bst dna polymerase  (New England Biolabs)


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    Name:
    Bst DNA Polymerase Full Length
    Description:
    Bst DNA Polymerase Full Length 500 units
    Catalog Number:
    m0328s
    Price:
    70
    Size:
    500 units
    Category:
    Thermostable DNA Polymerases
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    Structured Review

    New England Biolabs bst dna polymerase
    Bst DNA Polymerase Full Length
    Bst DNA Polymerase Full Length 500 units
    https://www.bioz.com/result/bst dna polymerase/product/New England Biolabs
    Average 94 stars, based on 73 article reviews
    Price from $9.99 to $1999.99
    bst dna polymerase - by Bioz Stars, 2020-05
    94/100 stars

    Images

    1) Product Images from "Flap endonuclease 1 is involved in cccDNA formation in the hepatitis B virus"

    Article Title: Flap endonuclease 1 is involved in cccDNA formation in the hepatitis B virus

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1007124

    FEN1 protein facilitates cccDNA formation in vitro . (A) Schematic presentation of in vitro cccDNA formation assay. Purified NC-DNA (10 8 copies) was incubated with recombinant FEN1, Bst DNA polymerase, and Taq DNA ligase. Following incubation, the DNA was purified and analyzed (B–F). Regions for qPCR amplification (E and F) were indicated as p. The 5.4-kb PstI fragment in HBV plasmid (Control) has a partial HBV sequence but does not have core and intact P genes. (B) cccDNA-selective qPCR. Each result represents the mean ± SEM of three independent experiments. Asterisks indicate statistically significant differences; *** P
    Figure Legend Snippet: FEN1 protein facilitates cccDNA formation in vitro . (A) Schematic presentation of in vitro cccDNA formation assay. Purified NC-DNA (10 8 copies) was incubated with recombinant FEN1, Bst DNA polymerase, and Taq DNA ligase. Following incubation, the DNA was purified and analyzed (B–F). Regions for qPCR amplification (E and F) were indicated as p. The 5.4-kb PstI fragment in HBV plasmid (Control) has a partial HBV sequence but does not have core and intact P genes. (B) cccDNA-selective qPCR. Each result represents the mean ± SEM of three independent experiments. Asterisks indicate statistically significant differences; *** P

    Techniques Used: In Vitro, Tube Formation Assay, Purification, Incubation, Recombinant, Real-time Polymerase Chain Reaction, Amplification, Plasmid Preparation, Sequencing

    2) Product Images from "Flap endonuclease 1 is involved in cccDNA formation in the hepatitis B virus"

    Article Title: Flap endonuclease 1 is involved in cccDNA formation in the hepatitis B virus

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1007124

    FEN1 protein facilitates cccDNA formation in vitro . (A) Schematic presentation of in vitro cccDNA formation assay. Purified NC-DNA (10 8 copies) was incubated with recombinant FEN1, Bst DNA polymerase, and Taq DNA ligase. Following incubation, the DNA was purified and analyzed (B–F). Regions for qPCR amplification (E and F) were indicated as p. The 5.4-kb PstI fragment in HBV plasmid (Control) has a partial HBV sequence but does not have core and intact P genes. (B) cccDNA-selective qPCR. Each result represents the mean ± SEM of three independent experiments. Asterisks indicate statistically significant differences; *** P
    Figure Legend Snippet: FEN1 protein facilitates cccDNA formation in vitro . (A) Schematic presentation of in vitro cccDNA formation assay. Purified NC-DNA (10 8 copies) was incubated with recombinant FEN1, Bst DNA polymerase, and Taq DNA ligase. Following incubation, the DNA was purified and analyzed (B–F). Regions for qPCR amplification (E and F) were indicated as p. The 5.4-kb PstI fragment in HBV plasmid (Control) has a partial HBV sequence but does not have core and intact P genes. (B) cccDNA-selective qPCR. Each result represents the mean ± SEM of three independent experiments. Asterisks indicate statistically significant differences; *** P

    Techniques Used: In Vitro, Tube Formation Assay, Purification, Incubation, Recombinant, Real-time Polymerase Chain Reaction, Amplification, Plasmid Preparation, Sequencing

    3) Product Images from "In vitro selection of an XNA aptamer capable of small-molecule recognition"

    Article Title: In vitro selection of an XNA aptamer capable of small-molecule recognition

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky667

    TNA SELEX to generate OTA-binding aptamers. The initial ssDNA library is amplified using a forward primer modified with a PEG spacer and polyT tail to enable separation and recovery by denaturing PAGE. The PEGylated DNA template is then annealed to the FAM-labelled TNA primer and extended using KOD RI polymerase to generate the TNA library for each selection round. The TNA library is incubated with OTA-functionalized magnetic beads, and bound sequences recovered by either heat (rounds 1–4) or ligand elution (rounds 5–9). These sequences are then treated with DNase I to digest any remaining DNA template. The TNA is then reverse transcribed back into DNA using Bst DNA polymerase and PCR amplified for the next round of selection.
    Figure Legend Snippet: TNA SELEX to generate OTA-binding aptamers. The initial ssDNA library is amplified using a forward primer modified with a PEG spacer and polyT tail to enable separation and recovery by denaturing PAGE. The PEGylated DNA template is then annealed to the FAM-labelled TNA primer and extended using KOD RI polymerase to generate the TNA library for each selection round. The TNA library is incubated with OTA-functionalized magnetic beads, and bound sequences recovered by either heat (rounds 1–4) or ligand elution (rounds 5–9). These sequences are then treated with DNase I to digest any remaining DNA template. The TNA is then reverse transcribed back into DNA using Bst DNA polymerase and PCR amplified for the next round of selection.

