A review of the development of Polymerase Chain Reaction technique and its uses in Scientific field

  • Lucyenne Angeline Giri Putra Department of Food Technology, Universitas Ciputra Surabaya, Region Citraland CBD Boulevard Made, Surabaya, Jawa Timur, 60219
  • Christianus Jodi Yonathan Department of Food Technology, Universitas Ciputra Surabaya, Region Citraland CBD Boulevard Made, Surabaya, Jawa Timur, 60219
  • Nabila Imania Niedhatrata Department of Food Technology, Universitas Ciputra Surabaya, Region Citraland CBD Boulevard Made, Surabaya, Jawa Timur, 60219
  • Mochammad Hilmy Rizka Firdaus Department of Food Technology, Universitas Ciputra Surabaya, Region Citraland CBD Boulevard Made, Surabaya, Jawa Timur, 60219
  • Jessica Renata Yoewono Department of Food Technology, Universitas Ciputra Surabaya, Region Citraland CBD Boulevard Made, Surabaya, Jawa Timur, 60219


PCR (Polymerase Chain Reaction) is a scientific term and technique in molecular biology which able to generate copies of a specific DNA from two short oligodeoxynucleotide sequences (also called primers) by a polymerase-dependent repetitive thermal reaction. PCR technique brought a revolution in science especially in molecular biology since its first discovery back in 1984 as its simplicity and not a time-consuming trait. Over the past decades, PCR techniques have been modified to make it suitable for the application in each scientific field. PCR nowadays is involved in almost all studies that required DNA fragments manipulation including in food and medical analysis. By taking advantage of this revolutionary technique and if developed and used well, it would become very beneficial for humanity in many aspects

Keywords: Polymerase Chain Reaction, DNA amplification, modified technique


Download data is not yet available.

Author Biography

Lucyenne Angeline Giri Putra, Department of Food Technology, Universitas Ciputra Surabaya, Region Citraland CBD Boulevard Made, Surabaya, Jawa Timur, 60219

Department of Food Technology, Faculty of Tourism, Universitas Ciputra, Surabaya


Atanassova, V., Meindl, A., & Ring, C. (2001). Prevalence of Staphylococcus aureus and Staphylococcal enterotoxins in raw pork and uncooked smoked ham - A comparison of classical culturing detection and RFLP-PCR. International Journal of Food Microbiology, 68(1–2),105–113. https://doi.org/10.1016/S0168-1605(01)00479-2

Atkins, T. (1995). Identification of cultivars and validation of genetic relationships in Mangifera indica L . using RAPD markers. 269–274.

Balacs, T. (1997). Research reports. International Journal of Aromatherapy, 8(2), 43–45. https://doi.org/10.1525/jlca.1992.4.2.99

Bintang, M. (2018). Biokimia Teknik Penelitian. In Biokimia Teknik Penelitian (Second Edition) (2nd ed.). Erlangga.

Boldura, O. M., & Popescu, S. (2016). PCR: A Powerful Method in Food Safety Field. Biochemistry, Genetics and Molecular Biology" Polymerase Chain Reaction for Biomedical Applications". Intech Publishers, USA, 135-158.

Bonin, S., Petrera, F., Niccolini, B., & Stanta, G. (2003). PCR analysis in archival postmortem tissues. Journal of Clinical Pathology - Molecular Pathology, 56(3), 184–186. http://dx.doi.org/10.5772/65738.

Bottero, M. T., Civera, T., Nucera, D., Rosati, S., Sacchi, P., & Turi, R. M. (2003). A multiplex polymerase chain reaction for the identification of cows’, goats’ and sheep’s milk in dairy products. International Dairy Journal, 13(4), 277–282. https://doi.org/10.1016/S0958-6946(02)00170-X

Bouzid, M., Heavens, D., Elwin, K., Chalmers, R. M., Hadfield, S. J., Hunter, P. R., & Tyler, K. M. (2010). Whole genome amplification (WGA) for archiving and genotyping of clinical isolates of Cryptosporidium species. Parasitology, 137(1), 27–36. https://doi.org/10.1017/S0031182009991132

