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  • 99
    New England Biolabs dpni
    Correlation between ori-plasmid replication and firefly luciferase expression (A) Levels of SV40 plasmid replication measured by quantitative real-time PCR (qPCR) or determined by measuring levels of firefly luciferase activity. C33A cells were transfected with the pFLORI40 plasmid and the LT expression vector (+LT). As controls, cells were transfected without the LT expression vector (No LT) or with a similar plasmid lacking the ori (No ori). The amounts of <t>DNA</t> replication measured by qPCR are reported in pg of <t>DpnI-resistant</t> plasmid per mg of total genomic DNA. Firefly luciferase (Fluc) activity is reported in relative light units (RLU). (B) A similar analysis was performed for HPV31 DNA replication with the exception that cells were transfected with the pFLORI31 plasmid, or a similar plasmid lacking the ori (No ori), and with expression vectors for E1 and E2, as indicated.
    Dpni, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 6590 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher dpni
    Identification of methylated recognition sequences in S. acidocaldarius genomic DNA by digestion assays. Restriction enzymes <t>BsuRI</t> (A) and BamHI, <t>DpnI,</t> and MboI (B) were used to highlight the presence/absence of methylated 5′-GGCC-3′ and 5′-GATC-3′ palindromes, respectively, in genomic DNA of S. acidocaldarius . Two types of substrates were digested: genomic DNA (gDNA) and a whole genome amplification of the genomic DNA (WGA). WGA is identical to gDNA in terms of nucleic sequence but it does not contain epigenetic marks (see material and methods). This negative control is only used in (A) . The addition of different restriction enzymes is symbolized by a positive sign “+” while reaction mix without restriction enzyme is represented by a negative sign “–”. Molecular size markers (GeneRuler DNA Ladder, Thermo Scientific) were loaded in both gels (M). Digestion patterns were obtained in 0.8% agarose gel stained with ethidium bromide and visualized under UV light.
    Dpni, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 2375 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Millipore dpni
    Identification of methylated recognition sequences in S. acidocaldarius genomic DNA by digestion assays. Restriction enzymes <t>BsuRI</t> (A) and BamHI, <t>DpnI,</t> and MboI (B) were used to highlight the presence/absence of methylated 5′-GGCC-3′ and 5′-GATC-3′ palindromes, respectively, in genomic DNA of S. acidocaldarius . Two types of substrates were digested: genomic DNA (gDNA) and a whole genome amplification of the genomic DNA (WGA). WGA is identical to gDNA in terms of nucleic sequence but it does not contain epigenetic marks (see material and methods). This negative control is only used in (A) . The addition of different restriction enzymes is symbolized by a positive sign “+” while reaction mix without restriction enzyme is represented by a negative sign “–”. Molecular size markers (GeneRuler DNA Ladder, Thermo Scientific) were loaded in both gels (M). Digestion patterns were obtained in 0.8% agarose gel stained with ethidium bromide and visualized under UV light.
    Dpni, supplied by Millipore, used in various techniques. Bioz Stars score: 93/100, based on 184 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Thermo Fisher fastdigest dpni
    Identification of methylated recognition sequences in S. acidocaldarius genomic DNA by digestion assays. Restriction enzymes <t>BsuRI</t> (A) and BamHI, <t>DpnI,</t> and MboI (B) were used to highlight the presence/absence of methylated 5′-GGCC-3′ and 5′-GATC-3′ palindromes, respectively, in genomic DNA of S. acidocaldarius . Two types of substrates were digested: genomic DNA (gDNA) and a whole genome amplification of the genomic DNA (WGA). WGA is identical to gDNA in terms of nucleic sequence but it does not contain epigenetic marks (see material and methods). This negative control is only used in (A) . The addition of different restriction enzymes is symbolized by a positive sign “+” while reaction mix without restriction enzyme is represented by a negative sign “–”. Molecular size markers (GeneRuler DNA Ladder, Thermo Scientific) were loaded in both gels (M). Digestion patterns were obtained in 0.8% agarose gel stained with ethidium bromide and visualized under UV light.
    Fastdigest Dpni, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 500 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    New England Biolabs endonuclease dpni
    (A) PAGE result of the proposed sensing platform. Line M: DNA marker, line 1: SDA proceeding on shortened MB without Nb.BbvcI, line 2: SDA proceeding on shortened MB with primer 0, line 3: SDA proceeding on shortened MB without primers, line 4: complete SDA proceeding on shortened MB only, line 5: <t>DpnI</t> treated MB without Dam MTase, line 6: shortened MB cut by DpnI, line 7: MB only. (B) Fluorescent spectrum in response to the addition of different components.
