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smai restriction enzyme  (New England Biolabs)


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    Structured Review

    New England Biolabs smai restriction enzyme
    Recombinant AAV genome element and heterogeneity analysis by native and alkaline electrophoresis (A) Graphic representation of the main recombinant AAV vector genome elements evaluated: wtITR (143 nt, black) versus dITR/wtITR (11-nt deletion in the 5′ C arm, 130 nt, red), EAlbAAT (albumin enhancer-alpha1-antitrypsin promoter, blue), Egfp (enhanced green fluorescent protein, green), pA (bovine/human growth hormone polyadenylation signal, yellow), and CBA (CMV (cytomegalovirus) enhancer-chicken beta actin promoter, orange). Vector genome sizes are shown next to each representation. (B) Native automated electrophoresis of <t>extracted</t> <t>rAAV</t> genomes from dITR/wtITR and wtITR. EalbAAT . Egfp vectors by TapeStation. From left to right: AAV2, AAV3B, AAV5, AAV8, AAV9, and AAVLK03 serotypes. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (C) Native automated electrophoresis of extracted rAAV genomes from AAV5 and AAV8 serotypes with dITR vs. wtITR and CBA versus EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (D) Native automated electrophoresis of extracted rAAV genomes from the AAVLK03 serotype with dITR and CBA vs. EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (E) Native electrophoresis of extracted rAAV genomes from AAV9 and AAVLK03 serotypes with dITR and CBA versus EalbAAT promoters, before and after digestion at 37°C for 1 h with <t>SmaI.</t> (F) Graphic representation of the dITR/tITR design (11-nt deletion in the 5′ C arm and 22-nt deletion of the 3′ B arm, 121 nt, purple), scITR (C arm deletion, 106 nt, green), and the dITR. AAT . Egfp expression cassette including an hypoxanthine phosphoribosyltransferase 1 ( HPRT 1 ) DNA stuffer sequence (GenBank: NG_012329.2 ) (bottom). Vector genome sizes are shown next to each design. (G) Alkaline electrophoresis of AAV8 vectors with different ITR configurations and CBA versus EalbAAT promoters. (H) Alkaline electrophoresis of AAV8 and AAV3B vectors with dITR/wtITR, dITR/tITR, and scITR configurations. (I) Alkaline electrophoresis of AAV8 and AAVLK03 vectors with the dITR/tITR configuration. (J) Alkaline electrophoresis of AAV3B, AAV5, and AAVLK03 vectors with dITR/wtITR configuration and CBA versus EalbAAT promoters. Combinations are displayed on top of each lane. Agarose gel ladder: FastGene 1 kb DNA marker (10,000–100 bp).
    Smai Restriction Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 2722 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/smai+restriction+enzyme/SmaI/pmc13049938-281-0-5
    Average 97 stars, based on 2722 article reviews
    smai restriction enzyme - by Bioz Stars, 2026-09
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    Images

    1) Product Images from "Orthogonal characterization of rAAV reveals vector attributes that drive ITR repair, self-complementary genome formation, and transgene expression"

    Article Title: Orthogonal characterization of rAAV reveals vector attributes that drive ITR repair, self-complementary genome formation, and transgene expression

