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Journal articles on the topic 'Phi29 DNA Polymerase'

Author: Grafiati

Published: 20 October 2023

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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 (2019): 648. http://dx.doi.org/10.3390/biom9110648.

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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 o

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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 (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 t

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3

Kamtekar, Satwik. "Phi29 DNA polymerase: structure and sequencing." Acta Crystallographica Section A Foundations and Advances 75, a1 (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 (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 (2018): e41. http://dx.doi.org/10.1002/cpch.41.

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7

Li, Shasha, Su Liu, Yicheng Xu, et al. "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 (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 (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 (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

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11

Lieberman, Kate R., Gerald M. Cherf, Michael J. Doody, Felix Olasagasti, Yvette Kolodji, and Mark Akeson. "Processive Replication of Single DNA Molecules in a Nanopore Catalyzed by phi29 DNA Polymerase." Journal of the American Chemical Society 132, no. 50 (2010): 17961–72. http://dx.doi.org/10.1021/ja1087612.

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12

Taniguchi, R., C. Masaki, Y. Murashima, et al. "DNA amplification using phi29 DNA polymerase validates gene polymorphism analysis from buccal mucosa samples." Journal of Prosthodontic Research 55, no. 3 (2011): 165–70. http://dx.doi.org/10.1016/j.jpor.2010.12.001.

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13

Povilaitis, Tadas, Gediminas Alzbutas, Rasa Sukackaite, Juozas Siurkus, and Remigijus Skirgaila. "In vitroevolution of phi29 DNA polymerase using isothermal compartmentalized self replication technique." Protein Engineering, Design and Selection 29, no. 12 (2016): 617–28. http://dx.doi.org/10.1093/protein/gzw052.

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14

Berman, Andrea J., Satwik Kamtekar, Jessica L. Goodman, et al. "Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases." EMBO Journal 26, no. 14 (2007): 3494–505. http://dx.doi.org/10.1038/sj.emboj.7601780.

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15

Manrao, Elizabeth A., Ian M. Derrington, Andrew H. Laszlo, et al. "Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase." Nature Biotechnology 30, no. 4 (2012): 349–53. http://dx.doi.org/10.1038/nbt.2171.

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16

Dean, F. B. "Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification." Genome Research 11, no. 6 (2001): 1095–99. http://dx.doi.org/10.1101/gr.180501.

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17

Kim, Subin, and Ja Yil Lee. "Study on biophysical properties of Phi29 DNA polymerase using a novel single-molecule imaging technique DNA curtain." Biophysical Journal 122, no. 3 (2023): 356a. http://dx.doi.org/10.1016/j.bpj.2022.11.1972.

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18

Liang, Jingjing, Jiaqi Zhou, Jianxi Tan, Zefeng Wang, and Le Deng. "Aptamer-Based Fluorescent Determination of Salmonella paratyphi A Using Phi29-DNA Polymerase-Assisted Cyclic Amplification." Analytical Letters 52, no. 6 (2018): 919–31. http://dx.doi.org/10.1080/00032719.2018.1505901.

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19

Sato, M. "Repeated GenomiPhi, phi29 DNA polymerase-based rolling circle amplification, is useful for generation of large amounts of plasmid DNA." Nucleic Acids Symposium Series 48, no. 1 (2004): 147–48. http://dx.doi.org/10.1093/nass/48.1.147.

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20

Gao, Yaping, Yun He, Liyi Chen, et al. "Chimeric Phi29 DNA polymerase with helix–hairpin–helix motifs shows enhanced salt tolerance and replication performance." Microbial Biotechnology 14, no. 4 (2021): 1642–56. http://dx.doi.org/10.1111/1751-7915.13830.

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21

Lagunavicius, A., Z. Kiveryte, V. Zimbaite-Ruskuliene, T. Radzvilavicius, and A. Janulaitis. "Duality of polynucleotide substrates for Phi29 DNA polymerase: 3'->5' RNase activity of the enzyme." RNA 14, no. 3 (2008): 503–13. http://dx.doi.org/10.1261/rna.622108.