    Endonuclease Dpni, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Agilent technologies dpni
    (A) PAGE result of the proposed sensing platform. Line M: DNA marker, line 1: SDA proceeding on shortened MB without Nb.BbvcI, line 2: SDA proceeding on shortened MB with primer 0, line 3: SDA proceeding on shortened MB without primers, line 4: complete SDA proceeding on shortened MB only, line 5: <t>DpnI</t> treated MB without Dam MTase, line 6: shortened MB cut by DpnI, line 7: MB only. (B) Fluorescent spectrum in response to the addition of different components.
    Dpni, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 470 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Promega dpni
    (A) PAGE result of the proposed sensing platform. Line M: DNA marker, line 1: SDA proceeding on shortened MB without Nb.BbvcI, line 2: SDA proceeding on shortened MB with primer 0, line 3: SDA proceeding on shortened MB without primers, line 4: complete SDA proceeding on shortened MB only, line 5: <t>DpnI</t> treated MB without Dam MTase, line 6: shortened MB cut by DpnI, line 7: MB only. (B) Fluorescent spectrum in response to the addition of different components.
    Dpni, supplied by Promega, used in various techniques. Bioz Stars score: 93/100, based on 442 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    dpni  (Roche)
    93
    Roche dpni
    (A) PAGE result of the proposed sensing platform. Line M: DNA marker, line 1: SDA proceeding on shortened MB without Nb.BbvcI, line 2: SDA proceeding on shortened MB with primer 0, line 3: SDA proceeding on shortened MB without primers, line 4: complete SDA proceeding on shortened MB only, line 5: <t>DpnI</t> treated MB without Dam MTase, line 6: shortened MB cut by DpnI, line 7: MB only. (B) Fluorescent spectrum in response to the addition of different components.
    Dpni, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 167 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dpni/product/Roche
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    92
    Stratagene dpni
    (A) PAGE result of the proposed sensing platform. Line M: DNA marker, line 1: SDA proceeding on shortened MB without Nb.BbvcI, line 2: SDA proceeding on shortened MB with primer 0, line 3: SDA proceeding on shortened MB without primers, line 4: complete SDA proceeding on shortened MB only, line 5: <t>DpnI</t> treated MB without Dam MTase, line 6: shortened MB cut by DpnI, line 7: MB only. (B) Fluorescent spectrum in response to the addition of different components.
    Dpni, supplied by Stratagene, used in various techniques. Bioz Stars score: 92/100, based on 562 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    dpni  (Toyobo)
    93
    Toyobo dpni
    (A) PAGE result of the proposed sensing platform. Line M: DNA marker, line 1: SDA proceeding on shortened MB without Nb.BbvcI, line 2: SDA proceeding on shortened MB with primer 0, line 3: SDA proceeding on shortened MB without primers, line 4: complete SDA proceeding on shortened MB only, line 5: <t>DpnI</t> treated MB without Dam MTase, line 6: shortened MB cut by DpnI, line 7: MB only. (B) Fluorescent spectrum in response to the addition of different components.
    Dpni, supplied by Toyobo, used in various techniques. Bioz Stars score: 93/100, based on 138 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Kapa Biosystems dpni
    (A) PAGE result of the proposed sensing platform. Line M: DNA marker, line 1: SDA proceeding on shortened MB without Nb.BbvcI, line 2: SDA proceeding on shortened MB with primer 0, line 3: SDA proceeding on shortened MB without primers, line 4: complete SDA proceeding on shortened MB only, line 5: <t>DpnI</t> treated MB without Dam MTase, line 6: shortened MB cut by DpnI, line 7: MB only. (B) Fluorescent spectrum in response to the addition of different components.
    Dpni, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Correlation between ori-plasmid replication and firefly luciferase expression (A) Levels of SV40 plasmid replication measured by quantitative real-time PCR (qPCR) or determined by measuring levels of firefly luciferase activity. C33A cells were transfected with the pFLORI40 plasmid and the LT expression vector (+LT). As controls, cells were transfected without the LT expression vector (No LT) or with a similar plasmid lacking the ori (No ori). The amounts of DNA replication measured by qPCR are reported in pg of DpnI-resistant plasmid per mg of total genomic DNA. Firefly luciferase (Fluc) activity is reported in relative light units (RLU). (B) A similar analysis was performed for HPV31 DNA replication with the exception that cells were transfected with the pFLORI31 plasmid, or a similar plasmid lacking the ori (No ori), and with expression vectors for E1 and E2, as indicated.