    Journal: Molecular Therapy. Nucleic Acids

    doi: 10.1016/j.omtn.2026.102899

    Recombinant AAV genome element and heterogeneity analysis by native and alkaline electrophoresis (A) Graphic representation of the main recombinant AAV vector genome elements evaluated: wtITR (143 nt, black) versus dITR/wtITR (11-nt deletion in the 5′ C arm, 130 nt, red), EAlbAAT (albumin enhancer-alpha1-antitrypsin promoter, blue), Egfp (enhanced green fluorescent protein, green), pA (bovine/human growth hormone polyadenylation signal, yellow), and CBA (CMV (cytomegalovirus) enhancer-chicken beta actin promoter, orange). Vector genome sizes are shown next to each representation. (B) Native automated electrophoresis of extracted rAAV genomes from dITR/wtITR and wtITR. EalbAAT . Egfp vectors by TapeStation. From left to right: AAV2, AAV3B, AAV5, AAV8, AAV9, and AAVLK03 serotypes. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (C) Native automated electrophoresis of extracted rAAV genomes from AAV5 and AAV8 serotypes with dITR vs. wtITR and CBA versus EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (D) Native automated electrophoresis of extracted rAAV genomes from the AAVLK03 serotype with dITR and CBA vs. EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (E) Native electrophoresis of extracted rAAV genomes from AAV9 and AAVLK03 serotypes with dITR and CBA versus EalbAAT promoters, before and after digestion at 37°C for 1 h with SmaI. (F) Graphic representation of the dITR/tITR design (11-nt deletion in the 5′ C arm and 22-nt deletion of the 3′ B arm, 121 nt, purple), scITR (C arm deletion, 106 nt, green), and the dITR. AAT . Egfp expression cassette including an hypoxanthine phosphoribosyltransferase 1 ( HPRT 1 ) DNA stuffer sequence (GenBank: NG_012329.2 ) (bottom). Vector genome sizes are shown next to each design. (G) Alkaline electrophoresis of AAV8 vectors with different ITR configurations and CBA versus EalbAAT promoters. (H) Alkaline electrophoresis of AAV8 and AAV3B vectors with dITR/wtITR, dITR/tITR, and scITR configurations. (I) Alkaline electrophoresis of AAV8 and AAVLK03 vectors with the dITR/tITR configuration. (J) Alkaline electrophoresis of AAV3B, AAV5, and AAVLK03 vectors with dITR/wtITR configuration and CBA versus EalbAAT promoters. Combinations are displayed on top of each lane. Agarose gel ladder: FastGene 1 kb DNA marker (10,000–100 bp).
    Figure Legend Snippet: Recombinant AAV genome element and heterogeneity analysis by native and alkaline electrophoresis (A) Graphic representation of the main recombinant AAV vector genome elements evaluated: wtITR (143 nt, black) versus dITR/wtITR (11-nt deletion in the 5′ C arm, 130 nt, red), EAlbAAT (albumin enhancer-alpha1-antitrypsin promoter, blue), Egfp (enhanced green fluorescent protein, green), pA (bovine/human growth hormone polyadenylation signal, yellow), and CBA (CMV (cytomegalovirus) enhancer-chicken beta actin promoter, orange). Vector genome sizes are shown next to each representation. (B) Native automated electrophoresis of extracted rAAV genomes from dITR/wtITR and wtITR. EalbAAT . Egfp vectors by TapeStation. From left to right: AAV2, AAV3B, AAV5, AAV8, AAV9, and AAVLK03 serotypes. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (C) Native automated electrophoresis of extracted rAAV genomes from AAV5 and AAV8 serotypes with dITR vs. wtITR and CBA versus EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (D) Native automated electrophoresis of extracted rAAV genomes from the AAVLK03 serotype with dITR and CBA vs. EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (E) Native electrophoresis of extracted rAAV genomes from AAV9 and AAVLK03 serotypes with dITR and CBA versus EalbAAT promoters, before and after digestion at 37°C for 1 h with SmaI. (F) Graphic representation of the dITR/tITR design (11-nt deletion in the 5′ C arm and 22-nt deletion of the 3′ B arm, 121 nt, purple), scITR (C arm deletion, 106 nt, green), and the dITR. AAT . Egfp expression cassette including an hypoxanthine phosphoribosyltransferase 1 ( HPRT 1 ) DNA stuffer sequence (GenBank: NG_012329.2 ) (bottom). Vector genome sizes are shown next to each design. (G) Alkaline electrophoresis of AAV8 vectors with different ITR configurations and CBA versus EalbAAT promoters. (H) Alkaline electrophoresis of AAV8 and AAV3B vectors with dITR/wtITR, dITR/tITR, and scITR configurations. (I) Alkaline electrophoresis of AAV8 and AAVLK03 vectors with the dITR/tITR configuration. (J) Alkaline electrophoresis of AAV3B, AAV5, and AAVLK03 vectors with dITR/wtITR configuration and CBA versus EalbAAT promoters. Combinations are displayed on top of each lane. Agarose gel ladder: FastGene 1 kb DNA marker (10,000–100 bp).

    Techniques Used: Recombinant, Electrophoresis, Plasmid Preparation, Marker, Expressing, Sequencing, Agarose Gel Electrophoresis

    Related Articles

    Polymerase Chain Reaction:

    Article Title: AAV serotype PHP.eB achieves superior neuronal transduction efficiency compared to AAV9 in pigtail macaques following intracerebroventricular administration
    Article Snippet: After isolation, DNA concentration was measured (NanoDrop, Thermo ScientificTM), and diluted to working concentrations ranging from 0.03-10ng/ul. .. Prior to PCR reaction, template DNA was treated with SmaI restriction enzyme (New England Biolabs). .. PCR was performed with PTC Tempo Deepwell Thermal Cycler (Bio-Rad).

