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plasmid pdup4-1  (Addgene inc)


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    Structured Review

    Addgene inc plasmid pdup4-1
    Plasmid Pdup4 1, supplied by Addgene inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/pdup4/vector+pdup4+1/pm38658687-365-19-4
    Average 90 stars, based on 1 article reviews
    plasmid pdup4-1 - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Plasmid Preparation:

    Article Title: Antisense oligonucleotide therapeutic approach for Timothy syndrome.
    Article Snippet: Cy5-labelled ASOs were synthesized by the addition of Cy5 to the 5′ of the ASO (Integrated DNA Technologies) followed by HPLC purification and Na+ salt exchange. .. pDup4-1 was obtained from Addgene (plasmid no. 23022) and was used as the backbone for the minigene splicing reporter. pDup4-1 was digested with ApaI and BglII (New England Biolabs) and the resulting 4,595 bp fragment was purified following loading on a 1% agarose gel using the QIAquick PCR Purification Kit (Qiagen, catalogue no. 28106). .. Genomic DNA from TS hiPS cells was purified with the DNeasy Blood & Tissue Kit (Qiagen, catalogue no. 69506).

    Article Title: Antisense oligonucleotide therapeutic approach for Timothy syndrome
    Article Snippet: Cy5-labelled ASOs were synthesized by the addition of Cy5 to the 5′ of the ASO (Integrated DNA Technologies) followed by HPLC purification and Na + salt exchange. .. pDup4-1 was obtained from Addgene (plasmid no. 23022) and was used as the backbone for the minigene splicing reporter. pDup4-1 was digested with ApaI and BglII (New England Biolabs) and the resulting 4,595 bp fragment was purified following loading on a 1% agarose gel using the QIAquick PCR Purification Kit (Qiagen, catalogue no. 28106). .. Genomic DNA from TS hiPS cells was purified with the DNeasy Blood & Tissue Kit (Qiagen, catalogue no. 69506).

    Purification:

    Article Title: Antisense oligonucleotide therapeutic approach for Timothy syndrome.
    Article Snippet: Cy5-labelled ASOs were synthesized by the addition of Cy5 to the 5′ of the ASO (Integrated DNA Technologies) followed by HPLC purification and Na+ salt exchange. .. pDup4-1 was obtained from Addgene (plasmid no. 23022) and was used as the backbone for the minigene splicing reporter. pDup4-1 was digested with ApaI and BglII (New England Biolabs) and the resulting 4,595 bp fragment was purified following loading on a 1% agarose gel using the QIAquick PCR Purification Kit (Qiagen, catalogue no. 28106). .. Genomic DNA from TS hiPS cells was purified with the DNeasy Blood & Tissue Kit (Qiagen, catalogue no. 69506).

    Article Title: Antisense oligonucleotide therapeutic approach for Timothy syndrome
    Article Snippet: Cy5-labelled ASOs were synthesized by the addition of Cy5 to the 5′ of the ASO (Integrated DNA Technologies) followed by HPLC purification and Na + salt exchange. .. pDup4-1 was obtained from Addgene (plasmid no. 23022) and was used as the backbone for the minigene splicing reporter. pDup4-1 was digested with ApaI and BglII (New England Biolabs) and the resulting 4,595 bp fragment was purified following loading on a 1% agarose gel using the QIAquick PCR Purification Kit (Qiagen, catalogue no. 28106). .. Genomic DNA from TS hiPS cells was purified with the DNeasy Blood & Tissue Kit (Qiagen, catalogue no. 69506).

    Agarose Gel Electrophoresis:

    Article Title: Antisense oligonucleotide therapeutic approach for Timothy syndrome.
    Article Snippet: Cy5-labelled ASOs were synthesized by the addition of Cy5 to the 5′ of the ASO (Integrated DNA Technologies) followed by HPLC purification and Na+ salt exchange. .. pDup4-1 was obtained from Addgene (plasmid no. 23022) and was used as the backbone for the minigene splicing reporter. pDup4-1 was digested with ApaI and BglII (New England Biolabs) and the resulting 4,595 bp fragment was purified following loading on a 1% agarose gel using the QIAquick PCR Purification Kit (Qiagen, catalogue no. 28106). .. Genomic DNA from TS hiPS cells was purified with the DNeasy Blood & Tissue Kit (Qiagen, catalogue no. 69506).