Bryksin, A. V., & Matsumura, I. (2010). Overlap extension PCR cloning: A simple and reliable way to create recombinant plasmids. BioTechniques, 48(6), 463–465. https://doi.org/10.2144/000113418

Calvo, J. H., Osta, R., & Zaragoza, P. (2002). Quantitative PCR detection of pork in raw and heated ground beef and pâté. Journal of Agricultural and Food Chemistry, 50(19), 5265–5267. https://doi.org/10.1021/jf0201576

Cao, M., Fu, Y., Guo, Y., & Pan, J. (2009). Chlamydomonas (Chlorophyceae) colony PCR. Protoplasma, 235(1–4), 107–110. https://doi.org/10.1007/s00709-009-0036-9

Carattoli, A., Bertini, A., Villa, L., Falbo, V., Hopkins, K. L., & Threlfall, E. J. (2005). Identification of plasmids by PCR-based replicon typing. Journal of Microbiological Methods, 63(3), 219–228. https://doi.org/10.1016/j.mimet.2005.03.018

Commission, C. A. (2006). Codex Alimentarius Commission. (2006). Draft revised standard for gluten-free foods. Report of the 28th Session of the Codex Committee on Nutrition and Foods for Special Dietary Uses (ALINORM 07/30/26). Joint FAO/WHO Food Standards Programme. Rome.

Darawi, M. N., Ai-Vyrn, C., Ramasamy, K., Hua, P. P. J., Pin, T. M., Kamaruzzaman, S. B., & Majeed, A. B. A. (2013). Allele-specific polymerase chain reaction for the detection of Alzheimer’s disease-related single nucleotide polymorphisms. BMC Medical Genetics, 14(1). https://doi.org/10.1186/1471-2350-14-27

Dary, O., Hurrell, R. (2006). Global Progress - Food Fortification. Unscn.Org, 341. https://doi.org/10.1242/jeb.02490

De Medici, D., Kuchta, T., Knutsson, R., Angelov, A., Auricchio, B., Barbanera, M., ... & Tomic, D. H. (2015). Rapid methods for quality assurance of foods: the next decade with polymerase chain reaction (PCR)-based food monitoring. Food analytical methods, 8(2), 255-271.doi:10.1007/s12161-014-9915-6.

European Commission. (2003). Regulation (Ec) No 1830/2003 ff The European Parliament and of The Council of 22 September 2003 concerning the traceability and labelling of genetically modified organisms and the traceability of food and feed products produced from genetically modified o. Official Journal of the European Union, 31(1830), 24–28.

Ferriol, M., Picó, M. B., & Nuez, F. (2003). Genetic diversity of some accessions of Cucurbita maxima from Spain using RAPD and SBAP markers. Genetic Resources and Crop Evolution, 50(3), 227–238. https://doi.org/10.1023/A:1023502925766

Garcı, T., Gonza, I., Rodrı, M. A., Martı, R., & Herna, P. E. (2005). MEAT TaqMan real-time PCR for the detection and quantitation of pork in meat mixtures. 70, 113–120. https://doi.org/10.1016/j.meatsci.2004.12.005

Garibyan, L., & Avashia, N. (2013). Research techniques made simple: polymerase chain reaction (PCR). The Journal of investigative dermatology, 133(3), e6. doi: 10.1038/jid.2013.1

Georgiou, M., Hatzaki, A., & Koutselinis, A. (2000). Identification of an alleged offender of murder by VNTR analysis: Case report. American Journal of Forensic Medicine and Pathology, 21(2), 162–165. https://doi.org/10.1097/00000433-200006000-00014

Germini, A., Zanetti, A., Salati, C., Rossi, S., Forré, C., Schmid, S., & Marchelli, R. (2004). Development of a seven-target multiplex PCR for the simultaneous detection of transgenic soybean and maize in feeds and foods. Journal of Agricultural and Food Chemistry, 52(11), 3275–3280. https://doi.org/10.1021/jf035052x

Gibson, D. G. (2011). Enzymatic assembly of overlapping DNA fragments. Methods in Enzymology, 498, 349–361. https://doi.org/10.1016/B978-0-12-385120-8.00015-2

Girish, P. S., Anjaneyulu, A. S. R., Viswas, K. N., Shivakumar, B. M., Anand, M., Patel, M., & Sharma, B. (2005). Meat species identification by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of mitochondrial 12S rRNA gene. Meat Science, 70(1), 107–112. https://doi.org/10.1016/j.meatsci.2004.12.004

Handoyo, D., & Rudiretna, A. (2001). Prinsip umum dan pelaksanaan Polymerase Chain Reaction (PCR). Unitas, 9(1), 17–29.

