Rolling circle amplification in molecular diagnostics: the power of simplicity
Amplificación por círculo rodante en el diagnóstico molecular: el poder de la simplicidad
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Rolling Circle Amplification (RCA) is an isothermal enzymatic process, mediated by certain DNA polymerases, in which long single-stranded (ss) DNA molecules are synthesized on a short circular ssDNA template using a single primer; a method
that allows phylogenetic, epidemiological and genome organization analysis studies. Recently, DNA polymerase from bacteriophage phi29 has been used for the efficient amplification of circular viral DNA genomes without the need for specific primers using the RCA mechanism, making the latter a highly versatile and important DNA amplification tool with wide applications in various research
fields. Based on this, the present review briefly highlights the theoretical model on which this technique is based for molecular diagnostic applications in different
research fields.
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Ali, M. M., Li, F. Z., Zhang, K., Kang, D.K., Ankrum, J. A., Le, X. C., & Zhao, W. (2014). Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine. Chem Soc Rev, 43(10), 3324-3341. doi:10.1039/c3cs60439j
Ali, M. M., Su, S., Filipe, C. D., Pelton, R., & Li, Y. (2007). Enzymatic manipulations of DNA oligonucleotides on microgel: towards development of DNA-microgel bioassays. Chemical Communications(43), 4459-4461. doi:https://doi.org/10.1039/B709817K
Asiello, P. J., & Baeumner, A. J. (2011). Miniaturized isothermal nucleic acid amplification, a review. Lab on Chip, 11, 1420-1430. doi:https://doi.org/10.1039/C0LC00666A
Berman, A. J., Kamtekar, S., Goodman, J. L., Lázaro, J. M., De Vega, M., Blanco, L., . . . Steitz, T. A. (2007). Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. Embo J, 26(14), 3494 - 3505. doi:10.1038/sj.emboj.7601780
Blab, G. A., Schmidt, T., & Nilsson, M. (2004). Homogeneous detection of single rolling circle replication products. Anal Chem, 76(2), 495-498. doi:10.1021/ac034987+
Blanco, L., & Salas, M. (1996). Relating structure to function in phi29 DNA polymerase. J Biol Chem, 271(15), 8509-8512. doi:10.1074/jbc.271.15.8509
Blanco, L., Bernad, A., Lázaro, J. M., Martín, G., Garmendia, C., & Salas, M. (1989). Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J Biol Chem, 264(15), 8935-8940. https://pubmed.ncbi.nlm.nih.gov/2498321/
Dahl, F., Banér, J., Gullberg, M., Mendel-Harving, M., Landegren, U., & Nilsson, M. (2004). Circle-to-circle amplification for precise and sensitive DNA analysis. Proc Natl Acad Sci U S A, 101(13), 4548-4553. doi:10.1073/pnas.0400834101
Davari, M., Van Diepeningen, A. D., Babai-Ahari, A., Arzanlou, M., Najafzadeh, M. J., Van der Lee, T. A., & De Hoog, G. S. (2012). Rapid identification of Fusarium graminearum species complex using Rolling Circle Amplification (RCA). J Microbiol Methods, 89(1), 63-70. doi:10.1016/j.mimet.2012.01.017
Dean, F. B., Nelson, J. R., Giesler, T. L., & Lasken, R. S. (2001). Dean FB, Nelson JR, Giesler TL, Lasken RS. 2001. Rapid amplification of plasmid and phage DNA using Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification. Genome Res, 11(6), 1095-1099. doi:10.1101/gr.180501
Demidov, V. V. (2005). Rolling-circle amplification (RCA). Encyclopedia of Diagnostic Genomics and Proteomics, 1175-1179.