    Techniques Used: Binding Assay, Amplification, Modification, Polyacrylamide Gel Electrophoresis, Selection, Incubation, Magnetic Beads, Polymerase Chain Reaction

    4) Product Images from "High-efficiency and integrable DNA arithmetic and logic system based on strand displacement synthesis"

    Article Title: High-efficiency and integrable DNA arithmetic and logic system based on strand displacement synthesis

    Journal: Nature Communications

    doi: 10.1038/s41467-019-13310-2

    Construction of six basic dual-rail systems and their performance. a Construction of the AND, OR, NAND, NOR, XOR, and XNOR dual-rail gates. The upper regular octagon shows a single-rail AND gate, and the lower regular hexagon shows a single-rail OR gate. The green and magenta colors mean defined TRUE and FALSE signals, respectively. Superscripts 1 and 0 also indicate the TRUE and FALSE inputs and outputs, respectively. When computations were performed, a set of input strands must be adder, e.g., inputs (1, 0) means adding inputs I A 1 (TURE) and I B 0 (FALSE). Detailed structures can be seen in Fig. S12. Reaction details of AND and XOR gates can be seen in Supplementary Figs. 7 and 8 . b , c Reaction kinetics of the dual-rail AND and XOR gates with all possible combinations of inputs. The reaction was performed with 3.2 U Bst polymerase (large fragment), TRI and FRI at 35 °C. The curve was plotted by transferring the cycle value into the reaction time. The outputs were normalized to the RFU values in the FAM and ROX channels with the highest signals. The FAM and ROX signals correspond to the TRUE and FALSE returns, respectively. Sequences of the DNA strands are listed in the Supplementary Information . d Summary of all the outputs computed by the six basic logic gates constructed from DNA.
    Figure Legend Snippet: Construction of six basic dual-rail systems and their performance. a Construction of the AND, OR, NAND, NOR, XOR, and XNOR dual-rail gates. The upper regular octagon shows a single-rail AND gate, and the lower regular hexagon shows a single-rail OR gate. The green and magenta colors mean defined TRUE and FALSE signals, respectively. Superscripts 1 and 0 also indicate the TRUE and FALSE inputs and outputs, respectively. When computations were performed, a set of input strands must be adder, e.g., inputs (1, 0) means adding inputs I A 1 (TURE) and I B 0 (FALSE). Detailed structures can be seen in Fig. S12. Reaction details of AND and XOR gates can be seen in Supplementary Figs. 7 and 8 . b , c Reaction kinetics of the dual-rail AND and XOR gates with all possible combinations of inputs. The reaction was performed with 3.2 U Bst polymerase (large fragment), TRI and FRI at 35 °C. The curve was plotted by transferring the cycle value into the reaction time. The outputs were normalized to the RFU values in the FAM and ROX channels with the highest signals. The FAM and ROX signals correspond to the TRUE and FALSE returns, respectively. Sequences of the DNA strands are listed in the Supplementary Information . d Summary of all the outputs computed by the six basic logic gates constructed from DNA.

    Techniques Used: Transferring, Construct

    Construction of DNA ALU with our DNA logic gates. a Abstract diagram of a typical ALU. b A typical construction of a 1-bit ALU with a digital logic circuit. A and B: inputs; C in : carry in; S 0 and S 1 : select signals; Y: output; C out : carry out. c Assembling the 4:1 multiplexer with DNA components. The sequences of the strands are listed in the Supplementary Table 2 . The details of the integrated logic gates are shown in Fig. S20. d Function table of the DNA ALU. e Summary of the outputs of the ALU. f , g Reaction kinetics of the ALU with all possible combinations of inputs. The reaction was performed with 12 U Bst polymerase (large fragment), TRIII, FRIII, TRII, and FRII. The curve was plotted by transferring the cycle values into the reaction time. The outputs were normalized to the RFU values in the FAM, ROX, HEX, and Cy5 channels with the highest signals. The TRIII (FAM) and FRIII (ROX) signals correspond to the TRUE and FALSE returns of Y, respectively. The TRII (HEX) and FRII (Cy5) signals correspond to the TRUE and FALSE returns of C out, respectively. The reaction kinetics of the individual gates can be seen in Supplementary Fig. 22 . The sequences of the DNA strands are listed in the Supplementary Table 2 .
    Figure Legend Snippet: Construction of DNA ALU with our DNA logic gates. a Abstract diagram of a typical ALU. b A typical construction of a 1-bit ALU with a digital logic circuit. A and B: inputs; C in : carry in; S 0 and S 1 : select signals; Y: output; C out : carry out. c Assembling the 4:1 multiplexer with DNA components. The sequences of the strands are listed in the Supplementary Table 2 . The details of the integrated logic gates are shown in Fig. S20. d Function table of the DNA ALU. e Summary of the outputs of the ALU. f , g Reaction kinetics of the ALU with all possible combinations of inputs. The reaction was performed with 12 U Bst polymerase (large fragment), TRIII, FRIII, TRII, and FRII. The curve was plotted by transferring the cycle values into the reaction time. The outputs were normalized to the RFU values in the FAM, ROX, HEX, and Cy5 channels with the highest signals. The TRIII (FAM) and FRIII (ROX) signals correspond to the TRUE and FALSE returns of Y, respectively. The TRII (HEX) and FRII (Cy5) signals correspond to the TRUE and FALSE returns of C out, respectively. The reaction kinetics of the individual gates can be seen in Supplementary Fig. 22 . The sequences of the DNA strands are listed in the Supplementary Table 2 .