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22

Chen, Anyi, Guo-Feng Gui, Ying Zhuo, Ya-Qin Chai, Yun Xiang, and Ruo Yuan. "Signal-off Electrochemiluminescence Biosensor Based on Phi29 DNA Polymerase Mediated Strand Displacement Amplification for MicroRNA Detection." Analytical Chemistry 87, no. 12 (2015): 6328–34. http://dx.doi.org/10.1021/acs.analchem.5b01168.

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23

Niel, Christian, Leonardo Diniz-Mendes, and Sylvie Devalle. "Rolling-circle amplification of Torque teno virus (TTV) complete genomes from human and swine sera and identification of a novel swine TTV genogroup." Journal of General Virology 86, no. 5 (2005): 1343–47. http://dx.doi.org/10.1099/vir.0.80794-0.

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Multiply primed rolling-circle amplification is a novel technology that uses bacteriophage phi29 DNA polymerase to amplify circular DNA molecules, without the need for prior knowledge of their sequences. In an attempt to detect Torque teno virus (TTV), rolling-circle amplification was used to amplify DNA extracted from eight human and four pig serum samples. All samples gave high molecular weight (>30 kb) amplification products. By restriction endonuclease digestion, these products generated DNA fragments whose sizes were consistent with those of human TTV (3·8 kb) and swine TTV (Sd-TTV; 2·

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24

Wang, Yuhan, Jiaxuan Xiao, Xiaona Lin, et al. "A Self-Assembled G-Quadruplex/Hemin DNAzyme-Driven DNA Walker Strategy for Sensitive and Rapid Detection of Lead Ions Based on Rolling Circle Amplification." Biosensors 13, no. 8 (2023): 761. http://dx.doi.org/10.3390/bios13080761.

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Herein, a sensitive biosensor is constructed based on a novel rolling circle amplification (RCA) for colorimetric quantification of lead ion (Pb2+). At the detection system, GR5 DNAzymes are modified on the surface of an immunomagnetic bead, and Pb2+ is captured by the aptamer, inducing the disintegration of the GR5 DNAzyme and the release of the DNA walker. After the introduction of the template DNA, T4 DNA ligase, and phi29 DNA polymerase, an RCA is initiated for the sensitivity improvement of this method. Moreover, a G4-hemin DNAzyme is formed as a colorimetric signal, owing to its peroxide

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25

Truniger, V. "A positively charged residue of phi29 DNA polymerase, highly conserved in DNA polymerases from families A and B, is involved in binding the incoming nucleotide." Nucleic Acids Research 30, no. 7 (2002): 1483–92. http://dx.doi.org/10.1093/nar/30.7.1483.

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26

Zhu, Qiang, Ting Fang, Yijun Zhou, et al. "Effect of phi29 polymerase-based multiple strand displacement whole genome amplification on the proportion in DNA mixtures." Forensic Science International: Genetics Supplement Series 7, no. 1 (2019): 841–42. http://dx.doi.org/10.1016/j.fsigss.2019.10.197.

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27

Gadkar, Vijay, and Matthias C. Rillig. "Application of Phi29 DNA polymerase mediated whole genome amplification on single spores of arbuscular mycorrhizal (AM) fungi." FEMS Microbiology Letters 242, no. 1 (2005): 65–71. http://dx.doi.org/10.1016/j.femsle.2004.10.041.

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28

Million, Matthieu, Maxime Gaudin, Cléa Melenotte, et al. "Metagenomic Analysis of Microdissected Valvular Tissue for Etiological Diagnosis of Blood Culture–Negative Endocarditis." Clinical Infectious Diseases 70, no. 11 (2019): 2405–12. http://dx.doi.org/10.1093/cid/ciz655.