    Article Title: Antisense oligonucleotide therapeutic approach for Timothy syndrome
    Article Snippet: Cy5-labelled ASOs were synthesized by the addition of Cy5 to the 5′ of the ASO (Integrated DNA Technologies) followed by HPLC purification and Na + salt exchange. .. pDup4-1 was obtained from Addgene (plasmid no. 23022) and was used as the backbone for the minigene splicing reporter. pDup4-1 was digested with ApaI and BglII (New England Biolabs) and the resulting 4,595 bp fragment was purified following loading on a 1% agarose gel using the QIAquick PCR Purification Kit (Qiagen, catalogue no. 28106). .. Genomic DNA from TS hiPS cells was purified with the DNeasy Blood & Tissue Kit (Qiagen, catalogue no. 69506).

    Polymerase Chain Reaction:

    Article Title: Antisense oligonucleotide therapeutic approach for Timothy syndrome.
    Article Snippet: Cy5-labelled ASOs were synthesized by the addition of Cy5 to the 5′ of the ASO (Integrated DNA Technologies) followed by HPLC purification and Na+ salt exchange. .. pDup4-1 was obtained from Addgene (plasmid no. 23022) and was used as the backbone for the minigene splicing reporter. pDup4-1 was digested with ApaI and BglII (New England Biolabs) and the resulting 4,595 bp fragment was purified following loading on a 1% agarose gel using the QIAquick PCR Purification Kit (Qiagen, catalogue no. 28106). .. Genomic DNA from TS hiPS cells was purified with the DNeasy Blood & Tissue Kit (Qiagen, catalogue no. 69506).

    Article Title: Antisense oligonucleotide therapeutic approach for Timothy syndrome
    Article Snippet: Cy5-labelled ASOs were synthesized by the addition of Cy5 to the 5′ of the ASO (Integrated DNA Technologies) followed by HPLC purification and Na + salt exchange. .. pDup4-1 was obtained from Addgene (plasmid no. 23022) and was used as the backbone for the minigene splicing reporter. pDup4-1 was digested with ApaI and BglII (New England Biolabs) and the resulting 4,595 bp fragment was purified following loading on a 1% agarose gel using the QIAquick PCR Purification Kit (Qiagen, catalogue no. 28106). .. Genomic DNA from TS hiPS cells was purified with the DNeasy Blood & Tissue Kit (Qiagen, catalogue no. 69506).

    Sequencing:

    Article Title: RBFOX PROTEINS REGULATE ALTERNATIVE SPLICING OF NEURONAL SODIUM CHANNEL SCN8A
    Article Snippet: .. To generate the SCN8A minigene, a 2.6 kb genomic DNA fragment containing exon 18N and exon 18A with 0.9 kb of upstream sequence and 1.2 kb of downstream sequence was amplified from genomic DNA from mouse strain 129X1/SvJ (The Jackson Laboratory, Bar Harbor, ME) and cloned in the vector pDUP4-1 ( Modafferi and Black, 1997 ) (Addgene, Cambridge, MA). pDUP4-1 contains exons 1 and 2 of the beta-globin gene, which provide initiation and termination signals and can be used to distinguish the minigene transcripts from endogenous Na v 1.6 transcripts. ..

    Amplification:

    Article Title: RBFOX PROTEINS REGULATE ALTERNATIVE SPLICING OF NEURONAL SODIUM CHANNEL SCN8A
    Article Snippet: .. To generate the SCN8A minigene, a 2.6 kb genomic DNA fragment containing exon 18N and exon 18A with 0.9 kb of upstream sequence and 1.2 kb of downstream sequence was amplified from genomic DNA from mouse strain 129X1/SvJ (The Jackson Laboratory, Bar Harbor, ME) and cloned in the vector pDUP4-1 ( Modafferi and Black, 1997 ) (Addgene, Cambridge, MA). pDUP4-1 contains exons 1 and 2 of the beta-globin gene, which provide initiation and termination signals and can be used to distinguish the minigene transcripts from endogenous Na v 1.6 transcripts. ..