Hayashi, K. (1992). PCR-SSCP: A method for detection of mutations. Genetic Analysis: Biomolecular Engineering, 9(3), 73–79. https://doi.org/10.1016/1050-3862(92)90001-L

Hayden, M. J., Nguyen, T. M., Waterman, A., & Chalmers, K. J. (2008). Multiplex-Ready PCR: A new method for multiplexed SSR and SNP genotyping. BMC Genomics, 9, 1–12. https://doi.org/10.1186/1471-2164-9-80

Heckman, K. L., & Pease, L. R. (2007). Gene splicing and mutagenesis by PCR-driven overlap extension. Nature Protocols, 2(4), 924–932. https://doi.org/10.1038/nprot.2007.132

Heiat, M., Ranjbar, R., Latifi, A. M., Rasaee, M. J., & Farnoosh, G. (2017). Essential strategies to optimize asymmetric PCR conditions as a reliable method to generate large amount of ssDNA aptamers. Biotechnology and Applied Biochemistry, 64(4), 541–548. https://doi.org/10.1002/bab.1507

Henegariu, O., Heerema, N. A., Dloughy, S. R., Vance, G.H., & Vogt, P. H. (1997). Multiplex PCR: critical parameters and step-by-step protocol (pp. 23,(3),504-511). pp. 23,(3),504-511. Biotechniques.

Herman, J. G., Graff, J. R., Myöhänen, S., Nelkin, B. D., & Baylin, S. B. (1996). Methylation-specific PCR: A novel PCR assay for methylation status of CpG islands. Proceedings of the National Academy of Sciences of the United States of America, 93(18), 9821–9826. https://doi.org/10.1073/pnas.93.18.9821

Hernández, M., Rodríguez-Lázaro, D., Zhang, D., Esteve, T., Pla, M., & Prat, S. (2005). Interlaboratory transfer of a PCR multiplex method for simultaneous detection of four genetically modified maize lines: Bt11, MON810, T25, and GA21. Journal of Agricultural and Food Chemistry, 53(9), 3333–3337. https://doi.org/10.1021/jf049192y

Higuchi, R., Krummel, B., & Saiki, R. (1988). A general method of in vitro preparation and specific mutagenesis of DNA fragments: study of protein and DNA interactions. (pp. 16 (15), 7351–7367). pp. 16 (15), 7351–7367.

Higuchi, R., Fockler, C., Dollinger, G., & Watson, R. (1993). Kinetic PCR analysis: Real-time monitoring of DNA amplification reactions. Bio/Technology, 11(9), 1026–1030. https://doi.org/10.1038/nbt0993-1026

Hömig-Hölzel, C., & Savola, S. (2012). Multiplex Ligation-dependent Probe Amplification (MLPA) in tumor diagnostics and prognostics. Diagnostic Molecular Pathology, 21(4), 189–206. https://doi.org/10.1097/PDM.0b013e3182595516

How Kit, A., Mazaleyrat, N., Daunay, A., Nielsen, H. M., Terris, B., & Tost, J. (2013). Sensitive detection of KRAS mutations using enhanced-ice-COLD-PCR mutation enrichment and direct sequence identification. Human Mutation, 34(11), 1568–1580. https://doi.org/10.1002/humu.22427

Hoy, M. A. (2013). Insect Molecular Genetics : An Introduction to Principles and Application (3rd ed.). Academic Press.