    Journal: Virology

    Article Title: DEVELOPMENT OF QUANTITATIVE AND HIGH-THROUGHPUT ASSAYS OF POLYOMAVIRUS AND PAPILLOMAVIRUS DNA REPLICATION

    doi: 10.1016/j.virol.2009.12.026

    Figure Lengend Snippet: Correlation between ori-plasmid replication and firefly luciferase expression (A) Levels of SV40 plasmid replication measured by quantitative real-time PCR (qPCR) or determined by measuring levels of firefly luciferase activity. C33A cells were transfected with the pFLORI40 plasmid and the LT expression vector (+LT). As controls, cells were transfected without the LT expression vector (No LT) or with a similar plasmid lacking the ori (No ori). The amounts of DNA replication measured by qPCR are reported in pg of DpnI-resistant plasmid per mg of total genomic DNA. Firefly luciferase (Fluc) activity is reported in relative light units (RLU). (B) A similar analysis was performed for HPV31 DNA replication with the exception that cells were transfected with the pFLORI31 plasmid, or a similar plasmid lacking the ori (No ori), and with expression vectors for E1 and E2, as indicated.

    Article Snippet: To measure the amount of replicated pFLORI31 or pFLORI40, 25 μl of total genomic DNA was digested with 10 units of DpnI (New England Biolabs) for 16 hrs in a final volume of 30 μl.

    Techniques: Plasmid Preparation, Luciferase, Expressing, Real-time Polymerase Chain Reaction, Activity Assay, Transfection

    ( A ) The click-oligonucleotides used for site directed mutagenesis contained a silent C to A mutation (shown in blue), that introduces a BamHI restriction site not present in the native mCherry gene. The click-linked bases are shown in red. ( B ) Assembly of the click-linked pRSET-mCherry plasmid by site directed mutagenesis, introducing a BamHI watermark. ( C ) Gel electrophoresis (0.8% agarose gel) of SDM products (expected size 3577 bp); Lane 1, 2-log DNA ladder (New England Biolabs); lane 2, pRSET-mCherry SDM with normal primers; lane 3, pRSET-mCherry SDM with normal primers followed by DpnI digestion; lane 4, pRSET-mCherry SDM using click primers; lane 5, pRSET-mCherry SDM using click primers followed by DpnI digestion; lane 6, negative control (pRSET-mCherry SDM using water instead of primers); lane 7, negative control followed by DpnI digestion; lane 8, pRSET-mCherry template plasmid.

    Journal: Nucleic Acids Research

    Article Title: Assessing the biocompatibility of click-linked DNA in Escherichia coli

    doi: 10.1093/nar/gks756

    Figure Lengend Snippet: ( A ) The click-oligonucleotides used for site directed mutagenesis contained a silent C to A mutation (shown in blue), that introduces a BamHI restriction site not present in the native mCherry gene. The click-linked bases are shown in red. ( B ) Assembly of the click-linked pRSET-mCherry plasmid by site directed mutagenesis, introducing a BamHI watermark. ( C ) Gel electrophoresis (0.8% agarose gel) of SDM products (expected size 3577 bp); Lane 1, 2-log DNA ladder (New England Biolabs); lane 2, pRSET-mCherry SDM with normal primers; lane 3, pRSET-mCherry SDM with normal primers followed by DpnI digestion; lane 4, pRSET-mCherry SDM using click primers; lane 5, pRSET-mCherry SDM using click primers followed by DpnI digestion; lane 6, negative control (pRSET-mCherry SDM using water instead of primers); lane 7, negative control followed by DpnI digestion; lane 8, pRSET-mCherry template plasmid.

    Article Snippet: DpnI digestion and purification of SDM products DpnI restriction endonuclease (NEB, Cat. No. R0176L) was directly added to the product of the above amplification reaction, and incubated at room temperature for 6 h. The SDM product was separated from any remaining template by gel purification from 0.8% agarose using the QIAquick Gel Extraction Kit (QIAgen) following the manufacturer’s instructions.