Di Giusto, D. A., Wlassoff, W. A., Gooding, J. J., Messerle, B. A., & King, G. C. (2005). Proximity extension of circular DNA aptamers with real-time protein detection. Nucleic Acids Research, 33(6), 1-7. doi:10.1093/nar/gni063
Esteban, J. A., M, S., & Blanco, L. (1993). Fidelity of phi 29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization. J Biol Chem, 268(4), 2719-2726. https://pubmed.ncbi.nlm.nih.gov/8428945/
Fakruddin, M., Mannan, K. S., Chowdhury, A., Mazumdar, R. M., Hossain, N., Islam, S., & Chowdhury, A. (2013). Nucleic acid amplification: Alternative methods of polymerase chain reaction. Journal of Pharmacy & BioAllied Sciences, 5(4), 245-252. doi:10.4103/0975-7406.120066
Fauquet, C. M., & Fargette, D. (2005). International Committee on Taxonomy of Viruses and the 3,142 unassigned species. Virology Journal, 2(64), 1-10. doi:https://doi.org/10.1186/1743-422X-2-64
Goo, N.-I., & Kim, D.-E. (2016). Rolling circle amplification as isothermal gene amplification in molecular diagnostics. Biochip J, 10(4), 262-271. doi:10.1007/s13206-016-0402-6
Gusev, Y., Sparkowski, J., Raghunathan, A., Ferguson, H., Montano, J., Bogdan, N., . . . Wheeler, V. (2001). Rolling circle amplification: a new approach to increase sensitivity for immunohistochemistry and flow cytometry. Am J Pathol, 159(1), 63-69. doi:10.1016/S0002-9440(10)61674-4
Haible, D., Kober, S., & Jeske, H. (2006). Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses. J Virol Methods, 135(1), 9-16. doi:10.1016/j.jviromet.2006.01.017
Inoue-Nagata, A. K., Albuquerque, L. C., Rocha, W. B., & Nagata, T. (2004). A simple method for cloning the complete begomovirus genome using the bacteriophage phi29 DNA polymerase. J Virol Methods, 116(2), 209-211. doi:10.1016/j.jviromet.2003.11.015
Johne, R., Müller, H., Rector, A., Van, R. M., & Stevens, H. (2009). Rolling-circle amplification of viral DNA genomes using phi29 polymerase. Trends in Microbiology, 17(5), 205-211. doi:https://doi.org/10.1016/j.tim.2009.02.004
Kamtekar, S., Berman, A. J., Wang, J., Lázaro, J. M., De Vega, M., Blanco, L., . . . Steitz, T. A. (2004). Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29. Mol Cell, 16(4), 609-618. doi:10.1016/j.molcel.2004.10.019
Kobori, T., & Takahashi, H. (2014). Expanding possibilities of Rolling Circle Amplification as a biosensing platform. Analytical Sciences, 30, 59-64. Obtenido de https://www.jstage.jst.go.jp/article/analsci/30/1/30_59/_pdf
Kuhn, H., Demidov, V. V., & Frank-Kamenetskii, M. D. (2002). Rolling-circle amplification under topological constraints. Nucleic Acids Research, 30(2), 574-580. doi:https://doi.org/10.1093/nar/30.2.574
Lagunavicius, A., Kiveryte, Z., Zimbaite-Ruskuliene, V., Radzvilavicius, & Janulaitis, A. (2008). Duality of polynucleotide substrates for Phi29 DNA polymerase: 3??5? RNase activity of the enzyme. RNA, 14(3), 503-513. doi:10.1261/rna.622108
Li, N., Li, J., & Zhong, W. (2008). CE combined with rolling circle amplification for sensitive DNA detection. Electrophoresis, 29(2), 424-432. doi:10.1002/elps.200700410
Lockhart, B., & Olszewski, N. (1993). Serologicaal nd genomic heterogeneity of banana streak badnavirus Implications for virus detection in Musa germplasm. InternationalSymposium on Genetic Improvement of Bananas for Resistance to Diseases and Pests (págs. 105-113). Montpellier: CIRAD-FLHOR.
López, M., Mayorquín, P. y Vega, M. (2005). Aplicación de los microarrays y biochips en salud humana. Madrid: Fundación Española para el Desarrollo de la Investigación en Genómica y Proteomica .
Mohsen, M. G., & Kool, E. T. (2016). The Discovery of Rolling Circle Amplification and Rolling Circle Transcription. Accounts of Chemical Research, 49(11), 2540-2550. doi:https://doi.org/10.1021/acs.accounts.6b00417
Najafzadeh, M. J., Dolatabadi, S., Saradeghi, K. M., Naseri, A., Feng, P., & De Hoog, G. S. (2013). Detection and identification of opportunistic Exophiala species using the rolling circle amplification of ribosomal internal transcribed spacers. J Microbiol Methods, 94(3), 338-342. doi:10.1016/j.mimet.2013.06.026
Nelson, J. R., Cai, Y. C., Giesler, T. L., Farchaus, J. W., Sundaram, S. T., Ortiz-Rivera, M., . . . Fuller, C. W. (2002). TempliPhi, phi29 DNA polymerase based rolling circle amplification of templates for DNA sequencing. Biotechniqueres, 44-47. https://pubmed.ncbi.nlm.nih.gov/12083397/