    Article Title: AAV-PHP.eB achieves superior neuronal transduction over AAV9 in pigtail macaques following intracerebroventricular administration
    Article Snippet: After isolation, DNA concentration was measured (NanoDrop, Thermo Fisher Scientific, USA) and diluted to working concentrations ranging from 0.03 to 10 ng/μL. .. Prior to PCR reaction, template DNA was treated with SmaI restriction enzyme (New England Biolabs, USA). .. PCR was performed with PTC Tempo Deepwell Thermal Cycler (Bio-Rad, USA).

    Plasmid Preparation:

    Article Title: A Redox-Enzyme Integrated Microbial Fuel Cell Design Using the Surface Display System in Shewanella oneidensis MR-1.
    Article Snippet: A biofuel cell is an electrochemical device using exoelectrogen or biocatalysts to transfer electrons from redox reactions to the electrodes.. While wild-type microbes and natural enzymes are often employed as exoelectrogen and biocatalysts, genetically engineered or modified organisms have been developed to enhance exoelectrogen activity.. Here, we demonstrated a redoxenzyme integrated microbial fuel cell (REI-MFC) design based on an exoelectrogen-enhancing strategy that reinforces the electrogenic activity of Shewanella oneidensis MR1 by displaying an extra redox enzyme on the cell surface.

    Article Title: A strategy for genome-wide seamless tagging of human protein-coding genes
    Article Snippet: .. Finally, 1.0 μg of each minicircle plasmid (P2A-Zeocin-MC, Zeocin-P2A-MC and linker-mClover3-P2A-Zeocin-MC) was digested with SmaI restriction enzyme (New England Biolabs) and then run on a 1.5% agarose gel to determine plasmid quality ( ). ..

    Modification:

    Article Title: A Redox-Enzyme Integrated Microbial Fuel Cell Design Using the Surface Display System in Shewanella oneidensis MR-1.
    Article Snippet: A biofuel cell is an electrochemical device using exoelectrogen or biocatalysts to transfer electrons from redox reactions to the electrodes.. While wild-type microbes and natural enzymes are often employed as exoelectrogen and biocatalysts, genetically engineered or modified organisms have been developed to enhance exoelectrogen activity.. Here, we demonstrated a redoxenzyme integrated microbial fuel cell (REI-MFC) design based on an exoelectrogen-enhancing strategy that reinforces the electrogenic activity of Shewanella oneidensis MR1 by displaying an extra redox enzyme on the cell surface.

    Pulsed-Field Gel:

    Article Title: Antimicrobial susceptibility and adaptative changes in MRSA lineages exposed to increasing concentrations of fluoroquinolones and chlorhexidine.
    Article Snippet: .. The characterization of the lineages was performed using the SmaI restriction enzyme (New England Biolabs; Ipswich, England) for chromosomal DNA fragmentation, followed by pulsed-field gel electrophoresis (PFGE) on a CHEF-DRIII® system (Bio-Rad, Richmond, CA, USA) [19]. ..

    Agarose Gel Electrophoresis:

    Article Title: A strategy for genome-wide seamless tagging of human protein-coding genes
    Article Snippet: .. Finally, 1.0 μg of each minicircle plasmid (P2A-Zeocin-MC, Zeocin-P2A-MC and linker-mClover3-P2A-Zeocin-MC) was digested with SmaI restriction enzyme (New England Biolabs) and then run on a 1.5% agarose gel to determine plasmid quality ( ). ..

    Gel Purification:

    Article Title: The Nematostella synaptonemal complex mediates divergent and sex-specific meiotic programs
    Article Snippet: The DNA was analyzed on a horizontal 1% agarose gel (agarose) with a 1 kb Plus DNA ladder (New England Biolabs # N3200L). .. DNA fragments at the appropriate size were cut out from the gel and DNA gel purification was performed with the Zymoclean Gel DNA Recovery Kit (Zymo Research #D4002) according to manufacturer’s recommendations. pGAD-C1 and pGBDU-C1 yeast two-hybrid vectors ( ) were linearized with the SmaI restriction enzyme (New England Biolabs #R0141L) according to manufacturer’s recommendations in a 60 min reaction. ..



