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Добірка наукової літератури з теми "Phi29 DNA Polymerase"

Автор: Grafiati
Опубліковано: 20 жовтня 2023

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Статті в журналах з теми "Phi29 DNA Polymerase"

1

del Prado, Santos, Lázaro, Salas, and de Vega. "The Loop of the TPR1 Subdomain of Phi29 DNA Polymerase Plays a Pivotal Role in Primer-Terminus Stabilization at the Polymerization Active Site." Biomolecules 9, no. 11 (October 24, 2019): 648. http://dx.doi.org/10.3390/biom9110648.

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Анотація:
Bacteriophage Phi29 DNA polymerase belongs to the protein-primed subgroup of family B DNA polymerases that use a terminal protein (TP) as a primer to initiate genome replication. The resolution of the crystallographic structure showed that it consists of an N-terminal domain with the exonuclease activity and a C-terminal polymerization domain. It also has two subdomains specific of the protein-primed DNA polymerases; the TP Regions 1 (TPR1) that interacts with TP and DNA, and 2 (TPR2), that couples both processivity and strand displacement to the enzyme. The superimposition of the structures of the apo polymerase and the polymerase in the polymerase/TP heterodimer shows that the structural changes are restricted almost to the TPR1 loop (residues 304–314). In order to study the role of this loop in binding the DNA and the TP, we changed the residues Arg306, Arg308, Phe309, Tyr310, and Lys311 into alanine, and also made the deletion mutant Δ6 lacking residues Arg306–Lys311. The results show a defective TP binding capacity in mutants R306A, F309A, Y310A, and Δ6. The additional impaired primer-terminus stabilization at the polymerization active site in mutants Y310A and Δ6 allows us to propose a role for the Phi29 DNA polymerase TPR1 loop in the proper positioning of the DNA and TP-priming 3’-OH termini at the preinsertion site of the polymerase to enable efficient initiation and further elongation steps during Phi29 TP-DNA replication.
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2

Sakatani, Yoshihiro, Ryo Mizuuchi, and Norikazu Ichihashi. "In vitro evolution of phi29 DNA polymerases through compartmentalized gene expression and rolling-circle replication." Protein Engineering, Design and Selection 32, no. 11 (November 2019): 481–87. http://dx.doi.org/10.1093/protein/gzaa011.

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Abstract Phi29 DNA polymerase is widely used for DNA amplification through rolling-circle replication or multiple displacement amplification. Here, we performed completely in vitro artificial evolution of phi29 DNA polymerase by combining the in vitro compartmentalization and the gene expression-coupled rolling-circle replication of a circular DNA encoding the polymerase. We conducted the experiments in six different conditions composed of three different levels of inhibitor concentrations with two different DNA labeling methods. One of the experiments was performed in our previous study and the other five experiments were newly conducted in this study. Under all conditions, we found several mutations that enhance the rolling-circle amplification by the polymerase when it was expressed in the reconstituted gene expression system. Especially, a combinatorial mutant polymerase (K555T/D570N) exhibits significantly higher rolling-circle activity than the wild type. These highly active mutant polymerases would be useful for various applications.
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3

Kamtekar, Satwik. "Phi29 DNA polymerase: structure and sequencing." Acta Crystallographica Section A Foundations and Advances 75, a1 (July 20, 2019): a139. http://dx.doi.org/10.1107/s010876731909860x.

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4

Krzywkowski, Tomasz, Malte Kühnemund, Di Wu, and Mats Nilsson. "Limited reverse transcriptase activity of phi29 DNA polymerase." Nucleic Acids Research 46, no. 7 (March 15, 2018): 3625–32. http://dx.doi.org/10.1093/nar/gky190.

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5

Tenaglia, Enrico, Yuki Imaizumi, Yuji Miyahara, and Carlotta Guiducci. "Isothermal multiple displacement amplification of DNA templates in minimally buffered conditions using phi29 polymerase." Chemical Communications 54, no. 17 (2018): 2158–61. http://dx.doi.org/10.1039/c7cc09609g.

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6

Torres, Leticia L., and Vitor B. Pinheiro. "Xenobiotic Nucleic Acid (XNA) Synthesis by Phi29 DNA Polymerase." Current Protocols in Chemical Biology 10, no. 2 (May 18, 2018): e41. http://dx.doi.org/10.1002/cpch.41.