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Abstract Background Etiological diagnosis is a key to therapeutic adaptation and improved prognosis, particularly for infections such as endocarditis. In blood culture–negative endocarditis (BCNE), 22% of cases remain undiagnosed despite an updated comprehensive syndromic approach. This prompted us to develop a new diagnostic approach. Methods Eleven valves from 10 BCNE patients were analyzed using a method that combines human RNA bait-depletion with phi29 DNA polymerase-based multiple displacement amplification and shotgun DNA sequencing. An additional case in which a microbe was serendipitou

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29

Takahashi, Hirokazu, Hiroyuki Yamazaki, Satoshi Akanuma, et al. "Preparation of Phi29 DNA Polymerase Free of Amplifiable DNA Using Ethidium Monoazide, an Ultraviolet-Free Light-Emitting Diode Lamp and Trehalose." PLoS ONE 9, no. 2 (2014): e82624. http://dx.doi.org/10.1371/journal.pone.0082624.

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30

Sato, Masahiro, Masato Ohtsuka, and Yuhsuke Ohmi. "Usefulness of repeated GenomiPhi, a phi29 DNA polymerase-based rolling circle amplification kit, for generation of large amounts of plasmid DNA." Biomolecular Engineering 22, no. 4 (2005): 129–32. http://dx.doi.org/10.1016/j.bioeng.2005.05.001.

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31

de Vega, M., J. M. Lazaro, M. Salas, and L. Blanco. "Primer-terminus stabilization at the 3′-5′ exonuclease active site of phi29 DNA polymerase. Involvement of two amino acid residues highly conserved in proofreading DNA polymerases." EMBO Journal 15, no. 5 (1996): 1182–92. http://dx.doi.org/10.1002/j.1460-2075.1996.tb00457.x.

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32

Kim, Min-Soo, Eun-Jin Park, Seong Woon Roh, and Jin-Woo Bae. "Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces." Applied and Environmental Microbiology 77, no. 22 (2011): 8062–70. http://dx.doi.org/10.1128/aem.06331-11.

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ABSTRACTIn this study, we investigated the abundance and diversity of single-stranded DNA (ssDNA) viruses in fecal samples from five healthy individuals through a combination of serial filtration and CsCl gradient ultracentrifugation. Virus abundance ranged from 108to 109per gram of feces, and virus-to-bacterium ratios were much lower (less than 0.1) than those observed in aquatic environments (5 to 10). Viral DNA was extracted and randomly amplified using phi29 polymerase and analyzed through high-throughput 454 pyrosequencing. Among 400,133 sequences, an average of 86.2% viromes were previou

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33

Sakatani, Yoshihiro, Norikazu Ichihashi, and Tetsuya Yomo. "2P262 Establishment of a self-replication system using phi29 DNA polymerase(20. Origin of life & Evolution,Poster)." Seibutsu Butsuri 54, supplement1-2 (2014): S238. http://dx.doi.org/10.2142/biophys.54.s238_4.

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34

Ye, Yan, Yao Lin, Zilin Chi, et al. "Rolling circle amplification (RCA) -based biosensor system for the fluorescent detection of miR-129-2-3p miRNA." PeerJ 10 (October 24, 2022): e14257. http://dx.doi.org/10.7717/peerj.14257.

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Herein, a versatile fluorescent bioanalysis platform for sensitive and specific screening of target miRNA (miR-129-2-3p) was innovatively designed by applying target-induced rolling circle amplification (RCA) for efficient signal amplification. Specifically, miR-129-2-3p was used as a ligation template to facilitate its ligation with padlock probes, followed by an RCA reaction in the presence of phi29 DNA polymerase. The dsDNA fragments and products were stained by SYBR Green I and then detected by fluorescence spectrophotometry. As a result, miR-129-2-3p concentrations as low as 50 nM could b

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35

Wu, Bingyun, Hiroyuki Kurokochi, and Taizo Hogetsu. "Development of 12 microsatellite markers in Euptelea polyandra by a random tailed genome-walking method using Phi29 DNA polymerase." Conservation Genetics Resources 1, no. 1 (2009): 59–61. http://dx.doi.org/10.1007/s12686-009-9014-y.