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    New England Biolabs smai restriction enzyme
    Recombinant AAV genome element and heterogeneity analysis by native and alkaline electrophoresis (A) Graphic representation of the main recombinant AAV vector genome elements evaluated: wtITR (143 nt, black) versus dITR/wtITR (11-nt deletion in the 5′ C arm, 130 nt, red), EAlbAAT (albumin enhancer-alpha1-antitrypsin promoter, blue), Egfp (enhanced green fluorescent protein, green), pA (bovine/human growth hormone polyadenylation signal, yellow), and CBA (CMV (cytomegalovirus) enhancer-chicken beta actin promoter, orange). Vector genome sizes are shown next to each representation. (B) Native automated electrophoresis of <t>extracted</t> <t>rAAV</t> genomes from dITR/wtITR and wtITR. EalbAAT . Egfp vectors by TapeStation. From left to right: AAV2, AAV3B, AAV5, AAV8, AAV9, and AAVLK03 serotypes. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (C) Native automated electrophoresis of extracted rAAV genomes from AAV5 and AAV8 serotypes with dITR vs. wtITR and CBA versus EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (D) Native automated electrophoresis of extracted rAAV genomes from the AAVLK03 serotype with dITR and CBA vs. EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (E) Native electrophoresis of extracted rAAV genomes from AAV9 and AAVLK03 serotypes with dITR and CBA versus EalbAAT promoters, before and after digestion at 37°C for 1 h with <t>SmaI.</t> (F) Graphic representation of the dITR/tITR design (11-nt deletion in the 5′ C arm and 22-nt deletion of the 3′ B arm, 121 nt, purple), scITR (C arm deletion, 106 nt, green), and the dITR. AAT . Egfp expression cassette including an hypoxanthine phosphoribosyltransferase 1 ( HPRT 1 ) DNA stuffer sequence (GenBank: NG_012329.2 ) (bottom). Vector genome sizes are shown next to each design. (G) Alkaline electrophoresis of AAV8 vectors with different ITR configurations and CBA versus EalbAAT promoters. (H) Alkaline electrophoresis of AAV8 and AAV3B vectors with dITR/wtITR, dITR/tITR, and scITR configurations. (I) Alkaline electrophoresis of AAV8 and AAVLK03 vectors with the dITR/tITR configuration. (J) Alkaline electrophoresis of AAV3B, AAV5, and AAVLK03 vectors with dITR/wtITR configuration and CBA versus EalbAAT promoters. Combinations are displayed on top of each lane. Agarose gel ladder: FastGene 1 kb DNA marker (10,000–100 bp).
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    Recombinant AAV genome element and heterogeneity analysis by native and alkaline electrophoresis (A) Graphic representation of the main recombinant AAV vector genome elements evaluated: wtITR (143 nt, black) versus dITR/wtITR (11-nt deletion in the 5′ C arm, 130 nt, red), EAlbAAT (albumin enhancer-alpha1-antitrypsin promoter, blue), Egfp (enhanced green fluorescent protein, green), pA (bovine/human growth hormone polyadenylation signal, yellow), and CBA (CMV (cytomegalovirus) enhancer-chicken beta actin promoter, orange). Vector genome sizes are shown next to each representation. (B) Native automated electrophoresis of <t>extracted</t> <t>rAAV</t> genomes from dITR/wtITR and wtITR. EalbAAT . Egfp vectors by TapeStation. From left to right: AAV2, AAV3B, AAV5, AAV8, AAV9, and AAVLK03 serotypes. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (C) Native automated electrophoresis of extracted rAAV genomes from AAV5 and AAV8 serotypes with dITR vs. wtITR and CBA versus EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (D) Native automated electrophoresis of extracted rAAV genomes from the AAVLK03 serotype with dITR and CBA vs. EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (E) Native electrophoresis of extracted rAAV genomes from AAV9 and AAVLK03 serotypes with dITR and CBA versus EalbAAT promoters, before and after digestion at 37°C for 1 h with <t>SmaI.</t> (F) Graphic representation of the dITR/tITR design (11-nt deletion in the 5′ C arm and 22-nt deletion of the 3′ B arm, 121 nt, purple), scITR (C arm deletion, 106 nt, green), and the dITR. AAT . Egfp expression cassette including an hypoxanthine phosphoribosyltransferase 1 ( HPRT 1 ) DNA stuffer sequence (GenBank: NG_012329.2 ) (bottom). Vector genome sizes are shown next to each design. (G) Alkaline electrophoresis of AAV8 vectors with different ITR configurations and CBA versus EalbAAT promoters. (H) Alkaline electrophoresis of AAV8 and AAV3B vectors with dITR/wtITR, dITR/tITR, and scITR configurations. (I) Alkaline electrophoresis of AAV8 and AAVLK03 vectors with the dITR/tITR configuration. (J) Alkaline electrophoresis of AAV3B, AAV5, and AAVLK03 vectors with dITR/wtITR configuration and CBA versus EalbAAT promoters. Combinations are displayed on top of each lane. Agarose gel ladder: FastGene 1 kb DNA marker (10,000–100 bp).
