (Biolab NEB Cat# 0101 S), KpnI (Biolab NEB Cat# 3142 S), and PstI (Biolab NEB Cat# 3140 S) enzymes were used for the mammalian expression vector. .. In contrast, BamHI (Biolab NEB Cat# 0136 S) was used to confirm the packaging vector pAAV2/rh10 and the helper vector pAdDeltaF6.

    Article Title: Systematic multi-reference vertebrate ACE2 sequence similarity analysis predicts species susceptibility to SARS-related sarbecoviruses
    Article Snippet: Codon-optimized ACE2 ORF sequences were synthesized as gene fragments (mouse, pig, narwhal, reindeer, Coquerel’s sifaka, sinicus bat allele 1443, affinis bat), which contain 5’ KpnI and 3’ MluI restriction sites for downstream cloning into above described the pCMV6-humanACE2-MYC-FLAG backbone, or directly synthesized as complete expression plasmids (hedgehog, ruff, Himalayan frog, sinicus bat allele 3358) by Twist Bioscience. .. ACE2 gene fragments were cloned into KpnI (NEB R3142S) and MluI (R3198S) double-digested pCMV6-MYC-FLAG plasmid backbone using the InFusion cloning kit (Takara 638,948). pCDNA3-SARS-CoV-2-beta-S ( QRN78347.1 ) expression plasmid was provided by Dr. Wilen (Yale University). pCAGGS-SARS-WIV1-S ( KF367457.1 ), pCAGGS-SARS-CoV-Tor2-S ( YP_009825051.1 ), pCAGGS -SARS-CoV-2-WA1-S ( QIQ50192.1 ), pCAGGS-SARS-CoV-2-delta-S ( UBG84005.1 ), pCAGGS- BANAL236-S ( MZ937003 ), and pCAGGS-BANAL52-S ( MZ937000 ) were synthesized as gene blocks by Twist Bioscience and subcloned into XbaI (NEB R0145S) and NotI (NEB R3189S) double-digested pCAGGS plasmids by Gibson Assembly (NEB HiFi M5520). pTwist-SARS-CoV-2-BA1-S ( UFO69279.1 ), pTwist-SARS-CoV-2-BA4-S ( UPP14409.1 ), expression plasmids were directly synthesized by Twist Bioscience. ..

    Article Title: Intrathecal delivery of AAVrh10-mHexa combined with anti-inflammatory treatment reduces neuropathological markers and extends the lifespan of mice with early-onset Tay-Sachs disease.
    Article Snippet: Vector verification was performed through restriction enzyme mapping. .. EcoRI (Biolab NEB Cat# 0101 S), KpnI (Biolab NEB Cat# 3142 S), and PstI (Biolab NEB Cat# 3140 S) enzymes were used for the mammalian expression vector. .. In contrast, BamHI (Biolab NEB Cat# 0136 S) was used to confirm the packaging vector pAAV2/rh10 and the helper vector pAdDeltaF6.

    Cloning:

    Article Title: Systematic multi-reference vertebrate ACE2 sequence similarity analysis predicts species susceptibility to SARS-related sarbecoviruses
    Article Snippet: Codon-optimized ACE2 ORF sequences were synthesized as gene fragments (mouse, pig, narwhal, reindeer, Coquerel’s sifaka, sinicus bat allele 1443, affinis bat), which contain 5’ KpnI and 3’ MluI restriction sites for downstream cloning into above described the pCMV6-humanACE2-MYC-FLAG backbone, or directly synthesized as complete expression plasmids (hedgehog, ruff, Himalayan frog, sinicus bat allele 3358) by Twist Bioscience. .. ACE2 gene fragments were cloned into KpnI (NEB R3142S) and MluI (R3198S) double-digested pCMV6-MYC-FLAG plasmid backbone using the InFusion cloning kit (Takara 638,948). pCDNA3-SARS-CoV-2-beta-S ( QRN78347.1 ) expression plasmid was provided by Dr. Wilen (Yale University). pCAGGS-SARS-WIV1-S ( KF367457.1 ), pCAGGS-SARS-CoV-Tor2-S ( YP_009825051.1 ), pCAGGS -SARS-CoV-2-WA1-S ( QIQ50192.1 ), pCAGGS-SARS-CoV-2-delta-S ( UBG84005.1 ), pCAGGS- BANAL236-S ( MZ937003 ), and pCAGGS-BANAL52-S ( MZ937000 ) were synthesized as gene blocks by Twist Bioscience and subcloned into XbaI (NEB R0145S) and NotI (NEB R3189S) double-digested pCAGGS plasmids by Gibson Assembly (NEB HiFi M5520). pTwist-SARS-CoV-2-BA1-S ( UFO69279.1 ), pTwist-SARS-CoV-2-BA4-S ( UPP14409.1 ), expression plasmids were directly synthesized by Twist Bioscience. ..

