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    New England Biolabs phi29 dna polymerase reaction buffer
    Plasmid <t>DNA</t> from the cecal sample after amplification with <t>phi29</t> polymerase. 1 , 1 kb ladder and 2 , Plasmid DNA amplified with Phi29 DNA polymerase.
    Phi29 Dna Polymerase Reaction Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 108 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi29 dna polymerase reaction buffer/product/New England Biolabs
    Average 99 stars, based on 108 article reviews
    Price from $9.99 to $1999.99
    phi29 dna polymerase reaction buffer - by Bioz Stars, 2020-10
    99/100 stars
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    99
    Thermo Fisher phi29 dna polymerase buffer
    Plasmid <t>DNA</t> from the cecal sample after amplification with <t>phi29</t> polymerase. 1 , 1 kb ladder and 2 , Plasmid DNA amplified with Phi29 DNA polymerase.
    Phi29 Dna Polymerase Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 94 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi29 dna polymerase buffer/product/Thermo Fisher
    Average 99 stars, based on 94 article reviews
    Price from $9.99 to $1999.99
    phi29 dna polymerase buffer - by Bioz Stars, 2020-10
    99/100 stars
      Buy from Supplier

    95
    Thermo Fisher reaction buffer for phi29 dna polymerase 10x
    Schematic illustration of in situ PLA using conventional and UnFold probes. ( a ) Conventional in situ PLA. ( b ) In situ PLA using UnFold probes. (i) After pairs of primary antibodies have bound a pair of interacting proteins (red and green) followed by washes, secondary conventional or UnFold in situ PLA probes are added, followed after an incubation by renewed washes. (ii) In the conventional design under ( a ) two more oligonucleotides are then added that can form a DNA circle. Using the UnFold design in ( b ) the probe carrying a hairpin-loop oligonucleotide is cleaved at the U residues, liberating a free 5′ end capable of being ligated to the 3′ end of the same DNA strand. Meanwhile, the U residues in the hairpin DNA strand of the other UnFold probe are cleaved presenting a single-stranded template for the enzymatic joining of the ends of the strand on the first UnFold probe. (iii) A DNA ligase is added to form DNA circles in the two variants of in situ PLA. (iv) Finally, <t>phi29</t> DNA polymerase is added to initiate RCA primed by oligonucleotides on one of the antibodies, and fluorescent oligonucleotides are used to visualize the RCA products.
    Reaction Buffer For Phi29 Dna Polymerase 10x, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 40 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/reaction buffer for phi29 dna polymerase 10x/product/Thermo Fisher
    Average 95 stars, based on 40 article reviews
    Price from $9.99 to $1999.99
    reaction buffer for phi29 dna polymerase 10x - by Bioz Stars, 2020-10
    95/100 stars
      Buy from Supplier

    99
    Thermo Fisher phi29 dna polymerase reaction buffer
    Schematic illustration of in situ PLA using conventional and UnFold probes. ( a ) Conventional in situ PLA. ( b ) In situ PLA using UnFold probes. (i) After pairs of primary antibodies have bound a pair of interacting proteins (red and green) followed by washes, secondary conventional or UnFold in situ PLA probes are added, followed after an incubation by renewed washes. (ii) In the conventional design under ( a ) two more oligonucleotides are then added that can form a DNA circle. Using the UnFold design in ( b ) the probe carrying a hairpin-loop oligonucleotide is cleaved at the U residues, liberating a free 5′ end capable of being ligated to the 3′ end of the same DNA strand. Meanwhile, the U residues in the hairpin DNA strand of the other UnFold probe are cleaved presenting a single-stranded template for the enzymatic joining of the ends of the strand on the first UnFold probe. (iii) A DNA ligase is added to form DNA circles in the two variants of in situ PLA. (iv) Finally, <t>phi29</t> DNA polymerase is added to initiate RCA primed by oligonucleotides on one of the antibodies, and fluorescent oligonucleotides are used to visualize the RCA products.
    Phi29 Dna Polymerase Reaction Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi29 dna polymerase reaction buffer/product/Thermo Fisher
    Average 99 stars, based on 25 article reviews
    Price from $9.99 to $1999.99
    phi29 dna polymerase reaction buffer - by Bioz Stars, 2020-10
    99/100 stars
      Buy from Supplier