    Techniques Used: Transferring

    Construction of the full adder and 4:1 multiplexer from our DNA logic gates. a , e A typical construction of the full adder and the 4:1 multiplexer with the digital logic circuit. D 0 –D 3 : inputs; S 0 and S 1 : select signals; Z: output. b , f Constructing a full adder and the 4:1 multiplexer with DNA logic gates. The sequences of the DNA strands are listed in the Supplementary table 2 . c , g Summary of all the outputs computed by the DNA full adder and 4:1 multiplexer. d , h Reaction kinetics of the full adder and the 4:1 multiplexer with all possible combinations of inputs. For the full adder, the reaction was performed with 12 U Bst polymerase (large fragment), TRI, FRI, TRII, and FRII. The outputs were normalized to the RFU values in the FAM, ROX, HEX, and Cy5 channels with the highest signals. For the full adder: The TRI (FAM) and FRI (ROX) signals correspond to TRUE and FALSE returns of S, respectively. The TRII (HEX) and FRII (Cy5) signals correspond to the TRUE and FALSE returns of C out, respectively. For the 4:1 multiplexer, the reaction was performed with 6.4 U Bst polymerase (large fragment), TRIII and FRII. The outputs were normalized to the RFU values in the FAM and ROX channels with the highest signals. The TRIII (FAM) and FRIII (ROX) signals correspond to TRUE and FALSE returns, respectively. The reaction kinetics of the individual gates can be seen in Supplementary Figs. 14 and 19 .
    Figure Legend Snippet: Construction of the full adder and 4:1 multiplexer from our DNA logic gates. a , e A typical construction of the full adder and the 4:1 multiplexer with the digital logic circuit. D 0 –D 3 : inputs; S 0 and S 1 : select signals; Z: output. b , f Constructing a full adder and the 4:1 multiplexer with DNA logic gates. The sequences of the DNA strands are listed in the Supplementary table 2 . c , g Summary of all the outputs computed by the DNA full adder and 4:1 multiplexer. d , h Reaction kinetics of the full adder and the 4:1 multiplexer with all possible combinations of inputs. For the full adder, the reaction was performed with 12 U Bst polymerase (large fragment), TRI, FRI, TRII, and FRII. The outputs were normalized to the RFU values in the FAM, ROX, HEX, and Cy5 channels with the highest signals. For the full adder: The TRI (FAM) and FRI (ROX) signals correspond to TRUE and FALSE returns of S, respectively. The TRII (HEX) and FRII (Cy5) signals correspond to the TRUE and FALSE returns of C out, respectively. For the 4:1 multiplexer, the reaction was performed with 6.4 U Bst polymerase (large fragment), TRIII and FRII. The outputs were normalized to the RFU values in the FAM and ROX channels with the highest signals. The TRIII (FAM) and FRIII (ROX) signals correspond to TRUE and FALSE returns, respectively. The reaction kinetics of the individual gates can be seen in Supplementary Figs. 14 and 19 .

    Techniques Used:

    Construction of AND and OR gates with DNA polymerase and their performance. a , c Right: structure of the AND and OR gates. The capital names are the sequence names; the lowercase names refer to the elementary sequences and asterisk indicates a complementary sequence. Each elementary sequence contains 18 bases. The gray parts are 4-mer spacer sequences used to reduce steric hinderance. The sequences of inputs A and B are the same as a and b. Left: abstract diagram of the AND and OR gates. The regular octagon shows the main structure of the DNA components; the two bold lines on the left indicate the binding sites of the two inputs in the DNA component; the vector line on the right indicates the potential output. b , d Mechanism of the AND and OR gates. e The fluorescent reporter used to visualize the devices. The letter Q denotes the quencher, and F denotes the fluorophore. f , g Reaction kinetics of the AND and OR gates with all possible combinations of inputs. The reaction was performed with 3.2 U Bst polymerase (large fragment) and TRI at 35 °C. The curve was plotted by transferring the cycle value into the reaction time. The outputs were normalized to the relative fluorescence unit (RFU) values in the FAM channel with the highest signals. The original signals are plotted in Supplementary Fig. 3 . The sequences of the DNA strands are listed in the Supplementary Table 2 .
    Figure Legend Snippet: Construction of AND and OR gates with DNA polymerase and their performance. a , c Right: structure of the AND and OR gates. The capital names are the sequence names; the lowercase names refer to the elementary sequences and asterisk indicates a complementary sequence. Each elementary sequence contains 18 bases. The gray parts are 4-mer spacer sequences used to reduce steric hinderance. The sequences of inputs A and B are the same as a and b. Left: abstract diagram of the AND and OR gates. The regular octagon shows the main structure of the DNA components; the two bold lines on the left indicate the binding sites of the two inputs in the DNA component; the vector line on the right indicates the potential output. b , d Mechanism of the AND and OR gates. e The fluorescent reporter used to visualize the devices. The letter Q denotes the quencher, and F denotes the fluorophore. f , g Reaction kinetics of the AND and OR gates with all possible combinations of inputs. The reaction was performed with 3.2 U Bst polymerase (large fragment) and TRI at 35 °C. The curve was plotted by transferring the cycle value into the reaction time. The outputs were normalized to the relative fluorescence unit (RFU) values in the FAM channel with the highest signals. The original signals are plotted in Supplementary Fig. 3 . The sequences of the DNA strands are listed in the Supplementary Table 2 .