Imyanitov, E. N., Buslov, K. G., Suspitsin, E. N., Kuligina, E. S., Belogubova, E. V., Grigoriev, M. Y., … Hanson, K. P. (2002). Improved reliability of allele-specific PCR. BioTechniques, 33(3), 484–490. https://doi.org/10.2144/02333bm04_11841a

Irvine, R. F., & Press, R. (1991). DNA Music : An Audio Aid Methods in lnositide Research PCR Protocols-A Guide to Methods and Applications. 19(1), 1991.

Jagtar Singh , Niti Birbian, S. S. and A. G. (2014). A critical review on PCR, its types and applications. International Journal of Advanced Research in Biological Sciences, 1(7), 65–80. Retrieved from http://www.ijarbs.com/pdfcopy/oct2014/ijarbs11.pdf

Joshi, M., & Deshpande, J. D. (2011). Polymerase Chain Reaction: Methods, Principles and Application. International Journal of Biomedical Research, 2(1). https://doi.org/10.7439/ijbr.v2i1.83

Klancnik, A., Kovac, M., Toplak, N., Piskernik, S., & Jersek, B. (2012). PCR in Food Analysis. Polymerase Chain Reaction, (May). https://doi.org/10.5772/38551

Kuchta, L. P. D. P. T. (2008). A novel real-time polymerase chain reaction ( PCR ) method for the detection of hazelnuts in food. 1155–1158. https://doi.org/10.1007/s00217-007-0644-6

Lasken, R. S., & Egholm, M. (2003). Whole genome amplification: Abundant supplies of DNA from precious samples or clinical specimens. Trends in Biotechnology, 21(12), 531–535. https://doi.org/10.1016/j.tibtech.2003.09.010

Laube, I., Spiegelberg, A., Butschke, A., Zagon, J., Schauzu, M., Kroh, L., & Broll, H. (2003). Methods for the detection of beef and pork in foods using real-time polymerase chain reaction. International Journal of Food Science and Technology, 38(2), 111–118. https://doi.org/10.1046/j.1365-2621.2003.00651.x

Liang, H., Chen, G.-J., Yu, Y., & Xiong, L.-K. (2018). Co-amplification at lower denaturation temperature-PCR: methodology and applications. Yi Chuan = Hereditas, 40(3), 227–236. https://doi.org/10.16288/j.yczz.17-369

Liu, Y. G., & Chen, Y. (2007). High-efficiency thermal asymmetric interlaced PCR for amplification of unknown flanking sequences. BioTechniques, 43(5), 649–656. https://doi.org/10.2144/000112601

Lo, A. C., & Feldman, S. R. (1994). Polymerase chain reaction: Basic concepts and clinical applications in dermatology. Journal of the American Academy of Dermatology, 30(2), 250–260. https://doi.org/10.1016/S0190-9622(94)70025-7

López-Calleja, I., González, I., Fajardo, V., Martín, I., Hernández, P. E., García, T., & Martín, R. (2007). Quantitative detection of goats’ milk in sheep’s milk by real-time PCR. Food Control, 18(11), 1466–1473. https://doi.org/10.1016/j.foodcont.2006.11.006

Ly-Chatain, M. H., Durand, L., Rigobello, V., Vera, A., & Demarigny, Y. (2011). Direct quantitative detection and identification of Lactococcal bacteriophages from milk and whey by real-time PCR: application for the detection of Lactococcal bacteriophages in Goat's raw milk whey in France. International journal of microbiology, 2011. doi:10.1155/2011/594369

Mano, J., Hatano, S., Futo, S., Yoshii, J., Nakae, H., Naito, S., ... & Kitta, K. (2014). Development of a reference material of a single DNA molecule for the quality control of PCR testing. Analytical chemistry, 86(17), 8621-8627.

Manimekalai, R., Nagarajan, P., & Bharathi, M. (2004). DNA polymorphism among coconut (Cocos nucifera L.) cultivars. Journal of Plantation Crops, 32, 117–122.