    91
    Monserate Biotechnology Group phi29 dna polymerase reaction buffer
    Schematic illustration of in situ PLA using conventional and UnFold probes. ( a ) Conventional in situ PLA. ( b ) In situ PLA using UnFold probes. (i) After pairs of primary antibodies have bound a pair of interacting proteins (red and green) followed by washes, secondary conventional or UnFold in situ PLA probes are added, followed after an incubation by renewed washes. (ii) In the conventional design under ( a ) two more oligonucleotides are then added that can form a DNA circle. Using the UnFold design in ( b ) the probe carrying a hairpin-loop oligonucleotide is cleaved at the U residues, liberating a free 5′ end capable of being ligated to the 3′ end of the same DNA strand. Meanwhile, the U residues in the hairpin DNA strand of the other UnFold probe are cleaved presenting a single-stranded template for the enzymatic joining of the ends of the strand on the first UnFold probe. (iii) A DNA ligase is added to form DNA circles in the two variants of in situ PLA. (iv) Finally, <t>phi29</t> DNA polymerase is added to initiate RCA primed by oligonucleotides on one of the antibodies, and fluorescent oligonucleotides are used to visualize the RCA products.
    Phi29 Dna Polymerase Reaction Buffer, supplied by Monserate Biotechnology Group, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phi29 dna polymerase reaction buffer/product/Monserate Biotechnology Group
    Average 91 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    phi29 dna polymerase reaction buffer - by Bioz Stars, 2020-10
    91/100 stars
      Buy from Supplier

    Image Search Results


    Plasmid DNA from the cecal sample after amplification with phi29 polymerase. 1 , 1 kb ladder and 2 , Plasmid DNA amplified with Phi29 DNA polymerase.

    Journal: Frontiers in Microbiology

    Article Title: A Comparison of Methods for the Extraction of Plasmids Capable of Conferring Antibiotic Resistance in a Human Pathogen From Complex Broiler Cecal Samples

    doi: 10.3389/fmicb.2018.01731

    Figure Lengend Snippet: Plasmid DNA from the cecal sample after amplification with phi29 polymerase. 1 , 1 kb ladder and 2 , Plasmid DNA amplified with Phi29 DNA polymerase.

    Article Snippet: Plasmid DNA was amplified by adding 1 μL of 10 μM Exo-Resistant Random Primer (Thermo Scientific), 2 μL phi29 DNA Polymerase Reaction Buffer (New England Biolabs) and 8.2 μL of MilliQ water to 5 μL of the purified treated DNA.

    Techniques: Plasmid Preparation, Amplification

    Digested plasmid DNA extracted from E. coli transformants after electroporation with the phi29 polymerase amplified DNA. 1 , 1 kb ladder; Plasmid DNA extracted from transformants selected on agar plates containing; 2 , ampicillin 32 mg/L (M_Amp_BC); 3 , ampicillin 32 mg/L (M_Amp_SC); 4 , tetracycline 16 mg/L (M_Tet_BC); 5 , tetracycline 16 mg/L (M_Tet_SC); 6 , kanamycin 25 mg/L (M_Kan); 7 , ciprofloxacin 16 mg/L (M_Cip). BC and SC refer to the two different colony morphology types, big or small colonies, on the same antibiotic plate.

    Journal: Frontiers in Microbiology

    Article Title: A Comparison of Methods for the Extraction of Plasmids Capable of Conferring Antibiotic Resistance in a Human Pathogen From Complex Broiler Cecal Samples

    doi: 10.3389/fmicb.2018.01731

    Figure Lengend Snippet: Digested plasmid DNA extracted from E. coli transformants after electroporation with the phi29 polymerase amplified DNA. 1 , 1 kb ladder; Plasmid DNA extracted from transformants selected on agar plates containing; 2 , ampicillin 32 mg/L (M_Amp_BC); 3 , ampicillin 32 mg/L (M_Amp_SC); 4 , tetracycline 16 mg/L (M_Tet_BC); 5 , tetracycline 16 mg/L (M_Tet_SC); 6 , kanamycin 25 mg/L (M_Kan); 7 , ciprofloxacin 16 mg/L (M_Cip). BC and SC refer to the two different colony morphology types, big or small colonies, on the same antibiotic plate.

    Article Snippet: Plasmid DNA was amplified by adding 1 μL of 10 μM Exo-Resistant Random Primer (Thermo Scientific), 2 μL phi29 DNA Polymerase Reaction Buffer (New England Biolabs) and 8.2 μL of MilliQ water to 5 μL of the purified treated DNA.