    Techniques Used: Sequencing, Binding Assay, Plasmid Preparation, Transferring, Fluorescence

    Related Articles

    Amplification:

    Article Title: Development of coupling controlled polymerizations by adapter-ligation in mate-pair sequencing for detection of various genomic variants in one single assay
    Article Snippet: .. Of note, after purification of Ad1 PCR products, a total of 20 µg amplified DNA, which could be a mixture of each amplified DNA with equal quantity (from the six patients) or from one single sample (Trisomy 2 or 8), was used for dsCir DNA formation. naCNT was performed with 1 pmol dsCir DNA; Bst DNA Polymerase, Full Length (NEB); Klenow fragment (Enzymatics, Inc.); and limited dNTPs. ..

    Article Title: In vitro selection of an XNA aptamer capable of small-molecule recognition
    Article Snippet: .. 1.6 U of Bst DNA polymerase I large fragment (New England Biolabs) was added to the primer-template complex and the reaction incubated at 55°C for 3.5 h. The RT reactions were divided into 5 μl aliquots and PCR amplified as previously described for the DNA library using unmodified versions of the forward and reverse PCR primers and an annealing temperature of 50°C. .. This material was purified using MinElute PCR clean up columns and re-amplified using the PEG-forward and FAM-reverse PCR primers to enable strand separation.

    Magnetic Beads:

    Article Title: Mapping vaccinia virus DNA replication origins at nucleotide level by deep sequencing
    Article Snippet: .. The primer complementary to the full-length 3′-end adaptor was annealed to the purified fragments while still on magnetic beads and was extended by Bst DNA polymerase, large fragment (New England BioLabs) to produce double-stranded DNA. ..

    Purification:

    Article Title: Development of coupling controlled polymerizations by adapter-ligation in mate-pair sequencing for detection of various genomic variants in one single assay
    Article Snippet: .. Of note, after purification of Ad1 PCR products, a total of 20 µg amplified DNA, which could be a mixture of each amplified DNA with equal quantity (from the six patients) or from one single sample (Trisomy 2 or 8), was used for dsCir DNA formation. naCNT was performed with 1 pmol dsCir DNA; Bst DNA Polymerase, Full Length (NEB); Klenow fragment (Enzymatics, Inc.); and limited dNTPs. ..

    Article Title: Mapping vaccinia virus DNA replication origins at nucleotide level by deep sequencing
    Article Snippet: .. The primer complementary to the full-length 3′-end adaptor was annealed to the purified fragments while still on magnetic beads and was extended by Bst DNA polymerase, large fragment (New England BioLabs) to produce double-stranded DNA. ..

    Concentration Assay:

    Article Title: Characterization of SNP and Structural Variations in the Mitochondrial Genomes of Tilletia indica and Its Closely Related Species Formed Basis for a Simple Diagnostic Assay
    Article Snippet: .. A LAMP assay mix of a 25 μl volume comprised a mix of the 3 pairs of primers, F3/B3, FIP/BIP and LF/LB primer pairs in a final concentration of 0.2 μM, 1.6 μM and 0.4 μM respectively, 6 mM MgSO4 , 1.4 mM each of the dNTP, 1 μl of the enzyme, Bst DNA Polymerase, Large Fragment (8000 U/ml) in 1X ThermoPol Buffer (New England Biolabs). ..

    Incubation:

    Article Title: Flap endonuclease 1 is involved in cccDNA formation in the hepatitis B virus
    Article Snippet: .. NC-DNA (108 copies) was incubated with 32 units (U) of Thermostable FEN1 in ThermoPol Buffer (New England Biolabs) at 65°C for 10 min, followed by incubation with 8 U of Bst DNA polymerase, 40 U of Taq DNA ligase, 100 μM dNTPs, and NAD+ (all from New England Biolabs). .. After further incubation at 37°C for 20 min, DNA was purified by phenol/chloroform extraction and ethanol precipitation, and subjected to cccDNA-selective qPCR or RCA, as described above.

    Article Title: In vitro selection of an XNA aptamer capable of small-molecule recognition
    Article Snippet: .. 1.6 U of Bst DNA polymerase I large fragment (New England Biolabs) was added to the primer-template complex and the reaction incubated at 55°C for 3.5 h. The RT reactions were divided into 5 μl aliquots and PCR amplified as previously described for the DNA library using unmodified versions of the forward and reverse PCR primers and an annealing temperature of 50°C. .. This material was purified using MinElute PCR clean up columns and re-amplified using the PEG-forward and FAM-reverse PCR primers to enable strand separation.