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    Recombinant AAV genome element and heterogeneity analysis by native and alkaline electrophoresis (A) Graphic representation of the main recombinant AAV vector genome elements evaluated: wtITR (143 nt, black) versus dITR/wtITR (11-nt deletion in the 5′ C arm, 130 nt, red), EAlbAAT (albumin enhancer-alpha1-antitrypsin promoter, blue), Egfp (enhanced green fluorescent protein, green), pA (bovine/human growth hormone polyadenylation signal, yellow), and CBA (CMV (cytomegalovirus) enhancer-chicken beta actin promoter, orange). Vector genome sizes are shown next to each representation. (B) Native automated electrophoresis of <t>extracted</t> <t>rAAV</t> genomes from dITR/wtITR and wtITR. EalbAAT . Egfp vectors by TapeStation. From left to right: AAV2, AAV3B, AAV5, AAV8, AAV9, and AAVLK03 serotypes. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (C) Native automated electrophoresis of extracted rAAV genomes from AAV5 and AAV8 serotypes with dITR vs. wtITR and CBA versus EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (D) Native automated electrophoresis of extracted rAAV genomes from the AAVLK03 serotype with dITR and CBA vs. EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (E) Native electrophoresis of extracted rAAV genomes from AAV9 and AAVLK03 serotypes with dITR and CBA versus EalbAAT promoters, before and after digestion at 37°C for 1 h with <t>SmaI.</t> (F) Graphic representation of the dITR/tITR design (11-nt deletion in the 5′ C arm and 22-nt deletion of the 3′ B arm, 121 nt, purple), scITR (C arm deletion, 106 nt, green), and the dITR. AAT . Egfp expression cassette including an hypoxanthine phosphoribosyltransferase 1 ( HPRT 1 ) DNA stuffer sequence (GenBank: NG_012329.2 ) (bottom). Vector genome sizes are shown next to each design. (G) Alkaline electrophoresis of AAV8 vectors with different ITR configurations and CBA versus EalbAAT promoters. (H) Alkaline electrophoresis of AAV8 and AAV3B vectors with dITR/wtITR, dITR/tITR, and scITR configurations. (I) Alkaline electrophoresis of AAV8 and AAVLK03 vectors with the dITR/tITR configuration. (J) Alkaline electrophoresis of AAV3B, AAV5, and AAVLK03 vectors with dITR/wtITR configuration and CBA versus EalbAAT promoters. Combinations are displayed on top of each lane. Agarose gel ladder: FastGene 1 kb DNA marker (10,000–100 bp).
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    Recombinant AAV genome element and heterogeneity analysis by native and alkaline electrophoresis (A) Graphic representation of the main recombinant AAV vector genome elements evaluated: wtITR (143 nt, black) versus dITR/wtITR (11-nt deletion in the 5′ C arm, 130 nt, red), EAlbAAT (albumin enhancer-alpha1-antitrypsin promoter, blue), Egfp (enhanced green fluorescent protein, green), pA (bovine/human growth hormone polyadenylation signal, yellow), and CBA (CMV (cytomegalovirus) enhancer-chicken beta actin promoter, orange). Vector genome sizes are shown next to each representation. (B) Native automated electrophoresis of <t>extracted</t> <t>rAAV</t> genomes from dITR/wtITR and wtITR. EalbAAT . Egfp vectors by TapeStation. From left to right: AAV2, AAV3B, AAV5, AAV8, AAV9, and AAVLK03 serotypes. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (C) Native automated electrophoresis of extracted rAAV genomes from AAV5 and AAV8 serotypes with dITR vs. wtITR and CBA versus EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (D) Native automated electrophoresis of extracted rAAV genomes from the AAVLK03 serotype with dITR and CBA vs. EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (E) Native electrophoresis of extracted rAAV genomes from AAV9 and AAVLK03 serotypes with dITR and CBA versus EalbAAT promoters, before and after digestion at 37°C for 1 h with <t>SmaI.</t> (F) Graphic representation of the dITR/tITR design (11-nt deletion in the 5′ C arm and 22-nt deletion of the 3′ B arm, 121 nt, purple), scITR (C arm deletion, 106 nt, green), and the dITR. AAT . Egfp expression cassette including an hypoxanthine phosphoribosyltransferase 1 ( HPRT 1 ) DNA stuffer sequence (GenBank: NG_012329.2 ) (bottom). Vector genome sizes are shown next to each design. (G) Alkaline electrophoresis of AAV8 vectors with different ITR configurations and CBA versus EalbAAT promoters. (H) Alkaline electrophoresis of AAV8 and AAV3B vectors with dITR/wtITR, dITR/tITR, and scITR configurations. (I) Alkaline electrophoresis of AAV8 and AAVLK03 vectors with the dITR/tITR configuration. (J) Alkaline electrophoresis of AAV3B, AAV5, and AAVLK03 vectors with dITR/wtITR configuration and CBA versus EalbAAT promoters. Combinations are displayed on top of each lane. Agarose gel ladder: FastGene 1 kb DNA marker (10,000–100 bp).