Marmiroli, N., & Maestri, E. (2007). Polymerase chain reaction (PCR). Food Toxicants Analysis, 5(6), 147–187. https://doi.org/10.1016/B978-044452843-8/50007-9

Masny, A. (2003). Ligation mediated PCR performed at low denaturation temperatures--PCR melting profiles. Nucleic Acids Research, 31(18), 114e – 114. https://doi.org/10.1093/nar/gng116

Maurya, R., Singh, R. K., Kumar, B., Salotra, P., Rai, M., & Sundar, S. (2005). Evaluation of PCR for diagnosis of Indian kala-azar and assessment of cure. Journal of Clinical Microbiology, 43(7), 3038–3041. https://doi.org/10.1128/JCM.43.7.3038-3041.2005

Milbury, C. A., Li, J., & Makrigiorgos, G. M. (2011). Ice-COLD-PCR enables rapid amplification and robust enrichment for low-abundance unknown DNA mutations. Nucleic Acids Research, 39(1), 1–10. https://doi.org/10.1093/nar/gkq899

Miller, S. A., Gallie, D. R., Sleat, D. E., Watts, J. W., Turner, P. C., & Wilson, T. M. a. (1988). Volume 16 Number 3 1988 Nucleic Acids Research. Nucleic Acids Research, 16(3), 883–893.

McPherson, M., & Møller, S. (2006). Pcr. Taylor & Francis.

Moras, D., & Argos, P. (1990). An attempt to unify the structure of polymerases. Protein Engineering, Design and Selection, 3(6), 461–467. https://doi.org/10.1093/protein/3.6.461

Mullis, K., Faloona, F., Scharf, S., Saiki, R., Horn, G., & Erlich, H. (1992). Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. 1986. Biotechnology (Reading, Mass.), 24(Table 1), 17–27.

Nalini, E., Jawali, N., Division, A., Atomic, B., Bhagwat, S. G., Agriculture, N., … Atomic, B. (1999). A simple method for isolation of dna from plants suitable for long term storage and dna marker analysis. (249), 208–214.

Nanvazadeh, F., Dokht, A., & Reza, M. (2013). Genotyping of Pseudomonas aeruginosa strains isolated from burn patients by RAPD-PCR. Burns, 39(7), 1409–1413. https://doi.org/10.1016/j.burns.2013.03.008

Park, G., Way, B., Park, A. B., & Road, N. (1989). volume 17 Number 7 1989 Nucleic Acids Research. 17(7), 2503–2516.

Patel, S. H., Bosamia, T. C., Bhalani, H. N., Singh, P., & Kumar, A. (2015). Polymerase Chain Reaction (PCR). In Agrobios Newsletter: A Monthly Magazine of Agricultural and Biological Sciences (XIII, p. 148). Agrobios newsletter: Magazine of Agricultural and Biological Science.

Pfaffl-Kubista-Vandesompele-real-time-PCR-chapter-5.pdf. (n.d.).

Pierce, K. E., & Wangh, L. J. (n.d.). 7. 65–85.

Poddar, S. K. (2000). Symmetric vs asymmetric PCR and molecular beacon probe in the detection of a target gene of adenovirus. 25–32. https://doi.org/10.1006/mcpr.1999.0278

Ponce, M. R., & Lmicol, J. (1992). PCR amplification of long DNA fragments. 20(3), 91125.

Quan, P., Sauzade, M., & Brouzes, E. (2018). dPCR : A Technology Review. https://doi.org/10.3390/s18041271

Q Nabi, A., Vernile, A., Spano, G., Lasalandra, G., Beneduce, L., Colelli, G., & Massa, S. (2011). PCR-based quality control of Listeria spp. and L. monocytogenes in ready-to-eat salads sold in Italy. Current Nutrition & Food Science, 7(1),57-62. doi:10.2174/157340111794941102

Raeymaekers, L. (2000). Basic principles of quantitative PCR. Molecular Biotechnology (pp. 15 (2) 115-122). pp. 15 (2) 115-122.

Rahman, M. T., Uddin, M. S., Sultana, R., Moue, A., & Setu, M. (n.d.). Polymerase Chain Reaction ( PCR ): A Short Review.

Rodríguez-Lázaro, D. (2013). Real-Time PCR in Food Science: Current Technology and Applications (Norfolk, UK: Caister Academic Press).