    Lamp Assay:

    Article Title: Characterization of SNP and Structural Variations in the Mitochondrial Genomes of Tilletia indica and Its Closely Related Species Formed Basis for a Simple Diagnostic Assay
    Article Snippet: .. A LAMP assay mix of a 25 μl volume comprised a mix of the 3 pairs of primers, F3/B3, FIP/BIP and LF/LB primer pairs in a final concentration of 0.2 μM, 1.6 μM and 0.4 μM respectively, 6 mM MgSO4 , 1.4 mM each of the dNTP, 1 μl of the enzyme, Bst DNA Polymerase, Large Fragment (8000 U/ml) in 1X ThermoPol Buffer (New England Biolabs). ..

    Polymerase Chain Reaction:

    Article Title: Development of coupling controlled polymerizations by adapter-ligation in mate-pair sequencing for detection of various genomic variants in one single assay
    Article Snippet: .. Of note, after purification of Ad1 PCR products, a total of 20 µg amplified DNA, which could be a mixture of each amplified DNA with equal quantity (from the six patients) or from one single sample (Trisomy 2 or 8), was used for dsCir DNA formation. naCNT was performed with 1 pmol dsCir DNA; Bst DNA Polymerase, Full Length (NEB); Klenow fragment (Enzymatics, Inc.); and limited dNTPs. ..

    Article Title: In vitro selection of an XNA aptamer capable of small-molecule recognition
    Article Snippet: .. 1.6 U of Bst DNA polymerase I large fragment (New England Biolabs) was added to the primer-template complex and the reaction incubated at 55°C for 3.5 h. The RT reactions were divided into 5 μl aliquots and PCR amplified as previously described for the DNA library using unmodified versions of the forward and reverse PCR primers and an annealing temperature of 50°C. .. This material was purified using MinElute PCR clean up columns and re-amplified using the PEG-forward and FAM-reverse PCR primers to enable strand separation.

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  • 94
    New England Biolabs bst dna polymerase
    FEN1 protein facilitates cccDNA formation in vitro . (A) Schematic presentation of in vitro cccDNA formation assay. Purified <t>NC-DNA</t> (10 8 copies) was incubated with recombinant FEN1, <t>Bst</t> DNA polymerase, and Taq DNA ligase. Following incubation, the DNA was purified and analyzed (B–F). Regions for qPCR amplification (E and F) were indicated as p. The 5.4-kb PstI fragment in HBV plasmid (Control) has a partial HBV sequence but does not have core and intact P genes. (B) cccDNA-selective qPCR. Each result represents the mean ± SEM of three independent experiments. Asterisks indicate statistically significant differences; *** P
    Bst Dna Polymerase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 62 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bst dna polymerase/product/New England Biolabs
    Average 94 stars, based on 62 article reviews
    Price from $9.99 to $1999.99
    bst dna polymerase - by Bioz Stars, 2020-05
    94/100 stars
      Buy from Supplier

    Image Search Results


    FEN1 protein facilitates cccDNA formation in vitro . (A) Schematic presentation of in vitro cccDNA formation assay. Purified NC-DNA (10 8 copies) was incubated with recombinant FEN1, Bst DNA polymerase, and Taq DNA ligase. Following incubation, the DNA was purified and analyzed (B–F). Regions for qPCR amplification (E and F) were indicated as p. The 5.4-kb PstI fragment in HBV plasmid (Control) has a partial HBV sequence but does not have core and intact P genes. (B) cccDNA-selective qPCR. Each result represents the mean ± SEM of three independent experiments. Asterisks indicate statistically significant differences; *** P

    Journal: PLoS Pathogens

    Article Title: Flap endonuclease 1 is involved in cccDNA formation in the hepatitis B virus

    doi: 10.1371/journal.ppat.1007124

    Figure Lengend Snippet: FEN1 protein facilitates cccDNA formation in vitro . (A) Schematic presentation of in vitro cccDNA formation assay. Purified NC-DNA (10 8 copies) was incubated with recombinant FEN1, Bst DNA polymerase, and Taq DNA ligase. Following incubation, the DNA was purified and analyzed (B–F). Regions for qPCR amplification (E and F) were indicated as p. The 5.4-kb PstI fragment in HBV plasmid (Control) has a partial HBV sequence but does not have core and intact P genes. (B) cccDNA-selective qPCR. Each result represents the mean ± SEM of three independent experiments. Asterisks indicate statistically significant differences; *** P

    Article Snippet: NC-DNA (108 copies) was incubated with 32 units (U) of Thermostable FEN1 in ThermoPol Buffer (New England Biolabs) at 65°C for 10 min, followed by incubation with 8 U of Bst DNA polymerase, 40 U of Taq DNA ligase, 100 μM dNTPs, and NAD+ (all from New England Biolabs).

