phi29 (New England Biolabs)


Name:
phi29 DNA Polymerase
Description:
phi29 DNA Polymerase 1 250 units
Catalog Number:
m0269l
Price:
228
Category:
DNA Polymerases
Size:
1 250 units
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Structured Review

phi29 DNA Polymerase 1 250 units
https://www.bioz.com/result/phi29/product/New England Biolabs
Average 98 stars, based on 1 article reviews
Price from $9.99 to $1999.99
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1) Product Images from "High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing"
Article Title: High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing
Journal: Nucleic Acids Research
doi: 10.1093/nar/gky296
![... D ) AMV RT and ( E ) Phi29 copying in ‘T’, ‘A’, ‘C’ and ‘G’ template ... DNA polymerase error preferences. Heat maps reflect nucleotide substitution and single nucleotide deletion preferences of ( A ) Dpo4, ( B ) Taq, ( C ) Sequenase 2.0, ( D ) AMV RT and ( E ) Phi29 copying in ‘T’, ‘A’, ‘C’ and ‘G’ template contexts. Error fraction was determined by normalizing individual error subtype frequencies to the total error rate measured at the lowest [dRTP] tested (10 −7 μM) for each template context. Values are the average of two experiments.](https://storage.googleapis.com/bioz_article_images/PMC6061839/gky296fig5.jpg)
Figure Legend Snippet: DNA polymerase error preferences. Heat maps reflect nucleotide substitution and single nucleotide deletion preferences of ( A ) Dpo4, ( B ) Taq, ( C ) Sequenase 2.0, ( D ) AMV RT and ( E ) Phi29 copying in ‘T’, ‘A’, ‘C’ and ‘G’ template contexts. Error fraction was determined by normalizing individual error subtype frequencies to the total error rate measured at the lowest [dRTP] tested (10 −7 μM) for each template context. Values are the average of two experiments.
Techniques Used:
![... dose response curves of Sequenase 2.0, AMV RT, Phi29, Dpo4 and Taq copying in ‘T’ template contexts. ... MagNIFi assay validation. ( A ) Fidelity dose response curves of Sequenase 2.0, AMV RT, Phi29, Dpo4 and Taq copying in ‘T’ template contexts. Values are the average of two experiments. Standard deviation error bars ( n = 2) are smaller than data points. Curves show qualitative agreement between DNA polymerase FC 50 values (indicated by black dotted line) and the expected rank order of natural DNA polymerase error rates ( Supplementary Table S4 ). In general, fidelity increases from right to left. ( B ) Calibration between error rate and [FC 50 ]. We show a calibration curve relating multiple reported error rates per DNA polymerase ( Supplementary Table S4 ) and the average FC 50 value of each DNA polymerase ( Supplementary Table S3 ). Nonlinear fitting on a log–log plot (line of best fit in grey) revealed the following equation: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$y = 10^{(2.063log(x) + 1.557)}$\end{document} , RMSE = 0.0008998 errors/bp.](https://storage.googleapis.com/bioz_article_images/PMC6061839/gky296fig3.jpg)
Figure Legend Snippet: MagNIFi assay validation. ( A ) Fidelity dose response curves of Sequenase 2.0, AMV RT, Phi29, Dpo4 and Taq copying in ‘T’ template contexts. Values are the average of two experiments. Standard deviation error bars ( n = 2) are smaller than data points. Curves show qualitative agreement between DNA polymerase FC 50 values (indicated by black dotted line) and the expected rank order of natural DNA polymerase error rates ( Supplementary Table S4 ). In general, fidelity increases from right to left. ( B ) Calibration between error rate and [FC 50 ]. We show a calibration curve relating multiple reported error rates per DNA polymerase ( Supplementary Table S4 ) and the average FC 50 value of each DNA polymerase ( Supplementary Table S3 ). Nonlinear fitting on a log–log plot (line of best fit in grey) revealed the following equation: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$y = 10^{(2.063log(x) + 1.557)}$\end{document} , RMSE = 0.0008998 errors/bp.
Techniques Used: Standard Deviation

Figure Legend Snippet: Assessing MagNIFi assay potential. ( A ) Simulation of the minimum number of sequencing reads required to accurately measure different error rates. Black line denotes a CV of 15%. ( B ) Sensitivity of FC 50 values to sampling error and DNA polymerase stochasticity. Distribution of calculated FC 50 values for 1000 simulated rare base titration experiments, with each rare base condition receiving 50 simulated reads. Each condition was simulated by drawing 50 samples from a Bernoulli process with an underlying error rate equal to the experimentally derived error rate. FC 50 values were determined using the fitting procedure described in Methods. Histograms are shown for simulations based on Dpo4 (blue) and Phi29 (pink) error rates in a ‘T’ template context. ( C ) Determination of MagNIFi assay sample variability across different read counts. Error rate data collected for Dpo4 copying in all four template contexts reveal that error rate differences between 36 sets of biological replicates ( n = 2) do not vary with read count differences between the same set of biological replicates. ( D ) Resolving power of the MagNIFi assay based on FC 50 sensitivity. Minimum detectable fold change in FC 50 was determined based on the 95% confidence interval of the fitted FC 50 (see Supplementary Table S3 for values). The ratio of the Upper Bound 95% CI: Fitted FC 50 was determined for Dpo4 copying in ‘T’, ‘A’, ‘C’ and ‘G’ template contexts.
Techniques Used: Sequencing, Sampling, Titration, Derivative Assay

Figure Legend Snippet: Local sequence context effects on DNA polymerase fidelity. ( A ) The identity and position of template bases neighboring a ‘T’ EES impact the measured FC 50 of Phi29 copying in a VVVTVVV template context. Change in logFC 50 (logFC 50 _Average – logFC 50 _Fixed Template Base) was calculated for each base identity/position. Positive ΔlogFC 50 values pertain to an increase in fidelity whereas negative values signify a decrease in fidelity. ( B ) The identity and position of template bases flanking ‘C’ and ‘G’ EESs impact the % total error Phi29 creates at 10 −7 μM dRTP when copying in DDDCDDD and HHHGHHH template contexts, respectively. A gray dotted line represents the average % total error made by Phi29 in a given context. ( C ) Base identity at the +1 template position in DDDCDDD, VVVTVVV, and BBBABBB contexts impacts the distribution of Dpo4 error preferences (nucleotide substitutions and single nucleotide deletions). Error preference was determined by normalizing error subtype frequency to the total error rate measured at 10 −7 μM dRTP. For all graphs in (A)–(C), values represent the average of two experiments. Error bars signify standard deviation ( n = 2).
Techniques Used: Sequencing, Standard Deviation
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