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36

Taniguchi, Ryoji, Chihiro Masaki, Yuhi Murashima, et al. "Erratum to “DNA amplification using phi29 DNA polymerase validates gene polymorphism analysis from buccal mucosa samples” [J. Prosthodont. Res. 55 (2011) 165–170]." Journal of Prosthodontic Research 55, no. 4 (2011): 266. http://dx.doi.org/10.1016/j.jpor.2011.08.001.

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37

Lagunavicius, A., E. Merkiene, Z. Kiveryte, et al. "Novel application of Phi29 DNA polymerase: RNA detection and analysis in vitro and in situ by target RNA-primed RCA." RNA 15, no. 5 (2009): 765–71. http://dx.doi.org/10.1261/rna.1279909.

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38

Pan, Xinghua, Alexander Eckehart Urban, Dean Palejev, et al. "A procedure for highly specific, sensitive, and unbiased whole-genome amplification." Proceedings of the National Academy of Sciences 105, no. 40 (2008): 15499–504. http://dx.doi.org/10.1073/pnas.0808028105.

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Highly specific amplification of complex DNA pools without bias or template-independent products (TIPs) remains a challenge. We have developed a method using phi29 DNA polymerase and trehalose and optimized control of amplification to create micrograms of specific amplicons without TIPs from down to subfemtograms of DNA. With an input of as little as 0.5–2.5 ng of human gDNA or a few cells, the product could be close to native DNA in locus representation. The amplicons from 5 and 0.5 ng of DNA faithfully demonstrated all previously known heterozygous segmental duplications and deletions (3 Mb

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39

Alsmadi, Osama, Fadi Alkayal, Dorota Monies, and Brian F. Meyer. "Specific and complete human genome amplification with improved yield achieved by phi29 DNA polymerase and a novel primer at elevated temperature." BMC Research Notes 2, no. 1 (2009): 48. http://dx.doi.org/10.1186/1756-0500-2-48.

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40

Eisenbrandt, R. "Phi29 DNA polymerase residues Tyr59, His61 and Phe69 of the highly conserved ExoII motif are essential for interaction with the terminal protein." Nucleic Acids Research 30, no. 6 (2002): 1379–86. http://dx.doi.org/10.1093/nar/30.6.1379.

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41

Knierim, D., and E. Maiss. "Application of Phi29 DNA polymerase in identification and full-length clone inoculation of tomato yellow leaf curl Thailand virus and tobacco leaf curl Thailand virus." Archives of Virology 152, no. 5 (2007): 941–54. http://dx.doi.org/10.1007/s00705-006-0914-9.

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42

Lu, Na, Junji Li, Changwei Bi, et al. "ChimeraMiner: An Improved Chimeric Read Detection Pipeline and Its Application in Single Cell Sequencing." International Journal of Molecular Sciences 20, no. 8 (2019): 1953. http://dx.doi.org/10.3390/ijms20081953.

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As the most widely-used single cell whole genome amplification (WGA) approach, multiple displacement amplification (MDA) has a superior performance, due to the high-fidelity and processivity of phi29 DNA polymerase. However, chimeric reads, generated in MDA, cause severe disruption in many single-cell studies. Herein, we constructed ChimeraMiner, an improved chimeric read detection pipeline for analyzing the sequencing data of MDA and classified the chimeric sequences. Two datasets (MDA1 and MDA2) were used for evaluating and comparing the efficiency of ChimeraMiner and previous pipeline. Unde

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43

Jung, S., M. Reichenbach, R. Fries, et al. "316 GENOMIC EVALUATION OF BOVINE EMBRYOS WITHIN 24 HOURS." Reproduction, Fertility and Development 27, no. 1 (2015): 247. http://dx.doi.org/10.1071/rdv27n1ab316.