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7

Li, Shasha, Su Liu, Yicheng Xu, Rufeng Zhang, Yihan Zhao, Xiaonan Qu, Yu Wang, Jiadong Huang, and Jinghua Yu. "Robust and highly specific fluorescence sensing of Salmonella typhimurium based on dual-functional phi29 DNA polymerase-mediated isothermal circular strand displacement polymerization." Analyst 144, no. 16 (2019): 4795–802. http://dx.doi.org/10.1039/c9an00843h.

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A simple and robust fluorescence sensing strategy has been developed for the detection of pathogenic bacteria by the combination of the dual functionality of phi29 DNA polymerase with isothermal circular strand displacement polymerization (ICSDP).
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8

Xu, Yun, Simon Gao, John F. Bruno, Benjamin J. Luft, and John J. Dunn. "Rapid detection and identification of a pathogen’s DNA using Phi29 DNA polymerase." Biochemical and Biophysical Research Communications 375, no. 4 (October 2008): 522–25. http://dx.doi.org/10.1016/j.bbrc.2008.08.082.

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9

Johne, Reimar, Hermann Müller, Annabel Rector, Marc van Ranst, and Hans Stevens. "Rolling-circle amplification of viral DNA genomes using phi29 polymerase." Trends in Microbiology 17, no. 5 (May 2009): 205–11. http://dx.doi.org/10.1016/j.tim.2009.02.004.

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10

Kesici, Merve-Zeynep, Philip Tinnefeld, and Andrés Manuel Vera. "A simple and general approach to generate photoactivatable DNA processing enzymes." Nucleic Acids Research 50, no. 6 (December 14, 2021): e31-e31. http://dx.doi.org/10.1093/nar/gkab1212.

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Abstract DNA processing enzymes, such as DNA polymerases and endonucleases, have found many applications in biotechnology, molecular diagnostics, and synthetic biology, among others. The development of enzymes with controllable activity, such as hot-start or light-activatable versions, has boosted their applications and improved the sensitivity and specificity of the existing ones. However, current approaches to produce controllable enzymes are experimentally demanding to develop and case-specific. Here, we introduce a simple and general method to design light-start DNA processing enzymes. In order to prove its versatility, we applied our method to three DNA polymerases commonly used in biotechnology, including the Phi29 (mesophilic), Taq, and Pfu polymerases, and one restriction enzyme. Light-start enzymes showed suppressed polymerase, exonuclease, and endonuclease activity until they were re-activated by an UV pulse. Finally, we applied our enzymes to common molecular biology assays and showed comparable performance to commercial hot-start enzymes.
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Більше джерел

Дисертації з теми "Phi29 DNA Polymerase"

1

Muharam, Firman Alamsyah. "Overcoming problems with limiting DNA samples in forensics and clinical diagnostics using multiple displacement amplification." Thesis, Queensland University of Technology, 2006. https://eprints.qut.edu.au/16207/1/Firman_Muharam_Thesis.pdf.

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The availability of DNA samples that are of adequate quality and quantity is essential for any genetic analysis. The fields of forensic biology and clinical diagnostic pathology testing often suffer from limited samples that yield insufficient DNA material to allow extensive analysis. This study examined the utility of a recently introduced whole genome amplification method termed Multiple Displacement Amplification (MDA) for amplifying a variety of limited sample types that are commonly encountered in the fields of forensic biology and clinical diagnostics. The MDA reaction, which employs the highly processive bacteriophage φ29 DNA polymerase, was found to generate high molecular weight template DNA suitable for a variety of downstream applications from low copy number DNA samples down to the single genome level. MDA of single cells yielded sufficient DNA for up to 20,000,000 PCR assays, allowing further confirmatory testing on samples of limited quantities or the archiving of precious DNA material for future work. The amplification of degraded DNA material using MDA identified a requirement for samples of sufficient quality to allow successful synthesis of product DNA templates. Furthermore, the utility of MDA products in comparative genomic hybridisation (CGH) assays identified the presence of amplification bias. However, this bias was overcome by introducing a novel modification to the MDA protocol. Future directions for this work include investigations into the utility of MDA products in short tandem repeat (STR) assays for human identifications and application of the modified MDA protocol for testing of single cell samples for genetic abnormalities.
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2

Muharam, Firman Alamsyah. "Overcoming problems with limiting DNA samples in forensics and clinical diagnostics using multiple displacement amplification." Queensland University of Technology, 2006. http://eprints.qut.edu.au/16207/.