    Techniques: In Vitro, Tube Formation Assay, Purification, Incubation, Recombinant, Real-time Polymerase Chain Reaction, Amplification, Plasmid Preparation, Sequencing

    FEN1 protein facilitates cccDNA formation in vitro . (A) Schematic presentation of in vitro cccDNA formation assay. Purified NC-DNA (10 8 copies) was incubated with recombinant FEN1, Bst DNA polymerase, and Taq DNA ligase. Following incubation, the DNA was purified and analyzed (B–F). Regions for qPCR amplification (E and F) were indicated as p. The 5.4-kb PstI fragment in HBV plasmid (Control) has a partial HBV sequence but does not have core and intact P genes. (B) cccDNA-selective qPCR. Each result represents the mean ± SEM of three independent experiments. Asterisks indicate statistically significant differences; *** P

    Journal: PLoS Pathogens

    Article Title: Flap endonuclease 1 is involved in cccDNA formation in the hepatitis B virus

    doi: 10.1371/journal.ppat.1007124

    Figure Lengend Snippet: FEN1 protein facilitates cccDNA formation in vitro . (A) Schematic presentation of in vitro cccDNA formation assay. Purified NC-DNA (10 8 copies) was incubated with recombinant FEN1, Bst DNA polymerase, and Taq DNA ligase. Following incubation, the DNA was purified and analyzed (B–F). Regions for qPCR amplification (E and F) were indicated as p. The 5.4-kb PstI fragment in HBV plasmid (Control) has a partial HBV sequence but does not have core and intact P genes. (B) cccDNA-selective qPCR. Each result represents the mean ± SEM of three independent experiments. Asterisks indicate statistically significant differences; *** P

    Article Snippet: NC-DNA (108 copies) was incubated with 32 units (U) of Thermostable FEN1 in ThermoPol Buffer (New England Biolabs) at 65°C for 10 min, followed by incubation with 8 U of Bst DNA polymerase, 40 U of Taq DNA ligase, 100 μM dNTPs, and NAD+ (all from New England Biolabs).

    Techniques: In Vitro, Tube Formation Assay, Purification, Incubation, Recombinant, Real-time Polymerase Chain Reaction, Amplification, Plasmid Preparation, Sequencing

    TNA SELEX to generate OTA-binding aptamers. The initial ssDNA library is amplified using a forward primer modified with a PEG spacer and polyT tail to enable separation and recovery by denaturing PAGE. The PEGylated DNA template is then annealed to the FAM-labelled TNA primer and extended using KOD RI polymerase to generate the TNA library for each selection round. The TNA library is incubated with OTA-functionalized magnetic beads, and bound sequences recovered by either heat (rounds 1–4) or ligand elution (rounds 5–9). These sequences are then treated with DNase I to digest any remaining DNA template. The TNA is then reverse transcribed back into DNA using Bst DNA polymerase and PCR amplified for the next round of selection.

    Journal: Nucleic Acids Research

    Article Title: In vitro selection of an XNA aptamer capable of small-molecule recognition

    doi: 10.1093/nar/gky667

    Figure Lengend Snippet: TNA SELEX to generate OTA-binding aptamers. The initial ssDNA library is amplified using a forward primer modified with a PEG spacer and polyT tail to enable separation and recovery by denaturing PAGE. The PEGylated DNA template is then annealed to the FAM-labelled TNA primer and extended using KOD RI polymerase to generate the TNA library for each selection round. The TNA library is incubated with OTA-functionalized magnetic beads, and bound sequences recovered by either heat (rounds 1–4) or ligand elution (rounds 5–9). These sequences are then treated with DNase I to digest any remaining DNA template. The TNA is then reverse transcribed back into DNA using Bst DNA polymerase and PCR amplified for the next round of selection.

    Article Snippet: 1.6 U of Bst DNA polymerase I large fragment (New England Biolabs) was added to the primer-template complex and the reaction incubated at 55°C for 3.5 h. The RT reactions were divided into 5 μl aliquots and PCR amplified as previously described for the DNA library using unmodified versions of the forward and reverse PCR primers and an annealing temperature of 50°C.

    Techniques: Binding Assay, Amplification, Modification, Polyacrylamide Gel Electrophoresis, Selection, Incubation, Magnetic Beads, Polymerase Chain Reaction

    Construction of six basic dual-rail systems and their performance. a Construction of the AND, OR, NAND, NOR, XOR, and XNOR dual-rail gates. The upper regular octagon shows a single-rail AND gate, and the lower regular hexagon shows a single-rail OR gate. The green and magenta colors mean defined TRUE and FALSE signals, respectively. Superscripts 1 and 0 also indicate the TRUE and FALSE inputs and outputs, respectively. When computations were performed, a set of input strands must be adder, e.g., inputs (1, 0) means adding inputs I A 1 (TURE) and I B 0 (FALSE). Detailed structures can be seen in Fig. S12. Reaction details of AND and XOR gates can be seen in Supplementary Figs. 7 and 8 . b , c Reaction kinetics of the dual-rail AND and XOR gates with all possible combinations of inputs. The reaction was performed with 3.2 U Bst polymerase (large fragment), TRI and FRI at 35 °C. The curve was plotted by transferring the cycle value into the reaction time. The outputs were normalized to the RFU values in the FAM and ROX channels with the highest signals. The FAM and ROX signals correspond to the TRUE and FALSE returns, respectively. Sequences of the DNA strands are listed in the Supplementary Information . d Summary of all the outputs computed by the six basic logic gates constructed from DNA.