    Techniques: Mutagenesis, Plasmid Preparation, Nucleic Acid Electrophoresis, Agarose Gel Electrophoresis, Negative Control

    Two-step derivation of mutations in E1B and E4. A. The mutant constructs were first amplified with two partially overlapping primers designed to incorporate the desired alteration (shown in green), using the corresponding wild type block as a template. The input template DNA was then eliminated by digestion with the restriction enzyme DpnI. In the second step, the PCR-derived plasmid was circularized in an assembly reaction, which merged and sealed the overlapping ends. B. Oligonucleotide pairs that were used to generate the mutants are illustrated. The mutant block 1-derived constructs were E1B19K-null, E1B55K-null or modified to express an endogenous E1B55K protein with a c-terminal FLAG epitope. Similarly, the E4ORF3 open reading frame was disrupted by a mutation at the initiation codon or the introduction of a c-terminal FLAG tag. The targeted codons are boxed, single base mutations are shown in red. At positions where the initiation codon of the target protein overlapped with a codon for a different protein, base substitutions were selected so that the mutation would be silent with respect to the second open reading frame. C. hTERT-RPE1 cells were infected with the synthetic Ad5 virus and the E1B mutant viruses generated in this study. Cells were lysed 16 h post-infection, and assessed by immunoblot with antibodies against p53 and the FLAG epitope, as indicated. D. hTERT-RPE1 cells were uninfected (no virus) or infected with wild type Ad5 and the E4 mutants. For all viruses, the MOI was 100. GAPDH was probed as a loading control.

    Journal: PLoS ONE

    Article Title: Seamless assembly of recombinant adenoviral genomes from high-copy plasmids

    doi: 10.1371/journal.pone.0199563

    Figure Lengend Snippet: Two-step derivation of mutations in E1B and E4. A. The mutant constructs were first amplified with two partially overlapping primers designed to incorporate the desired alteration (shown in green), using the corresponding wild type block as a template. The input template DNA was then eliminated by digestion with the restriction enzyme DpnI. In the second step, the PCR-derived plasmid was circularized in an assembly reaction, which merged and sealed the overlapping ends. B. Oligonucleotide pairs that were used to generate the mutants are illustrated. The mutant block 1-derived constructs were E1B19K-null, E1B55K-null or modified to express an endogenous E1B55K protein with a c-terminal FLAG epitope. Similarly, the E4ORF3 open reading frame was disrupted by a mutation at the initiation codon or the introduction of a c-terminal FLAG tag. The targeted codons are boxed, single base mutations are shown in red. At positions where the initiation codon of the target protein overlapped with a codon for a different protein, base substitutions were selected so that the mutation would be silent with respect to the second open reading frame. C. hTERT-RPE1 cells were infected with the synthetic Ad5 virus and the E1B mutant viruses generated in this study. Cells were lysed 16 h post-infection, and assessed by immunoblot with antibodies against p53 and the FLAG epitope, as indicated. D. hTERT-RPE1 cells were uninfected (no virus) or infected with wild type Ad5 and the E4 mutants. For all viruses, the MOI was 100. GAPDH was probed as a loading control.

    Article Snippet: Input plasmid DNA templates were digested with 20 U of the restriction enzyme DpnI (New England Biolabs) for 30 min at 37°C.

    Techniques: Mutagenesis, Construct, Amplification, Blocking Assay, Polymerase Chain Reaction, Derivative Assay, Plasmid Preparation, Modification, FLAG-tag, Infection, Generated

    Real-time PCR analysis of viral DNA synthesis in Sf9 cells. Total DNA was isolated from Sf9 cells transfected with vAc ac76-KO-PH-GFP or vAc-GP64-KO at selected time points, digested with the restriction enzyme DpnI to eliminate input bacmid DNA, and assayed

    Journal: Journal of Virology

    Article Title: Autographa californica Multiple Nucleopolyhedrovirus ac76 Is Involved in Intranuclear Microvesicle Formation ▿

    doi: 10.1128/JVI.02103-09

    Figure Lengend Snippet: Real-time PCR analysis of viral DNA synthesis in Sf9 cells. Total DNA was isolated from Sf9 cells transfected with vAc ac76-KO-PH-GFP or vAc-GP64-KO at selected time points, digested with the restriction enzyme DpnI to eliminate input bacmid DNA, and assayed

    Article Snippet: Prior to PCR, 5 μl of total DNA from each time point was digested with 20 units of DpnI restriction enzyme (NEB) overnight in a 50-μl reaction volume to eliminate input bacmid DNA.