    Synthesized:

    Article Title: Systematic multi-reference vertebrate ACE2 sequence similarity analysis predicts species susceptibility to SARS-related sarbecoviruses
    Article Snippet: Codon-optimized ACE2 ORF sequences were synthesized as gene fragments (mouse, pig, narwhal, reindeer, Coquerel’s sifaka, sinicus bat allele 1443, affinis bat), which contain 5’ KpnI and 3’ MluI restriction sites for downstream cloning into above described the pCMV6-humanACE2-MYC-FLAG backbone, or directly synthesized as complete expression plasmids (hedgehog, ruff, Himalayan frog, sinicus bat allele 3358) by Twist Bioscience. .. ACE2 gene fragments were cloned into KpnI (NEB R3142S) and MluI (R3198S) double-digested pCMV6-MYC-FLAG plasmid backbone using the InFusion cloning kit (Takara 638,948). pCDNA3-SARS-CoV-2-beta-S ( QRN78347.1 ) expression plasmid was provided by Dr. Wilen (Yale University). pCAGGS-SARS-WIV1-S ( KF367457.1 ), pCAGGS-SARS-CoV-Tor2-S ( YP_009825051.1 ), pCAGGS -SARS-CoV-2-WA1-S ( QIQ50192.1 ), pCAGGS-SARS-CoV-2-delta-S ( UBG84005.1 ), pCAGGS- BANAL236-S ( MZ937003 ), and pCAGGS-BANAL52-S ( MZ937000 ) were synthesized as gene blocks by Twist Bioscience and subcloned into XbaI (NEB R0145S) and NotI (NEB R3189S) double-digested pCAGGS plasmids by Gibson Assembly (NEB HiFi M5520). pTwist-SARS-CoV-2-BA1-S ( UFO69279.1 ), pTwist-SARS-CoV-2-BA4-S ( UPP14409.1 ), expression plasmids were directly synthesized by Twist Bioscience. ..

    RNA Expression:

    Article Title: Compositions and methods for targeted delivery of CRISPR-Cas effector polypeptides and transgenes
    Article Snippet: In-Fusion (Takara Bio) cloning was used to clone Gag-Cas9 and Env into the pCAGGS expression vector. pCF221 (Addgene plasmid #121669) was modified to express mNeonGreen (Allele Biotechnology) or the α-CD19-4-1BBζ-P2A-mCherry (CAR-P2A-mCherry) construct (Hill et al., 2018; Muller et al., 2020) in place of mCherry and was used as the sgRNA-expressing lentiviral transfer plasmid. .. For generation of hybrid Cas9-VLPs, the guide RNA expression cassette was removed from the CAR-P2A-mCherry lentiviral plasmid via digestion with EcoRI and KpnI (NEB). .. The following primers (IDT) were phosphorylated, annealed, and ligated into the digested vector: 5′-cATCGATCTTAAGTCGCGACTCGAg (SEQ ID NO:164) and 5′-aattcTCGAGTCGCGACTTAAGATCGATggtac (SEQ ID NO:165).



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