    Techniques: Plasmid Preparation, Electroporation, Amplification

    Effect of RNA substitutions in circular templates on rolling circle amplification with phi29 DNA polymerase. ( A ) Total amount of RCA products (y-axis) generated for padlock probes with/without a terminal 3′ RNA and in the absence of synthetic RNA ligation template (template -). ( B ) Circles with 0–7 RNA substitutions in the backbone were amplified and digitally counted. The y-axis shows the number of rolling circle products (RCPs); error bars ± S.D.; n = 2. The same RCA reactions with chimeric circles were also monitored in real-time by measuring SYBR Gold incorporation on qPCR instrument ( C and E ). (C) RCA reaction curves of circles with 0, 1 and 2 RNA substitutions. ( D ) RCPs from C were imaged on microscope slides and size and intensity of individual RCPs were quantified. Black line, median; upper whisker, highest value that is within 1.5 the interquartile range of the hinge; lower whisker, lowest value within 1.5 the interquartile range of the hinge. (E) Real-time data of the same RCA reactions as in B with 0–7 RNA substitutes are displayed. Representative samples are presented from a duplicated experiment. To highlight the initial stages of RCA and to show the difference between the samples with low RCA efficiency, fluorescence intensity readout between 3000 and 6000 is presented.

    Journal: Nucleic Acids Research

    Article Title: Limited reverse transcriptase activity of phi29 DNA polymerase

    doi: 10.1093/nar/gky190

    Figure Lengend Snippet: Effect of RNA substitutions in circular templates on rolling circle amplification with phi29 DNA polymerase. ( A ) Total amount of RCA products (y-axis) generated for padlock probes with/without a terminal 3′ RNA and in the absence of synthetic RNA ligation template (template -). ( B ) Circles with 0–7 RNA substitutions in the backbone were amplified and digitally counted. The y-axis shows the number of rolling circle products (RCPs); error bars ± S.D.; n = 2. The same RCA reactions with chimeric circles were also monitored in real-time by measuring SYBR Gold incorporation on qPCR instrument ( C and E ). (C) RCA reaction curves of circles with 0, 1 and 2 RNA substitutions. ( D ) RCPs from C were imaged on microscope slides and size and intensity of individual RCPs were quantified. Black line, median; upper whisker, highest value that is within 1.5 the interquartile range of the hinge; lower whisker, lowest value within 1.5 the interquartile range of the hinge. (E) Real-time data of the same RCA reactions as in B with 0–7 RNA substitutes are displayed. Representative samples are presented from a duplicated experiment. To highlight the initial stages of RCA and to show the difference between the samples with low RCA efficiency, fluorescence intensity readout between 3000 and 6000 is presented.

    Article Snippet: Next, RCA products were digested with AluI restriction enzyme in a reaction mixture containing 1 × phi29 DNA polymerase buffer, 0.2 μg/μl BSA, 100 nM restriction oligonucleotide , 120 mU/μl AluI (NEB) and RCA products at a final concentration of 10 pM during 10 min incubation at 37°C.

    Techniques: Amplification, Generated, Ligation, Real-time Polymerase Chain Reaction, Microscopy, Whisker Assay, Fluorescence

    Phi29 DNA polymerase exhibits higher RCA rate with circles containing pyrimidine RNA substitutions. ( A ) Real-time RCA curves of circles containing 1, 2, 3 or 4 consecutive RNA substations of rG, rU, rA, rC RNA bases are displayed (number of consecutive substitutions is indicated above plots). Rate of RCA was monitored by measuring fluorescence build-up (y-axis) resulted from SYBR Gold incorporation into RCPs. Averaged fluorescence intensity for each RCA time point was calculated from a duplicated experiment. RCA was conducted in the presence of Mg 2+ and Mn 2+ (solid and dashed lines respectively). ( B ) Linear, early stage RCA velocity (y-axis) is presented for PLPs from (A) in the presence of Mg 2+ (solid lines) and Mn 2+ (dashed lines). ( C ) RCA for the control PLP (non-chimeric DNA circle, with Mg 2+ (solid) and Mn 2+ (dashed line) are displayed.

    Journal: Nucleic Acids Research

    Article Title: Limited reverse transcriptase activity of phi29 DNA polymerase

    doi: 10.1093/nar/gky190

    Figure Lengend Snippet: Phi29 DNA polymerase exhibits higher RCA rate with circles containing pyrimidine RNA substitutions. ( A ) Real-time RCA curves of circles containing 1, 2, 3 or 4 consecutive RNA substations of rG, rU, rA, rC RNA bases are displayed (number of consecutive substitutions is indicated above plots). Rate of RCA was monitored by measuring fluorescence build-up (y-axis) resulted from SYBR Gold incorporation into RCPs. Averaged fluorescence intensity for each RCA time point was calculated from a duplicated experiment. RCA was conducted in the presence of Mg 2+ and Mn 2+ (solid and dashed lines respectively). ( B ) Linear, early stage RCA velocity (y-axis) is presented for PLPs from (A) in the presence of Mg 2+ (solid lines) and Mn 2+ (dashed lines). ( C ) RCA for the control PLP (non-chimeric DNA circle, with Mg 2+ (solid) and Mn 2+ (dashed line) are displayed.