    Journal: Nature Communications

    Article Title: High-efficiency and integrable DNA arithmetic and logic system based on strand displacement synthesis

    doi: 10.1038/s41467-019-13310-2

    Figure Lengend Snippet: Construction of six basic dual-rail systems and their performance. a Construction of the AND, OR, NAND, NOR, XOR, and XNOR dual-rail gates. The upper regular octagon shows a single-rail AND gate, and the lower regular hexagon shows a single-rail OR gate. The green and magenta colors mean defined TRUE and FALSE signals, respectively. Superscripts 1 and 0 also indicate the TRUE and FALSE inputs and outputs, respectively. When computations were performed, a set of input strands must be adder, e.g., inputs (1, 0) means adding inputs I A 1 (TURE) and I B 0 (FALSE). Detailed structures can be seen in Fig. S12. Reaction details of AND and XOR gates can be seen in Supplementary Figs. 7 and 8 . b , c Reaction kinetics of the dual-rail AND and XOR gates with all possible combinations of inputs. The reaction was performed with 3.2 U Bst polymerase (large fragment), TRI and FRI at 35 °C. The curve was plotted by transferring the cycle value into the reaction time. The outputs were normalized to the RFU values in the FAM and ROX channels with the highest signals. The FAM and ROX signals correspond to the TRUE and FALSE returns, respectively. Sequences of the DNA strands are listed in the Supplementary Information . d Summary of all the outputs computed by the six basic logic gates constructed from DNA.

    Article Snippet: Typically, we used Bst DNA polymerase, large fragment (New England Biolabs), and the reactions were performed in 1 × ThermoPol buffer containing 4 mM of MgSO4 , 0.31 mM each dNTP.

    Techniques: Transferring, Construct

    Construction of DNA ALU with our DNA logic gates. a Abstract diagram of a typical ALU. b A typical construction of a 1-bit ALU with a digital logic circuit. A and B: inputs; C in : carry in; S 0 and S 1 : select signals; Y: output; C out : carry out. c Assembling the 4:1 multiplexer with DNA components. The sequences of the strands are listed in the Supplementary Table 2 . The details of the integrated logic gates are shown in Fig. S20. d Function table of the DNA ALU. e Summary of the outputs of the ALU. f , g Reaction kinetics of the ALU with all possible combinations of inputs. The reaction was performed with 12 U Bst polymerase (large fragment), TRIII, FRIII, TRII, and FRII. The curve was plotted by transferring the cycle values into the reaction time. The outputs were normalized to the RFU values in the FAM, ROX, HEX, and Cy5 channels with the highest signals. The TRIII (FAM) and FRIII (ROX) signals correspond to the TRUE and FALSE returns of Y, respectively. The TRII (HEX) and FRII (Cy5) signals correspond to the TRUE and FALSE returns of C out, respectively. The reaction kinetics of the individual gates can be seen in Supplementary Fig. 22 . The sequences of the DNA strands are listed in the Supplementary Table 2 .

    Journal: Nature Communications

    Article Title: High-efficiency and integrable DNA arithmetic and logic system based on strand displacement synthesis

    doi: 10.1038/s41467-019-13310-2

    Figure Lengend Snippet: Construction of DNA ALU with our DNA logic gates. a Abstract diagram of a typical ALU. b A typical construction of a 1-bit ALU with a digital logic circuit. A and B: inputs; C in : carry in; S 0 and S 1 : select signals; Y: output; C out : carry out. c Assembling the 4:1 multiplexer with DNA components. The sequences of the strands are listed in the Supplementary Table 2 . The details of the integrated logic gates are shown in Fig. S20. d Function table of the DNA ALU. e Summary of the outputs of the ALU. f , g Reaction kinetics of the ALU with all possible combinations of inputs. The reaction was performed with 12 U Bst polymerase (large fragment), TRIII, FRIII, TRII, and FRII. The curve was plotted by transferring the cycle values into the reaction time. The outputs were normalized to the RFU values in the FAM, ROX, HEX, and Cy5 channels with the highest signals. The TRIII (FAM) and FRIII (ROX) signals correspond to the TRUE and FALSE returns of Y, respectively. The TRII (HEX) and FRII (Cy5) signals correspond to the TRUE and FALSE returns of C out, respectively. The reaction kinetics of the individual gates can be seen in Supplementary Fig. 22 . The sequences of the DNA strands are listed in the Supplementary Table 2 .

    Article Snippet: Typically, we used Bst DNA polymerase, large fragment (New England Biolabs), and the reactions were performed in 1 × ThermoPol buffer containing 4 mM of MgSO4 , 0.31 mM each dNTP.

    Techniques: Transferring

    Construction of the full adder and 4:1 multiplexer from our DNA logic gates. a , e A typical construction of the full adder and the 4:1 multiplexer with the digital logic circuit. D 0 –D 3 : inputs; S 0 and S 1 : select signals; Z: output. b , f Constructing a full adder and the 4:1 multiplexer with DNA logic gates. The sequences of the DNA strands are listed in the Supplementary table 2 . c , g Summary of all the outputs computed by the DNA full adder and 4:1 multiplexer. d , h Reaction kinetics of the full adder and the 4:1 multiplexer with all possible combinations of inputs. For the full adder, the reaction was performed with 12 U Bst polymerase (large fragment), TRI, FRI, TRII, and FRII. The outputs were normalized to the RFU values in the FAM, ROX, HEX, and Cy5 channels with the highest signals. For the full adder: The TRI (FAM) and FRI (ROX) signals correspond to TRUE and FALSE returns of S, respectively. The TRII (HEX) and FRII (Cy5) signals correspond to the TRUE and FALSE returns of C out, respectively. For the 4:1 multiplexer, the reaction was performed with 6.4 U Bst polymerase (large fragment), TRIII and FRII. The outputs were normalized to the RFU values in the FAM and ROX channels with the highest signals. The TRIII (FAM) and FRIII (ROX) signals correspond to TRUE and FALSE returns, respectively. The reaction kinetics of the individual gates can be seen in Supplementary Figs. 14 and 19 .