Paez, J. G., Lin, M., Beroukhim, R., Lee, J. C., Zhao, X., Richter, D. J., . . . Sellers, W. R. (2004). Genome coverage and sequence fidelity of phi29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Res, 32(9). doi:10.1093/nar/gnh069
Pang, S., Qureshi, F., Shanahan, D., & Harris, N. (2007). Investigation of the use of rolling circle amplification for the detection of GM food. Eur Food Res Techno, 225(59), 59-66. doi:10.1007/s00217-006-0382-1
Reagin, M. J., Giesler, T. L., Merla, A. L., Resetar-Gerke, J. M., Kapolka, K. M., & Mamone, J. A. (2003). TempliPhi: A Sequencing Template Preparation Procedure That Eliminates Overnight Cultures and DNA Purification. J Biomol Tech, 14(2), 143-148. https://acortar.link/RXNzUb
Rector, A., Tachezy, R., & Van, R. M. (2004). A Sequence-Independent Strategy for Detection and Cloning of Circular DNA Virus Genomes by Using Multiply Primed Rolling-Circle Amplification. Journal of Virology, 78(10), 4993-4998. doi:10.1128/JVI.78.10.4993-4998.2004
Schubert, J., Habekuss, A., Kazmaier, K., & Jeske, H. (2007). Surveying cereal-infecting geminiviruses in Germany--diagnostics and direct sequencing using rolling circle amplification. Virus Res, 127(1), 61-70. doi:10.1016/j.virusres.2007.03.018
Silander, K., & Saarela, J. (2008). Whole genome amplification with Phi29 DNA polymerase to enable genetic or genomic analysis of samples of low DNA yield. Methods Mol Biol, 439, 1-18. doi:10.1007/978-1-59745-188-8_1
Spits, C., Le Caignec, C., De Rycke, M., Van Haute, L., Van Steirteghem, A., Liebaers, I., & Sermon, K. (2006). Whole-genome multiple displacement amplification from single cells. Nat Protoc, 1(4), 1965-1970. doi:10.1038/nprot.2006.326
Sun, J., Najafzadeh, M. J., Zhang, J., Vicente, V. A., Xi, L., & De Hoog, G. S. (2011). Molecular identification of Penicillium marneffei using rolling circle amplification. Mycoses, 54(6), 751-759. doi:10.1111/j.1439-0507.2011.02017.x
Tavares, R. G., Staggemeier, R., P, B. A., Rodrigues, M. T., Castelan, L. A., Vasconcelos, J., . . . Spalding, S. M. (2011). Molecular techniques for the study and diagnosis of parasite infection. Journal of Venomous Animals and Toxins including Tropical Diseases, 17(3), 239-248. doi:https://doi.org/10.1590/S1678-91992011000300003
Tong, Z., Kong, F., Wang, B., Zeng, X., & Gilbert, G. L. (2007). A practical method for subtyping of Streptococcus agalactiae serotype III, of human origin, using rolling circle amplification. J Microbiol Methods, 70(1), 39-44. doi:10.1016/j.mimet.2007.03.010
Tsui, C. K., Wang, B., Khadempour, L., Alamouti, S. M., Bohlmann, J., Murray, B. W., & Hamelin, R. C. (2010). Rapid identification and detection of pine pathogenic fungi associated with mountain pine beetles by padlock probes. J Microbiol Methods, 1, 26-33. doi:0.1016/j.mimet.2010.07.016
Vera, M. S., Jiménez, M. P., & Franco-Lara, L. (2012). Uso de herramientas bioinformáticas en la evaluación de secuencias "DNA barcode" para la identificación a nivel de especie. Revista Facultad de Ciencias Básicas 8: 196-209. Facultad de Ciencias Básicas, 196-209. doi:https://doi.org/10.18359/rfcb.2035
Wang, B., Potter, S. J., Lin, Y., Cunningham, A. L., Dwyer, D. E., Su.,. . . . Saksena, N. K. (2005). Rapid and sensitive detection of severe acute respiratory syndrome coronavirus by rolling circle amplification. J Clin Microbiol, 43(5), 2339-2344. doi:10.1128/JCM.43.5.2339-2344.2005
Yi, J., Zhang, W., & Zhang, D. Y. (2006). Molecular Zipper: a fluorescent probe for real-time isothermal DNA amplification. Nucleic Acids Research, 34(11), 1-5. doi:10.1093/nar/gkl261
Zhang, D., Wu, J., Ye, F., Feng, T., Lee, I., & Yin, B. (2006). Amplification of circularizable probes for the detection of target nucleic acids and proteins. Clin Chim Acta, 363(1-2), 61-70. doi:10.1016/j.cccn.2005.05.039
Zhao, W., Ali, M. M., Brook, M. A., & Li, Y. (2008). Rolling circle amplification: applications in nanotechnology and biodetection with functional nucleic acids. Angew Chem Int Ed Engl, 47(34), 6330-6337. doi:10.1002/anie.200705982
Zhong, X. B., Lizardi, P. M., Huang, X. H.-W., & Ward, D. C. (2001). Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification. Proc Natl Acad Sci U S A, 98(7), 3940-3945. doi:10.1073/pnas.061026198
Zhou, H., Bouwman, K., Schotanus, M., Verwejj, C., Marrero, J. A., Dillon, D., . . . Haab, B. B. (2004). Two-color, rolling-circle amplification on antibody microarrays for sensitive, multiplexed serum-protein measurements. Genome Biology, 5(R28), 1-12. doi:https://doi.org/10.1186/gb-2004-5-4-r28