    Clone Assay:

    Article Title: RBFOX PROTEINS REGULATE ALTERNATIVE SPLICING OF NEURONAL SODIUM CHANNEL SCN8A
    Article Snippet: .. To generate the SCN8A minigene, a 2.6 kb genomic DNA fragment containing exon 18N and exon 18A with 0.9 kb of upstream sequence and 1.2 kb of downstream sequence was amplified from genomic DNA from mouse strain 129X1/SvJ (The Jackson Laboratory, Bar Harbor, ME) and cloned in the vector pDUP4-1 ( Modafferi and Black, 1997 ) (Addgene, Cambridge, MA). pDUP4-1 contains exons 1 and 2 of the beta-globin gene, which provide initiation and termination signals and can be used to distinguish the minigene transcripts from endogenous Na v 1.6 transcripts. ..



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    a , Schematics illustrating the TS pathogenic variant in the alternatively spliced exon 8A (left) and the resulting gain-of-function channel variant (right). The heterozygous G>A variant (black arrow) is located towards the 3′ end of exon 8A. b , Generation of hCO from control (Ctrl) and TS hiPS cells. c , Schematic of the RFLP assay. Left, PCR products amplified from hCO cDNA; the exon 8-containing amplicon is recognized by restriction enzyme BamHI; exon 8A, 8 and 7–9 amplicons have different molecular weights on agarose gel. Right, RFLP gel image of control and TS hCO at days 30, 60 and 90 of differentiation. Each column represents a hCO derived from different hiPS cell lines. L, ladder. d , Next-generation sequencing of amplicons generated from day 60 hCO. Left, PCR products were obtained using a forward primer targeting exon 7 and a reverse primer targeting exon 9; both primers have an Illumina adaptor at their 5′. Right, proportions of exon 8A WT, exon 8A TS, exon 8 and exons 7–9 are shown ( n = 3 for WT hCO, n = 3 for TS hCO). Data presented as mean ± s.d. One-way analysis of variance (ANOVA) with Tukey’s post hoc test: for control hCO, F 2,6 = 3.246, P = 0.1108; for TS hCO, F 3,8 = 50.28, P < 0.0001. **** P < 0.0001, *** P < 0.001, ** P < 0.01. e , Generation of minigene splicing reporters for exons 8 and 8A of CACNA1C . Left, experimental strategy for testing minisplicing reporters in HEK293T cells. Right, a CACNA1C DNA fragment (isolated from TS hiPS cells) was inserted into a <t>pDup4-1backbone</t> resulting in two vectors, pDup8-8A-WT and pDup8-8A-TS. bp, base pairs.
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    a , Schematics illustrating the TS pathogenic variant in the alternatively spliced exon 8A (left) and the resulting gain-of-function channel variant (right). The heterozygous G>A variant (black arrow) is located towards the 3′ end of exon 8A. b , Generation of hCO from control (Ctrl) and TS hiPS cells. c , Schematic of the RFLP assay. Left, PCR products amplified from hCO cDNA; the exon 8-containing amplicon is recognized by restriction enzyme BamHI; exon 8A, 8 and 7–9 amplicons have different molecular weights on agarose gel. Right, RFLP gel image of control and TS hCO at days 30, 60 and 90 of differentiation. Each column represents a hCO derived from different hiPS cell lines. L, ladder. d , Next-generation sequencing of amplicons generated from day 60 hCO. Left, PCR products were obtained using a forward primer targeting exon 7 and a reverse primer targeting exon 9; both primers have an Illumina adaptor at their 5′. Right, proportions of exon 8A WT, exon 8A TS, exon 8 and exons 7–9 are shown ( n = 3 for WT hCO, n = 3 for TS hCO). Data presented as mean ± s.d. One-way analysis of variance (ANOVA) with Tukey’s post hoc test: for control hCO, F 2,6 = 3.246, P = 0.1108; for TS hCO, F 3,8 = 50.28, P < 0.0001. **** P < 0.0001, *** P < 0.001, ** P < 0.01. e , Generation of minigene splicing reporters for exons 8 and 8A of CACNA1C . Left, experimental strategy for testing minisplicing reporters in HEK293T cells. Right, a CACNA1C DNA fragment (isolated from TS hiPS cells) was inserted into a <t>pDup4-1backbone</t> resulting in two vectors, pDup8-8A-WT and pDup8-8A-TS. bp, base pairs.