    Article Snippet: Next, RCA products were digested with AluI restriction enzyme in a reaction mixture containing 1 × phi29 DNA polymerase buffer, 0.2 μg/μl BSA, 100 nM restriction oligonucleotide , 120 mU/μl AluI (NEB) and RCA products at a final concentration of 10 pM during 10 min incubation at 37°C.

    Techniques: Fluorescence, Plasmid Purification

    DNA sequencing-based analysis of rolling circle products reveals reverse transcription activity of phi29 DNA polymerase. ( A ) After RCA, short DNA oligonucleotides were hybridized to an AluI restriction site in the RCA products and RCPs were digested with AluI restriction enzyme, resulting in RCA monomers. Following digestion, monomers were PCR-amplified using primers containing Ilumina adapter sequences. PCR products were extended using IIlumina indexed primers. Finally, sequencing library was prepared using indexed primers-specific P5/7 PCR primers. The region of interest containing RNA substitutions in the original padlock probe sequence is indicated with green boxes. ( B ) Logos showing sequencing frequencies for each position within RCA monomers generated from the control DNA circle (P1 = dG), and circles containing single rG, rU, rA and rC substitutions at the RNA position (P1). Positions P1 and P2 are indicated and position P1 was additionally highlighted with the red box. ( C ) Incorporation of incorrect nucleotides for every position in the sequenced monomers from (B). Error rates, calculated as Incorporation error [%] = 1 – number of reads with expected nucleotide/total number of reads, is presented for padlock probes with single- (upper plot) and double-RNA substitutions (lower plots). P1 position for the first RNA substitution is indicated with the box.

    Journal: Nucleic Acids Research

    Article Title: Limited reverse transcriptase activity of phi29 DNA polymerase

    doi: 10.1093/nar/gky190

    Figure Lengend Snippet: DNA sequencing-based analysis of rolling circle products reveals reverse transcription activity of phi29 DNA polymerase. ( A ) After RCA, short DNA oligonucleotides were hybridized to an AluI restriction site in the RCA products and RCPs were digested with AluI restriction enzyme, resulting in RCA monomers. Following digestion, monomers were PCR-amplified using primers containing Ilumina adapter sequences. PCR products were extended using IIlumina indexed primers. Finally, sequencing library was prepared using indexed primers-specific P5/7 PCR primers. The region of interest containing RNA substitutions in the original padlock probe sequence is indicated with green boxes. ( B ) Logos showing sequencing frequencies for each position within RCA monomers generated from the control DNA circle (P1 = dG), and circles containing single rG, rU, rA and rC substitutions at the RNA position (P1). Positions P1 and P2 are indicated and position P1 was additionally highlighted with the red box. ( C ) Incorporation of incorrect nucleotides for every position in the sequenced monomers from (B). Error rates, calculated as Incorporation error [%] = 1 – number of reads with expected nucleotide/total number of reads, is presented for padlock probes with single- (upper plot) and double-RNA substitutions (lower plots). P1 position for the first RNA substitution is indicated with the box.

    Article Snippet: Next, RCA products were digested with AluI restriction enzyme in a reaction mixture containing 1 × phi29 DNA polymerase buffer, 0.2 μg/μl BSA, 100 nM restriction oligonucleotide , 120 mU/μl AluI (NEB) and RCA products at a final concentration of 10 pM during 10 min incubation at 37°C.

    Techniques: DNA Sequencing, Activity Assay, Polymerase Chain Reaction, Amplification, Sequencing, Generated

    SNES method and WGA quality control. (a) Nuclear suspensions were prepared from tissues, stained with DAPI and flow-sorted. Single nuclei were isolated by gating the G1/0 or G2/M ploidy distributions and deposited nuclei singly into a 96-well plate. Multiple-displacement-amplification is performed using Φ29 to perform WGA. (b) Time-course of WGA showing total DNA yield from single nuclei. (c) Quality control assay using a panel of 22 chromosome-specific qPCR primers to determine the WGA amplification efficiency of each single nucleus.