    Journal: Nature Communications

    Article Title: High-efficiency and integrable DNA arithmetic and logic system based on strand displacement synthesis

    doi: 10.1038/s41467-019-13310-2

    Figure Lengend Snippet: Construction of the full adder and 4:1 multiplexer from our DNA logic gates. a , e A typical construction of the full adder and the 4:1 multiplexer with the digital logic circuit. D 0 –D 3 : inputs; S 0 and S 1 : select signals; Z: output. b , f Constructing a full adder and the 4:1 multiplexer with DNA logic gates. The sequences of the DNA strands are listed in the Supplementary table 2 . c , g Summary of all the outputs computed by the DNA full adder and 4:1 multiplexer. d , h Reaction kinetics of the full adder and the 4:1 multiplexer with all possible combinations of inputs. For the full adder, the reaction was performed with 12 U Bst polymerase (large fragment), TRI, FRI, TRII, and FRII. The outputs were normalized to the RFU values in the FAM, ROX, HEX, and Cy5 channels with the highest signals. For the full adder: The TRI (FAM) and FRI (ROX) signals correspond to TRUE and FALSE returns of S, respectively. The TRII (HEX) and FRII (Cy5) signals correspond to the TRUE and FALSE returns of C out, respectively. For the 4:1 multiplexer, the reaction was performed with 6.4 U Bst polymerase (large fragment), TRIII and FRII. The outputs were normalized to the RFU values in the FAM and ROX channels with the highest signals. The TRIII (FAM) and FRIII (ROX) signals correspond to TRUE and FALSE returns, respectively. The reaction kinetics of the individual gates can be seen in Supplementary Figs. 14 and 19 .

    Article Snippet: Typically, we used Bst DNA polymerase, large fragment (New England Biolabs), and the reactions were performed in 1 × ThermoPol buffer containing 4 mM of MgSO4 , 0.31 mM each dNTP.

    Techniques:

    Construction of AND and OR gates with DNA polymerase and their performance. a , c Right: structure of the AND and OR gates. The capital names are the sequence names; the lowercase names refer to the elementary sequences and asterisk indicates a complementary sequence. Each elementary sequence contains 18 bases. The gray parts are 4-mer spacer sequences used to reduce steric hinderance. The sequences of inputs A and B are the same as a and b. Left: abstract diagram of the AND and OR gates. The regular octagon shows the main structure of the DNA components; the two bold lines on the left indicate the binding sites of the two inputs in the DNA component; the vector line on the right indicates the potential output. b , d Mechanism of the AND and OR gates. e The fluorescent reporter used to visualize the devices. The letter Q denotes the quencher, and F denotes the fluorophore. f , g Reaction kinetics of the AND and OR gates with all possible combinations of inputs. The reaction was performed with 3.2 U Bst polymerase (large fragment) and TRI at 35 °C. The curve was plotted by transferring the cycle value into the reaction time. The outputs were normalized to the relative fluorescence unit (RFU) values in the FAM channel with the highest signals. The original signals are plotted in Supplementary Fig. 3 . The sequences of the DNA strands are listed in the Supplementary Table 2 .

    Journal: Nature Communications

    Article Title: High-efficiency and integrable DNA arithmetic and logic system based on strand displacement synthesis

    doi: 10.1038/s41467-019-13310-2

    Figure Lengend Snippet: Construction of AND and OR gates with DNA polymerase and their performance. a , c Right: structure of the AND and OR gates. The capital names are the sequence names; the lowercase names refer to the elementary sequences and asterisk indicates a complementary sequence. Each elementary sequence contains 18 bases. The gray parts are 4-mer spacer sequences used to reduce steric hinderance. The sequences of inputs A and B are the same as a and b. Left: abstract diagram of the AND and OR gates. The regular octagon shows the main structure of the DNA components; the two bold lines on the left indicate the binding sites of the two inputs in the DNA component; the vector line on the right indicates the potential output. b , d Mechanism of the AND and OR gates. e The fluorescent reporter used to visualize the devices. The letter Q denotes the quencher, and F denotes the fluorophore. f , g Reaction kinetics of the AND and OR gates with all possible combinations of inputs. The reaction was performed with 3.2 U Bst polymerase (large fragment) and TRI at 35 °C. The curve was plotted by transferring the cycle value into the reaction time. The outputs were normalized to the relative fluorescence unit (RFU) values in the FAM channel with the highest signals. The original signals are plotted in Supplementary Fig. 3 . The sequences of the DNA strands are listed in the Supplementary Table 2 .

    Article Snippet: Typically, we used Bst DNA polymerase, large fragment (New England Biolabs), and the reactions were performed in 1 × ThermoPol buffer containing 4 mM of MgSO4 , 0.31 mM each dNTP.

    Techniques: Sequencing, Binding Assay, Plasmid Preparation, Transferring, Fluorescence