Amplification of DNA Template Using Polymerase Chain Reaction (PCR) and Using Different Methods in Order PCR Optimization Which Includes Real-Time Quantitative PCR (qPCR)
DOI:
https://doi.org/10.59743/Keywords:
Amplifying, DNA, PCR, Mg concentration, MT temperatureAbstract
Polymerase chain reaction (PCR) is used to amplify a sample of DNA to produce from thousands up to millions of DNA copies and different optimization techniques such as real-time quantitative PCR (q PCR) can be used to optimize the PCR reaction. The results it can be seen that the neat sample had an increased DNA template while contain more than . The optimal temperature for the specific products was 65°C which is the highest annealing temperature and there was no PCR products. However, the low temperature bands of 46°C and the high-temperature ones 58°C had the nearly same brightness as did the bands at 52°C and 55°C. the optimal amplification of the DNA sample occurs with 2.0 and 3.0 mMol concentration of Mg+2 though the alternative Mg+2 concentrations have amplification, but not as specific and the primer dimer gel has nonspecific bands.Downloads
References
Abd-Elsalam, K. A. (2003). Bioinformatic tools and guideline for PCR primer design. african Journal of biotechnology, 2(5), 91-95.
Ali, N., Rampazzo, R. D. C. P., Costa, A. D. T., & Krieger, M. A. (2017). Current nucleic acid extraction methods and their implications to point‐of‐care diagnostics. BioMed research international, 2017(1), 9306564.
Arya, M., Shergill, I. S., Williamson, M., Gommersall, L., Arya, N., & Patel, H. R. (2005). Basic principles of real-time quantitative PCR. Expert review of molecular diagnostics, 5(2), 209-219.
Bartlett, J. M., & Stirling, D. (Eds.). (2003). PCR protocols (Vol. 226, pp. 3-525). Totowa, NJ: Humana Press.
Birch, D. E., Kolmodin, L., Wong, J., Zangenberg, G. A., Zoccoli, M. A., McKinney, N., & Young, K. K. Y. (1996). Simplified hot start PCR. Nature, 381(6581), 445-446.
Dieffenbach, C. W., Lowe, T. M., & Dveksler, G. S. (1993). General concepts for PCR primer design. PCR methods appl, 3(3), S30-S37.
Dorak, M. T. (Ed.). (2007). Real-time PCR. Garland Science.
Ekman, S. (1999). PCR optimization and troubleshooting, with special reference to the amplification of ribosomal DNA in lichenized fungi. The lichenologist, 31(5), 517-531.
Evans, M. F. (2009). The polymerase chain reaction and pathology practice. Diagnostic histopathology, 15(7), 344-356.
Harzandi, N., Jamshidi, S., Dezfulian, M., Bahonar, A., Bakhtiari, A., & Banihashemi, K. (2016). Molecular detection and speciation of Campylobacter species in children with gastroenteritis using polymerase chain reaction in Bahonar Hospital of Karaj City. International Journal of Enteric Pathogens, 3(2), 3-21796.
Innis, M.A., Gelfand, D.H., Sninsky, J.J. and White, T.J. (2012) Optimization of PCRs. Academic Press: San Diego, CA, USA.
Johnson, M. P., Haupt, L. M., & Griffiths, L. R. (2004). Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real‐time PCR. Nucleic acids research, 32(6), e55-e55.
Joshi, M., & Deshpande, J. D. (2010). Polymerase chain reaction: methods, principles and application. International Journal of Biomedical Research, 2(1), 81-97.
Lee, S. J., Park, S. Y., Lee, K. H., Lee, M. W., Yu, C. Y., Maeng, J., ... & Kim, S. W. (2023). Development of a Simple Direct and Hot-Start PCR Using Escherichia coli-Expressing Taq DNA Polymerase. International journal of molecular sciences, 24(14), 11405.
Lorenz, T. C. (2012). Polymerase chain reaction: basic protocol plus troubleshooting and optimization strategies. JoVE (Journal of Visualized Experiments), (63), e3998.
Metzenberg, S. (2007). Working with DNA. New York: Taylor & Francis Group.
Metzker, M.L. and Caskey, C.T., (2009). Polymerase chain reaction (PCR). eLS,.
Newton, C. and Graham, A., (1994). Introduction to biotechniques PCR. Billington D,.
Nolan, T., & Bustin, S. A. (Eds.). (2013). PCR technology: current innovations. CRC press.
Orce, I. G., Sendín, L. N., Marano, M. R., Vojnov, A. A., Castagnaro, A. P., & Filippone, M. P. (2015). Novel set of real-time PCR primers for simultaneous detection of Liberibacter species associated with citrus Huanglongbing. Scientia Agricola, 72(3), 252-259.
Rebrikov, D. V., & Trofimov, D. Y. (2006). Real-time PCR: a review of approaches to data analysis. Applied biochemistry and microbiology, 42, 455-463.
Rychlik, W. J. S. W., Spencer, W. J., & Rhoads, R. E. (1990). Optimization of the annealing temperature for DNA amplification in vitro. Nucleic acids research, 18(21), 6409-6412.
Saunders, N.A. and Lee, M.A., (2013). Real-time PCR: advanced technologies and applications. Horizon Scientific Press.
Soliman, M. A., Azab, M. S., Hussein, H. A., & Abu El-naga, M. N. (2024). Validation and Application of FBPP: Software to Design Foodborne Pathogen PCR Primers and Probes. Egyptian Academic Journal of Biological Sciences. C, Physiology and Molecular Biology, 16(2), 105-112.
Valasek, M. A., & Repa, J. J. (2005). The power of real-time PCR. Advances in physiology education, 29(3), 151-159.
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