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    a , Schematics illustrating the TS pathogenic variant in the alternatively spliced exon 8A (left) and the resulting gain-of-function channel variant (right). The heterozygous G>A variant (black arrow) is located towards the 3′ end of exon 8A. b , Generation of hCO from control (Ctrl) and TS hiPS cells. c , Schematic of the RFLP assay. Left, PCR products amplified from hCO cDNA; the exon 8-containing amplicon is recognized by restriction enzyme BamHI; exon 8A, 8 and 7–9 amplicons have different molecular weights on agarose gel. Right, RFLP gel image of control and TS hCO at days 30, 60 and 90 of differentiation. Each column represents a hCO derived from different hiPS cell lines. L, ladder. d , Next-generation sequencing of amplicons generated from day 60 hCO. Left, PCR products were obtained using a forward primer targeting exon 7 and a reverse primer targeting exon 9; both primers have an Illumina adaptor at their 5′. Right, proportions of exon 8A WT, exon 8A TS, exon 8 and exons 7–9 are shown ( n = 3 for WT hCO, n = 3 for TS hCO). Data presented as mean ± s.d. One-way analysis of variance (ANOVA) with Tukey’s post hoc test: for control hCO, F 2,6 = 3.246, P = 0.1108; for TS hCO, F 3,8 = 50.28, P < 0.0001. **** P < 0.0001, *** P < 0.001, ** P < 0.01. e , Generation of minigene splicing reporters for exons 8 and 8A of CACNA1C . Left, experimental strategy for testing minisplicing reporters in HEK293T cells. Right, a CACNA1C DNA fragment (isolated from TS hiPS cells) was inserted into a <t>pDup4-1backbone</t> resulting in two vectors, pDup8-8A-WT and pDup8-8A-TS. bp, base pairs.
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    a , Schematics illustrating the TS pathogenic variant in the alternatively spliced exon 8A (left) and the resulting gain-of-function channel variant (right). The heterozygous G>A variant (black arrow) is located towards the 3′ end of exon 8A. b , Generation of hCO from control (Ctrl) and TS hiPS cells. c , Schematic of the RFLP assay. Left, PCR products amplified from hCO cDNA; the exon 8-containing amplicon is recognized by restriction enzyme BamHI; exon 8A, 8 and 7–9 amplicons have different molecular weights on agarose gel. Right, RFLP gel image of control and TS hCO at days 30, 60 and 90 of differentiation. Each column represents a hCO derived from different hiPS cell lines. L, ladder. d , Next-generation sequencing of amplicons generated from day 60 hCO. Left, PCR products were obtained using a forward primer targeting exon 7 and a reverse primer targeting exon 9; both primers have an Illumina adaptor at their 5′. Right, proportions of exon 8A WT, exon 8A TS, exon 8 and exons 7–9 are shown ( n = 3 for WT hCO, n = 3 for TS hCO). Data presented as mean ± s.d. One-way analysis of variance (ANOVA) with Tukey’s post hoc test: for control hCO, F 2,6 = 3.246, P = 0.1108; for TS hCO, F 3,8 = 50.28, P < 0.0001. **** P < 0.0001, *** P < 0.001, ** P < 0.01. e , Generation of minigene splicing reporters for exons 8 and 8A of CACNA1C . Left, experimental strategy for testing minisplicing reporters in HEK293T cells. Right, a CACNA1C DNA fragment (isolated from TS hiPS cells) was inserted into a <t>pDup4-1backbone</t> resulting in two vectors, pDup8-8A-WT and pDup8-8A-TS. bp, base pairs.
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    Image Search Results