    Journal: Genome Biology

    Article Title: SNES: single nucleus exome sequencing

    doi: 10.1186/s13059-015-0616-2

    Figure Lengend Snippet: SNES method and WGA quality control. (a) Nuclear suspensions were prepared from tissues, stained with DAPI and flow-sorted. Single nuclei were isolated by gating the G1/0 or G2/M ploidy distributions and deposited nuclei singly into a 96-well plate. Multiple-displacement-amplification is performed using Φ29 to perform WGA. (b) Time-course of WGA showing total DNA yield from single nuclei. (c) Quality control assay using a panel of 22 chromosome-specific qPCR primers to determine the WGA amplification efficiency of each single nucleus.

    Article Snippet: Whole-genome amplification by time-limited multiple-displacement amplification Whole-genome amplification was performed on single flow-sorted nuclei using 10 units of Φ29 polymerase and 10× Φ29 buffer (NEB cat#M0269L), 1 mM dNTP (GE Healthcare, cat#28-4065-51), and 50 μM random hexamer (phosphorothioate modification on the two 3’-terminal nucleotide - NNNN*N*N - synthesized by Sigma Aldrich) to each well.

    Techniques: Whole Genome Amplification, Staining, Flow Cytometry, Isolation, Multiple Displacement Amplification, Control Assay, Real-time Polymerase Chain Reaction, Amplification

    Schematic illustration of in situ PLA using conventional and UnFold probes. ( a ) Conventional in situ PLA. ( b ) In situ PLA using UnFold probes. (i) After pairs of primary antibodies have bound a pair of interacting proteins (red and green) followed by washes, secondary conventional or UnFold in situ PLA probes are added, followed after an incubation by renewed washes. (ii) In the conventional design under ( a ) two more oligonucleotides are then added that can form a DNA circle. Using the UnFold design in ( b ) the probe carrying a hairpin-loop oligonucleotide is cleaved at the U residues, liberating a free 5′ end capable of being ligated to the 3′ end of the same DNA strand. Meanwhile, the U residues in the hairpin DNA strand of the other UnFold probe are cleaved presenting a single-stranded template for the enzymatic joining of the ends of the strand on the first UnFold probe. (iii) A DNA ligase is added to form DNA circles in the two variants of in situ PLA. (iv) Finally, phi29 DNA polymerase is added to initiate RCA primed by oligonucleotides on one of the antibodies, and fluorescent oligonucleotides are used to visualize the RCA products.

    Journal: Scientific Reports

    Article Title: Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes

    doi: 10.1038/s41598-018-23582-1

    Figure Lengend Snippet: Schematic illustration of in situ PLA using conventional and UnFold probes. ( a ) Conventional in situ PLA. ( b ) In situ PLA using UnFold probes. (i) After pairs of primary antibodies have bound a pair of interacting proteins (red and green) followed by washes, secondary conventional or UnFold in situ PLA probes are added, followed after an incubation by renewed washes. (ii) In the conventional design under ( a ) two more oligonucleotides are then added that can form a DNA circle. Using the UnFold design in ( b ) the probe carrying a hairpin-loop oligonucleotide is cleaved at the U residues, liberating a free 5′ end capable of being ligated to the 3′ end of the same DNA strand. Meanwhile, the U residues in the hairpin DNA strand of the other UnFold probe are cleaved presenting a single-stranded template for the enzymatic joining of the ends of the strand on the first UnFold probe. (iii) A DNA ligase is added to form DNA circles in the two variants of in situ PLA. (iv) Finally, phi29 DNA polymerase is added to initiate RCA primed by oligonucleotides on one of the antibodies, and fluorescent oligonucleotides are used to visualize the RCA products.

    Article Snippet: The slides were then washed twice in TBS-T for 3 min. Circularization oligonucleotides for the two probe designs were ligated using 0.02 U/µl T4 DNA ligase (Thermo Scientific) in T4 DNA ligase buffer supplemented with 0.25 mg/ml BSA for 30 min at 37 °C, thereafter the slides were washed twice for 3 min in TBS-T. RCA was performed by addition of 0.5 U/µl phi29 polymerase (Thermo scientific) in phi29 polymerase buffer (Thermo Scientific) supplemented with 7.5 ng/ml PolyA (Sigma-Aldrich), 0.25 mM dNTP and 0.25 mg/ml BSA for 60 min at 37 °C, followed by two 3 min washes in TBS-T.

    Techniques: In Situ, Proximity Ligation Assay, Incubation