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Анотація:
The availability of DNA samples that are of adequate quality and quantity is essential for any genetic analysis. The fields of forensic biology and clinical diagnostic pathology testing often suffer from limited samples that yield insufficient DNA material to allow extensive analysis. This study examined the utility of a recently introduced whole genome amplification method termed Multiple Displacement Amplification (MDA) for amplifying a variety of limited sample types that are commonly encountered in the fields of forensic biology and clinical diagnostics. The MDA reaction, which employs the highly processive bacteriophage φ29 DNA polymerase, was found to generate high molecular weight template DNA suitable for a variety of downstream applications from low copy number DNA samples down to the single genome level. MDA of single cells yielded sufficient DNA for up to 20,000,000 PCR assays, allowing further confirmatory testing on samples of limited quantities or the archiving of precious DNA material for future work. The amplification of degraded DNA material using MDA identified a requirement for samples of sufficient quality to allow successful synthesis of product DNA templates. Furthermore, the utility of MDA products in comparative genomic hybridisation (CGH) assays identified the presence of amplification bias. However, this bias was overcome by introducing a novel modification to the MDA protocol. Future directions for this work include investigations into the utility of MDA products in short tandem repeat (STR) assays for human identifications and application of the modified MDA protocol for testing of single cell samples for genetic abnormalities.
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3

Zahoransky, Viktor Wendelin. "Information Transmission Across Generations : Thermodynamics and Evolutionary Implications." Electronic Thesis or Diss., Université Paris sciences et lettres, 2023. http://www.theses.fr/2023UPSLS012.

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Анотація:
La Phi29 ADN polymérase (DNAP) dérive du bactériophage Phi29 et réplique l'ADN dans des conditions isothermes par amplification en cercle roulant. Il s'agit d'une enzyme particulièrement intéressante en raison de son exceptionnelle processivité et de son faible taux d'erreur, de l'ordre d'une paire de bases mésapparente pour chaque 10^(-5) à 10^(-6) nucléotides incorporés. La Phi29 DNAP atteint cette haute fidélité grâce à une fonction catalytique supplémentaire: La capacité à corriger les erreurs d'incorporation de bases par excision de nucléotides. Malgré les nombreuses études qui ont déjà été menées sur cette enzyme, la coordination entre ses principales fonctions catalytiques, la synthèse de l'ADN et la correction des erreurs, n'est pas entièrement comprise. Dans ce travail, nous développons plusieurs essais massivement parallélisés et à très haut débit, basés sur de grandes bibliothèques de gènes (10^(6)), afin de tester et de cribler les variants de la Phi29 DNAP dans un contexte évolutif. Pour la première fois, une technique d'émulsification membranaire est adaptée aux réactions d'auto-réplication compartimentée isotherme in vitro (iviCSR) facilitant le criblage simultané de variants dans différentes conditions environnementales. Nous avons trouvé des preuves que le variant R223T de la Phi29 DNAP peut répliquer l'ADN de manière plus progressive que l'enzyme WT dans des conditions éprouvantes et que la position de l'acide aminé 223 contribue à la coordination du compromis activité-fidélité de l'enzyme
Phi29 DNA polymerase (DNAP) derives from bacteriophage Phi29 and replicates DNA under isothermal conditions by rolling circle amplification. It is a particularly interesting enzyme due to its outstanding processivity and low error rates in the range of one base-pair mismatch for every 10^(-5) to 10^(-6) nucleotides incorporated. Phi29 DNAP achieves such high fidelity by means of an additional catalytic function: The ability to correct for base misincorporations by nucleotide excision. Despite the many studies that have already been conducted on this enzyme, the coordination between its main catalytic functions, DNA synthesis and error correction, is not fully understood.In this work we develop several massively parallelised, ultra-high-throughput assays, based on large (10^(6)) gene libraries, to challenge and screen for Phi29 DNAP variants in an evolutionary setting. For the first time, a membrane emulsification technique is adapted to in vitro isothermal compartmentalised self-replication (iviCSR) reactions facilitating simultaneous screenings of variants in different environmental conditions. We found evidence that Phi29 DNAP variant R223T can replicate DNA more processively than the WT enzyme under challenging conditions and that amino acid position 223 contributes to the coordination of the enzyme's activity-fidelity trade-off
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4

Schoenborn, Veit. "Whole Genome Amplification von Plasma-DNA und Entwicklung eines Ausschlusskriteriums zur Verbesserung der Genotypisierungsqualität." Doctoral thesis, 2008. https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-37136.