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The aim of this study was to develop a reliable procedure for genomic evaluation of bovine embryos to determine gender, polled status, and hereditary defects within 24 h after collection. German Simmental animals (n = 15) were superovulated (n = 25) using a standard protocol. Embryos were recovered on Day 7 (Day 0 = oestrus). A total of 217 embryos (morula, n = 130; early blastocyst, n = 43; blastocyst, n = 44) were biopsied with a steel blade attached to a micromanipulator. Biopsied cells were immediately transferred into 1 µL TE buffer to a 500 µL reaction tube and embryos were in vitro cult

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44

"5198543 Phi29 DNA polymerase." Biotechnology Advances 12, no. 1 (1994): 127. http://dx.doi.org/10.1016/0734-9750(94)90402-2.

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45

"5001050 PH phi29 DNA polymerase." Biotechnology Advances 9, no. 3 (1991): 445. http://dx.doi.org/10.1016/0734-9750(91)90880-5.

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46

Zhang, Jia, Xiaolu Su, Yefei Wang, et al. "Improved single-cell genome amplification by a high-efficiency phi29 DNA polymerase." Frontiers in Bioengineering and Biotechnology 11 (June 29, 2023). http://dx.doi.org/10.3389/fbioe.2023.1233856.

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Single-cell genomic whole genome amplification (WGA) is a crucial step in single-cell sequencing, yet its low amplification efficiency, incomplete and uneven genome amplification still hinder the throughput and efficiency of single-cell sequencing workflows. Here we introduce a process called Improved Single-cell Genome Amplification (iSGA), in which the whole single-cell sequencing cycle is completed in a high-efficient and high-coverage manner, through phi29 DNA polymerase engineering and process engineering. By establishing a disulfide bond of F137C-A377C, the amplification ability of the e

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47

Nelson, John R. "Random‐Primed, Phi29 DNA Polymerase‐Based Whole Genome Amplification." Current Protocols in Molecular Biology 105, no. 1 (2014). http://dx.doi.org/10.1002/0471142727.mb1513s105.

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48

Zhang, Jia, Xiaolu Su, Yefei Wang, et al. "Corrigendum: Improved single-cell genome amplification by a high-efficiency phi29 DNA polymerase." Frontiers in Bioengineering and Biotechnology 11 (August 28, 2023). http://dx.doi.org/10.3389/fbioe.2023.1263634.

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49

Zhang, Xi, Jingjing Chen, Pengfei Jiang, et al. "A Phi29-based unbiased exponential amplification and genotyping approach improves pathogen detection in tick samples." Frontiers in Veterinary Science 9 (November 7, 2022). http://dx.doi.org/10.3389/fvets.2022.1025911.

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Ticks are vectors for many infectious diseases, such as spotted fever group (SFG) rickettsioses and borreliosis, and are valuable in the study of pathogen ecology. Ticks have several growth stages that vary considerably in size; therefore, in most cases, DNA extracted from ticks is insufficient for subsequent studies, particularly for multiple pathogen screening and genotyping. Unbiased amplification of DNA from tick samples before analysis is a major requirement for subsequent ecological surveys and other studies. Phi29 DNA polymerase, an enzyme that exhibits strand displacement activity, can

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50

Tsuruta, Haruka, Yuina Sonohara, Kosuke Tohashi, Narumi Aoki Shioi, Shigenori Iwai, and Isao Kuraoka. "Effects of acetaldehyde-induced DNA lesions on DNA metabolism." Genes and Environment 42, no. 1 (2020). http://dx.doi.org/10.1186/s41021-019-0142-7.

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Abstract Background Acetaldehyde, produced upon exposure to alcohol, cigarette smoke, polluted air and sugar, is a highly reactive compound that is carcinogenic to humans and causes a variety of DNA lesions in living human cells. Previously, we reported that acetaldehyde reacts with adjacent deoxyguanosine residues on oligonucleotides, but not with single deoxyguanosine residues or other deoxyadenosine, deoxycytosine, or thymidine residues, and revealed that it forms reversible intrastrand crosslinks with the dGpdG sequence (GG dimer). Results Here, we show that restriction enzymes that recogn

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