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    New England Biolabs sma i restriction enzyme
    Recombinant AAV genome element and heterogeneity analysis by native and alkaline electrophoresis (A) Graphic representation of the main recombinant AAV vector genome elements evaluated: wtITR (143 nt, black) versus dITR/wtITR (11-nt deletion in the 5′ C arm, 130 nt, red), EAlbAAT (albumin enhancer-alpha1-antitrypsin promoter, blue), Egfp (enhanced green fluorescent protein, green), pA (bovine/human growth hormone polyadenylation signal, yellow), and CBA (CMV (cytomegalovirus) enhancer-chicken beta actin promoter, orange). Vector genome sizes are shown next to each representation. (B) Native automated electrophoresis of <t>extracted</t> <t>rAAV</t> genomes from dITR/wtITR and wtITR. EalbAAT . Egfp vectors by TapeStation. From left to right: AAV2, AAV3B, AAV5, AAV8, AAV9, and AAVLK03 serotypes. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (C) Native automated electrophoresis of extracted rAAV genomes from AAV5 and AAV8 serotypes with dITR vs. wtITR and CBA versus EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (D) Native automated electrophoresis of extracted rAAV genomes from the AAVLK03 serotype with dITR and CBA vs. EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (E) Native electrophoresis of extracted rAAV genomes from AAV9 and AAVLK03 serotypes with dITR and CBA versus EalbAAT promoters, before and after digestion at 37°C for 1 h with <t>SmaI.</t> (F) Graphic representation of the dITR/tITR design (11-nt deletion in the 5′ C arm and 22-nt deletion of the 3′ B arm, 121 nt, purple), scITR (C arm deletion, 106 nt, green), and the dITR. AAT . Egfp expression cassette including an hypoxanthine phosphoribosyltransferase 1 ( HPRT 1 ) DNA stuffer sequence (GenBank: NG_012329.2 ) (bottom). Vector genome sizes are shown next to each design. (G) Alkaline electrophoresis of AAV8 vectors with different ITR configurations and CBA versus EalbAAT promoters. (H) Alkaline electrophoresis of AAV8 and AAV3B vectors with dITR/wtITR, dITR/tITR, and scITR configurations. (I) Alkaline electrophoresis of AAV8 and AAVLK03 vectors with the dITR/tITR configuration. (J) Alkaline electrophoresis of AAV3B, AAV5, and AAVLK03 vectors with dITR/wtITR configuration and CBA versus EalbAAT promoters. Combinations are displayed on top of each lane. Agarose gel ladder: FastGene 1 kb DNA marker (10,000–100 bp).
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    Recombinant AAV genome element and heterogeneity analysis by native and alkaline electrophoresis (A) Graphic representation of the main recombinant AAV vector genome elements evaluated: wtITR (143 nt, black) versus dITR/wtITR (11-nt deletion in the 5′ C arm, 130 nt, red), EAlbAAT (albumin enhancer-alpha1-antitrypsin promoter, blue), Egfp (enhanced green fluorescent protein, green), pA (bovine/human growth hormone polyadenylation signal, yellow), and CBA (CMV (cytomegalovirus) enhancer-chicken beta actin promoter, orange). Vector genome sizes are shown next to each representation. (B) Native automated electrophoresis of <t>extracted</t> <t>rAAV</t> genomes from dITR/wtITR and wtITR. EalbAAT . Egfp vectors by TapeStation. From left to right: AAV2, AAV3B, AAV5, AAV8, AAV9, and AAVLK03 serotypes. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (C) Native automated electrophoresis of extracted rAAV genomes from AAV5 and AAV8 serotypes with dITR vs. wtITR and CBA versus EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (D) Native automated electrophoresis of extracted rAAV genomes from the AAVLK03 serotype with dITR and CBA vs. EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (E) Native electrophoresis of extracted rAAV genomes from AAV9 and AAVLK03 serotypes with dITR and CBA versus EalbAAT promoters, before and after digestion at 37°C for 1 h with <t>SmaI.</t> (F) Graphic representation of the dITR/tITR design (11-nt deletion in the 5′ C arm and 22-nt deletion of the 3′ B arm, 121 nt, purple), scITR (C arm deletion, 106 nt, green), and the dITR. AAT . Egfp expression cassette including an hypoxanthine phosphoribosyltransferase 1 ( HPRT 1 ) DNA stuffer sequence (GenBank: NG_012329.2 ) (bottom). Vector genome sizes are shown next to each design. (G) Alkaline electrophoresis of AAV8 vectors with different ITR configurations and CBA versus EalbAAT promoters. (H) Alkaline electrophoresis of AAV8 and AAV3B vectors with dITR/wtITR, dITR/tITR, and scITR configurations. (I) Alkaline electrophoresis of AAV8 and AAVLK03 vectors with the dITR/tITR configuration. (J) Alkaline electrophoresis of AAV3B, AAV5, and AAVLK03 vectors with dITR/wtITR configuration and CBA versus EalbAAT promoters. Combinations are displayed on top of each lane. Agarose gel ladder: FastGene 1 kb DNA marker (10,000–100 bp).