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Plasma- und Serumproben waren in früheren epidemiologischen Studien häufig das einzige biologische Material, das gesammelt und untersucht wurde. Diese Studien besitzen gerade durch ihren sehr langen Untersuchungszeitraum einen riesigen Informationsgehalt und wären ein unbezahlbarer Schatz für genetische Analysen. Oft ist aufgrund damals mangelnder Akquirierung jedoch keine genomische DNA verfügbar. Um die in Plasmaproben in geringer Menge vorkommende DNA verwenden zu können, extrahierten wir die DNA mit Hilfe von magnetischen Partikeln und setzten sie in eine Whole Genome Amplification (WGA) mittels Φ29-DNA-Polymerase ein. Wir stellten 88 Probenpärchen, bestehend aus einer WGA-Plasma-DNA und der korrespondierenden Vollblut-DNA derselben Person, zusammen und genotypisierten bei diesen neun hochpolymorphe Short Tandem Repeats (STR) und 25 SNPs. Die durchschnittliche innerhalb der Probenpaare auftretende Diskordanzrate betrug 3,8% für SNPs sowie 15,9% für STRs. Basierend auf den Ergebnissen der Hälfte der Probenpaare entwickelten wir einen Ausschlussalgorithmus und validierten diesen in der anderen Hälfte der Probenpaare. Mit diesem ist es möglich, zum Einen diejenigen Proben mit einer guten DNA-Qualität herauszufiltern, um Genotypisierungsfehler zu vermeiden, und zum Anderen jene Proben mit insuffizienter DNA-Qualität auszuschließen. Nachdem Proben, die fünf oder mehr homozygote Loci in dem 9-STR-Markerset aufwiesen, ausgeschlossen wurden, resultierte dies in einer Ausschlussrate von 22,7% und senkte die durchschnittliche Diskordanzrate auf 3,92% für STRs bzw. 0,63% für SNPs. Bei SNPs entspricht dieser Wert ungefähr der Fehlerquote, wie er auch bei Genotypisierungen mit Vollblut-DNA in vielen Laboratorien auftritt. Unsere Methode und das Ausschlusskriterium bieten damit neue Möglichkeiten, um zuverlässige DNA aus archivierten Plasmaproben wiederzugewinnen. Dieser Algorithmus ist auch besser geeignet, als nur die eingesetzte DNA-Menge in die WGA-Reaktion als Kriterium zu benützen
Plasma and serum samples were often the only biological material collected for earlier epidemiological studies. These studies have a huge informative content, especially due to their long follow-up and would be an invaluable treasure for genetic investigations. However, often no banked DNA is available. To use the small amounts of DNA present in plasma, in a first step, we applied magnetic bead technology to extract this DNA, followed by a whole-genome amplification (WGA) using phi29-polymerase. We assembled 88 sample pairs, each consisting of WGA plasma DNA and the corresponding whole-blood DNA. We genotyped nine highly polymorphic short tandem repeats (STRs) and 23 SNPs in both DNA sources. The average within-pair discordance was 3.8% for SNPs and 15.9% for STR genotypes, respectively. We developed an algorithm based on one-half of the sample pairs and validated on the other one-half to identify the samples with high WGA plasma DNA quality to assure low genotyping error and to exclude plasma DNA samples with insufficient quality: excluding samples showing homozygosity at five or more of the nine STR loci yielded exclusion of 22.7% of all samples and decreased average discordance for STR and SNP markers to 3.92% and 0.63%, respectively. For SNPs, this is very close to the error observed for genomic DNA in many laboratories. Our workflow and sample selection algorithm offers new opportunities to recover reliable DNA from stored plasma material. This algorithm is superior to testing the amount of input DNA
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Частини книг з теми "Phi29 DNA Polymerase"

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Kroneis, Thomas, and Amin El-Heliebi. "Whole Genome Amplification by Isothermal Multiple Strand Displacement Using Phi29 DNA Polymerase." In Whole Genome Amplification, 111–17. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2990-0_8.

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2

Silander, Kaisa, and Janna Saarela. "Whole Genome Amplification with Phi29 DNA Polymerase to Enable Genetic or Genomic Analysis of Samples of Low DNA Yield." In Methods in Molecular Biology, 1–18. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-188-8_1.

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3

del Prado, Alicia, and Margarita Salas. "Strand Displacement and Unwinding Assays to Study the Concerted Action of the DNA Polymerase and SSB During Phi29 TP-DNA Replication." In Methods in Molecular Biology, 333–42. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1290-3_22.

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