    a , Schematics illustrating the TS pathogenic variant in the alternatively spliced exon 8A (left) and the resulting gain-of-function channel variant (right). The heterozygous G>A variant (black arrow) is located towards the 3′ end of exon 8A. b , Generation of hCO from control (Ctrl) and TS hiPS cells. c , Schematic of the RFLP assay. Left, PCR products amplified from hCO cDNA; the exon 8-containing amplicon is recognized by restriction enzyme BamHI; exon 8A, 8 and 7–9 amplicons have different molecular weights on agarose gel. Right, RFLP gel image of control and TS hCO at days 30, 60 and 90 of differentiation. Each column represents a hCO derived from different hiPS cell lines. L, ladder. d , Next-generation sequencing of amplicons generated from day 60 hCO. Left, PCR products were obtained using a forward primer targeting exon 7 and a reverse primer targeting exon 9; both primers have an Illumina adaptor at their 5′. Right, proportions of exon 8A WT, exon 8A TS, exon 8 and exons 7–9 are shown ( n = 3 for WT hCO, n = 3 for TS hCO). Data presented as mean ± s.d. One-way analysis of variance (ANOVA) with Tukey’s post hoc test: for control hCO, F 2,6 = 3.246, P = 0.1108; for TS hCO, F 3,8 = 50.28, P < 0.0001. **** P < 0.0001, *** P < 0.001, ** P < 0.01. e , Generation of minigene splicing reporters for exons 8 and 8A of CACNA1C . Left, experimental strategy for testing minisplicing reporters in HEK293T cells. Right, a CACNA1C DNA fragment (isolated from TS hiPS cells) was inserted into a pDup4-1backbone resulting in two vectors, pDup8-8A-WT and pDup8-8A-TS. bp, base pairs.

    Journal: Nature

    Article Title: Antisense oligonucleotide therapeutic approach for Timothy syndrome

    doi: 10.1038/s41586-024-07310-6

    Figure Lengend Snippet: a , Schematics illustrating the TS pathogenic variant in the alternatively spliced exon 8A (left) and the resulting gain-of-function channel variant (right). The heterozygous G>A variant (black arrow) is located towards the 3′ end of exon 8A. b , Generation of hCO from control (Ctrl) and TS hiPS cells. c , Schematic of the RFLP assay. Left, PCR products amplified from hCO cDNA; the exon 8-containing amplicon is recognized by restriction enzyme BamHI; exon 8A, 8 and 7–9 amplicons have different molecular weights on agarose gel. Right, RFLP gel image of control and TS hCO at days 30, 60 and 90 of differentiation. Each column represents a hCO derived from different hiPS cell lines. L, ladder. d , Next-generation sequencing of amplicons generated from day 60 hCO. Left, PCR products were obtained using a forward primer targeting exon 7 and a reverse primer targeting exon 9; both primers have an Illumina adaptor at their 5′. Right, proportions of exon 8A WT, exon 8A TS, exon 8 and exons 7–9 are shown ( n = 3 for WT hCO, n = 3 for TS hCO). Data presented as mean ± s.d. One-way analysis of variance (ANOVA) with Tukey’s post hoc test: for control hCO, F 2,6 = 3.246, P = 0.1108; for TS hCO, F 3,8 = 50.28, P < 0.0001. **** P < 0.0001, *** P < 0.001, ** P < 0.01. e , Generation of minigene splicing reporters for exons 8 and 8A of CACNA1C . Left, experimental strategy for testing minisplicing reporters in HEK293T cells. Right, a CACNA1C DNA fragment (isolated from TS hiPS cells) was inserted into a pDup4-1backbone resulting in two vectors, pDup8-8A-WT and pDup8-8A-TS. bp, base pairs.

    Article Snippet: pDup4-1 was obtained from Addgene (plasmid no. 23022) and was used as the backbone for the minigene splicing reporter. pDup4-1 was digested with ApaI and BglII (New England Biolabs) and the resulting 4,595 bp fragment was purified following loading on a 1% agarose gel using the QIAquick PCR Purification Kit (Qiagen, catalogue no. 28106).

    Techniques: Variant Assay, Control, RFLP Assay, Amplification, Agarose Gel Electrophoresis, Derivative Assay, Next-Generation Sequencing, Generated, Isolation