    Techniques: Real-time Polymerase Chain Reaction, DNA Synthesis, Isolation, Transfection

    Identification of methylated recognition sequences in S. acidocaldarius genomic DNA by digestion assays. Restriction enzymes BsuRI (A) and BamHI, DpnI, and MboI (B) were used to highlight the presence/absence of methylated 5′-GGCC-3′ and 5′-GATC-3′ palindromes, respectively, in genomic DNA of S. acidocaldarius . Two types of substrates were digested: genomic DNA (gDNA) and a whole genome amplification of the genomic DNA (WGA). WGA is identical to gDNA in terms of nucleic sequence but it does not contain epigenetic marks (see material and methods). This negative control is only used in (A) . The addition of different restriction enzymes is symbolized by a positive sign “+” while reaction mix without restriction enzyme is represented by a negative sign “–”. Molecular size markers (GeneRuler DNA Ladder, Thermo Scientific) were loaded in both gels (M). Digestion patterns were obtained in 0.8% agarose gel stained with ethidium bromide and visualized under UV light.

    Journal: Frontiers in Microbiology

    Article Title: The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius

    doi: 10.3389/fmicb.2018.00137

    Figure Lengend Snippet: Identification of methylated recognition sequences in S. acidocaldarius genomic DNA by digestion assays. Restriction enzymes BsuRI (A) and BamHI, DpnI, and MboI (B) were used to highlight the presence/absence of methylated 5′-GGCC-3′ and 5′-GATC-3′ palindromes, respectively, in genomic DNA of S. acidocaldarius . Two types of substrates were digested: genomic DNA (gDNA) and a whole genome amplification of the genomic DNA (WGA). WGA is identical to gDNA in terms of nucleic sequence but it does not contain epigenetic marks (see material and methods). This negative control is only used in (A) . The addition of different restriction enzymes is symbolized by a positive sign “+” while reaction mix without restriction enzyme is represented by a negative sign “–”. Molecular size markers (GeneRuler DNA Ladder, Thermo Scientific) were loaded in both gels (M). Digestion patterns were obtained in 0.8% agarose gel stained with ethidium bromide and visualized under UV light.

    Article Snippet: Genomic DNA isolated from asynchronous S. acidocaldarius cells was cleaved independently with a specific REase in order to decipher the presence or the absence of m4C or m6A: BsuRI, BamHI, MboI, and DpnI (Thermo Scientific).

    Techniques: Methylation, Whole Genome Amplification, Sequencing, Negative Control, Agarose Gel Electrophoresis, Staining

    (A) PAGE result of the proposed sensing platform. Line M: DNA marker, line 1: SDA proceeding on shortened MB without Nb.BbvcI, line 2: SDA proceeding on shortened MB with primer 0, line 3: SDA proceeding on shortened MB without primers, line 4: complete SDA proceeding on shortened MB only, line 5: DpnI treated MB without Dam MTase, line 6: shortened MB cut by DpnI, line 7: MB only. (B) Fluorescent spectrum in response to the addition of different components.

    Journal: Chemical Science

    Article Title: An integrated-molecular-beacon based multiple exponential strand displacement amplification strategy for ultrasensitive detection of DNA methyltransferase activity integrated-molecular-beacon based multiple exponential strand displacement amplification strategy for ultrasensitive detection of DNA methyltransferase activity †Electronic supplementary information (ESI) available: Fig. S1 to S7 and Table S1. See DOI: 10.1039/c8sc05102j

    doi: 10.1039/c8sc05102j

    Figure Lengend Snippet: (A) PAGE result of the proposed sensing platform. Line M: DNA marker, line 1: SDA proceeding on shortened MB without Nb.BbvcI, line 2: SDA proceeding on shortened MB with primer 0, line 3: SDA proceeding on shortened MB without primers, line 4: complete SDA proceeding on shortened MB only, line 5: DpnI treated MB without Dam MTase, line 6: shortened MB cut by DpnI, line 7: MB only. (B) Fluorescent spectrum in response to the addition of different components.

    Article Snippet: Dam and M. SssI methyltransferase (MTase), endonuclease DpnI, Klenow Fragment Polymerase (3′–5′ exo-) (KFP), nicking enzyme Nb.BbvcI, S -adenyl methionine (SAM), EcoRI enzyme and the corresponding buffer solution were obtained from New England Biolabs (Beijing, China).

    Techniques: Polyacrylamide Gel Electrophoresis, Marker