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    Recombinant AAV genome element and heterogeneity analysis by native and alkaline electrophoresis (A) Graphic representation of the main recombinant AAV vector genome elements evaluated: wtITR (143 nt, black) versus dITR/wtITR (11-nt deletion in the 5′ C arm, 130 nt, red), EAlbAAT (albumin enhancer-alpha1-antitrypsin promoter, blue), Egfp (enhanced green fluorescent protein, green), pA (bovine/human growth hormone polyadenylation signal, yellow), and CBA (CMV (cytomegalovirus) enhancer-chicken beta actin promoter, orange). Vector genome sizes are shown next to each representation. (B) Native automated electrophoresis of <t>extracted</t> <t>rAAV</t> genomes from dITR/wtITR and wtITR. EalbAAT . Egfp vectors by TapeStation. From left to right: AAV2, AAV3B, AAV5, AAV8, AAV9, and AAVLK03 serotypes. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (C) Native automated electrophoresis of extracted rAAV genomes from AAV5 and AAV8 serotypes with dITR vs. wtITR and CBA versus EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (D) Native automated electrophoresis of extracted rAAV genomes from the AAVLK03 serotype with dITR and CBA vs. EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (E) Native electrophoresis of extracted rAAV genomes from AAV9 and AAVLK03 serotypes with dITR and CBA versus EalbAAT promoters, before and after digestion at 37°C for 1 h with <t>SmaI.</t> (F) Graphic representation of the dITR/tITR design (11-nt deletion in the 5′ C arm and 22-nt deletion of the 3′ B arm, 121 nt, purple), scITR (C arm deletion, 106 nt, green), and the dITR. AAT . Egfp expression cassette including an hypoxanthine phosphoribosyltransferase 1 ( HPRT 1 ) DNA stuffer sequence (GenBank: NG_012329.2 ) (bottom). Vector genome sizes are shown next to each design. (G) Alkaline electrophoresis of AAV8 vectors with different ITR configurations and CBA versus EalbAAT promoters. (H) Alkaline electrophoresis of AAV8 and AAV3B vectors with dITR/wtITR, dITR/tITR, and scITR configurations. (I) Alkaline electrophoresis of AAV8 and AAVLK03 vectors with the dITR/tITR configuration. (J) Alkaline electrophoresis of AAV3B, AAV5, and AAVLK03 vectors with dITR/wtITR configuration and CBA versus EalbAAT promoters. Combinations are displayed on top of each lane. Agarose gel ladder: FastGene 1 kb DNA marker (10,000–100 bp).
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    Recombinant AAV genome element and heterogeneity analysis by native and alkaline electrophoresis (A) Graphic representation of the main recombinant AAV vector genome elements evaluated: wtITR (143 nt, black) versus dITR/wtITR (11-nt deletion in the 5′ C arm, 130 nt, red), EAlbAAT (albumin enhancer-alpha1-antitrypsin promoter, blue), Egfp (enhanced green fluorescent protein, green), pA (bovine/human growth hormone polyadenylation signal, yellow), and CBA (CMV (cytomegalovirus) enhancer-chicken beta actin promoter, orange). Vector genome sizes are shown next to each representation. (B) Native automated electrophoresis of extracted rAAV genomes from dITR/wtITR and wtITR. EalbAAT . Egfp vectors by TapeStation. From left to right: AAV2, AAV3B, AAV5, AAV8, AAV9, and AAVLK03 serotypes. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (C) Native automated electrophoresis of extracted rAAV genomes from AAV5 and AAV8 serotypes with dITR vs. wtITR and CBA versus EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (D) Native automated electrophoresis of extracted rAAV genomes from the AAVLK03 serotype with dITR and CBA vs. EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (E) Native electrophoresis of extracted rAAV genomes from AAV9 and AAVLK03 serotypes with dITR and CBA versus EalbAAT promoters, before and after digestion at 37°C for 1 h with SmaI. (F) Graphic representation of the dITR/tITR design (11-nt deletion in the 5′ C arm and 22-nt deletion of the 3′ B arm, 121 nt, purple), scITR (C arm deletion, 106 nt, green), and the dITR. AAT . Egfp expression cassette including an hypoxanthine phosphoribosyltransferase 1 ( HPRT 1 ) DNA stuffer sequence (GenBank: NG_012329.2 ) (bottom). Vector genome sizes are shown next to each design. (G) Alkaline electrophoresis of AAV8 vectors with different ITR configurations and CBA versus EalbAAT promoters. (H) Alkaline electrophoresis of AAV8 and AAV3B vectors with dITR/wtITR, dITR/tITR, and scITR configurations. (I) Alkaline electrophoresis of AAV8 and AAVLK03 vectors with the dITR/tITR configuration. (J) Alkaline electrophoresis of AAV3B, AAV5, and AAVLK03 vectors with dITR/wtITR configuration and CBA versus EalbAAT promoters. Combinations are displayed on top of each lane. Agarose gel ladder: FastGene 1 kb DNA marker (10,000–100 bp).

    Journal: Molecular Therapy. Nucleic Acids

    Article Title: Orthogonal characterization of rAAV reveals vector attributes that drive ITR repair, self-complementary genome formation, and transgene expression

    doi: 10.1016/j.omtn.2026.102899

    Figure Lengend Snippet: Recombinant AAV genome element and heterogeneity analysis by native and alkaline electrophoresis (A) Graphic representation of the main recombinant AAV vector genome elements evaluated: wtITR (143 nt, black) versus dITR/wtITR (11-nt deletion in the 5′ C arm, 130 nt, red), EAlbAAT (albumin enhancer-alpha1-antitrypsin promoter, blue), Egfp (enhanced green fluorescent protein, green), pA (bovine/human growth hormone polyadenylation signal, yellow), and CBA (CMV (cytomegalovirus) enhancer-chicken beta actin promoter, orange). Vector genome sizes are shown next to each representation. (B) Native automated electrophoresis of extracted rAAV genomes from dITR/wtITR and wtITR. EalbAAT . Egfp vectors by TapeStation. From left to right: AAV2, AAV3B, AAV5, AAV8, AAV9, and AAVLK03 serotypes. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (C) Native automated electrophoresis of extracted rAAV genomes from AAV5 and AAV8 serotypes with dITR vs. wtITR and CBA versus EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (D) Native automated electrophoresis of extracted rAAV genomes from the AAVLK03 serotype with dITR and CBA vs. EalbAAT promoters. As a run reference, the upper marker (10,000 bp) and lower marker (15 bp) of the ladder are highlighted in purple and green, respectively. (E) Native electrophoresis of extracted rAAV genomes from AAV9 and AAVLK03 serotypes with dITR and CBA versus EalbAAT promoters, before and after digestion at 37°C for 1 h with SmaI. (F) Graphic representation of the dITR/tITR design (11-nt deletion in the 5′ C arm and 22-nt deletion of the 3′ B arm, 121 nt, purple), scITR (C arm deletion, 106 nt, green), and the dITR. AAT . Egfp expression cassette including an hypoxanthine phosphoribosyltransferase 1 ( HPRT 1 ) DNA stuffer sequence (GenBank: NG_012329.2 ) (bottom). Vector genome sizes are shown next to each design. (G) Alkaline electrophoresis of AAV8 vectors with different ITR configurations and CBA versus EalbAAT promoters. (H) Alkaline electrophoresis of AAV8 and AAV3B vectors with dITR/wtITR, dITR/tITR, and scITR configurations. (I) Alkaline electrophoresis of AAV8 and AAVLK03 vectors with the dITR/tITR configuration. (J) Alkaline electrophoresis of AAV3B, AAV5, and AAVLK03 vectors with dITR/wtITR configuration and CBA versus EalbAAT promoters. Combinations are displayed on top of each lane. Agarose gel ladder: FastGene 1 kb DNA marker (10,000–100 bp).

    Article Snippet: SmaI restriction enzyme (20,000 units/mL; New England Biolabs) was used to digest rAAV genomes for 1 h at 37°C.

    Techniques: Recombinant, Electrophoresis, Plasmid Preparation, Marker, Expressing, Sequencing, Agarose Gel Electrophoresis