Rodríguez-Lázaro, D., & Hernández, M. (2013). Real-time PCR in food science: introduction. Curr. Issues Mol. Biol, 15, 25-38.

Sandberg, M., Lundberg, L., & Ferm, M. (2003). Real Time PCR for the detection and discrimination of cereal contamination in gluten free foods. 344–349. https://doi.org/10.1007/s00217-003-0758-4

Schnell, R. J., Ronning, C. M., & Knight, R. J. (1995). Identification of cultivars and validation of genetic relationships in Mangifera indica L. using RAPD markers.Theoretical and Applied Genetics (pp. 90 (2), 269–274). pp. 90 (2), 269–274.

Shokohi, T., Soteh, M. B. H., Pouri, Z. S., Hedayati, M. T., & Mayahi, S. (2010). Identification of Candida species using PCR-RFLP in cancer patients in Iran. 28(June), 147–152. https://doi.org/10.4103/0255-0857.62493

Singer, T., & Burke, E. (n.d.). DNA Flanking Insertions. 236.

Smith, C. J., & Osborn, A. M. (2009). Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS microbiology ecology, 67(1), 6-20. https://doi.org/10.1111/j.1574-6941.2008.00629.x

Stanek, G., & Hirschl, A. M. (2001). Multicenter Comparison Trial of DNA Extraction Methods and PCR Assays for Detection of. Society, 39(2), 519–524. https://doi.org/10.1128/JCM.39.2.519

Tabarzad, M., Kazemi, B., Vahidi, H., Aboofazeli,R., Shahhosseini, S., & Nafissi-Varcheh, N. (2014). Challenges to design and develop of DNA aptamers for protein targets. I. optimization of asymmetric PCR for generation of a single stranded DNA library. Iranian Journal of Pharmaceutical Research, 13(SUPPL), 133–141. https://doi.org/10.22037/ijpr.2014.1468

Tahmasebi, P., Farnia, P., Sheikholslami, F. M., & Velayati, A. A. (2012). Rapid identification of extensively and extremely drug resistant tuberculosis from multidrug resistant strains; using PCR-RFLP and PCR-SSCP. Iranian Journal of Microbiology, 4(4), 165–170.

Taylor, P., Poms, R. E., Klein, C. L., & Anklam, E. (2007). Methods for allergen analysis in food : a review Methods for allergen analysis in food : a review. https://doi.org/10.1080/02652030310001620423

Ugozzoli, L., Yam, P., Petz, L. D., Ferrara, G. B., Champlin, R. E., Forman, S. J., … Wallace, R. B. (1991). Amplification by the polymerase chain reaction of hypervariable regions of the human genome for evaluation of chimerism after bone marrow transplantation. Blood, 77(7), 1607–1615. https://doi.org/10.1182/blood.v77.7.1607.bloodjournal7771607

Valasek, M. A., & Repa, J. J. (2005). The power of real-time PCR. Advances in physiology education, 29(3), 151-159. doi:10.1152/advan.00019.2005.

Vos, P., Hogers, R., Bleeker, M., Reijans, M., Lee, T. Van De, Hornes, M., … Zabeau, M. (1995). AFLP: A new technique for DNA fingerprinting. Nucleic Acids Research, 23(21), 4407–4414. https://doi.org/10.1093/nar/23.21.4407

Wahyuni, S., Xu, D. H., Bermawie, N., Tsunematsu, H., & Ban, T. (2004).Wahyuni, S., Xu, D. H., Bermawie, N., Tsunematsu, H., & Ban, T. (2004). (n.d.). Skrining Issr Primer Studi Pendahuluan. 33–42.

Zhiqing Huang , Christopher F. Bassil, and S. K. M. (2017). Ovarian Cancer Including Fallopian Tube Cancer and Primary Peritoneal Cancer. Clinical Practice Guidelines, 1049(version 4), 1–124. https://doi.org/10.1007/978-1-62703-547-7

Zietkiewicz, E., Rafalski, A., & Labuda, D. (1994). Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics, Vol. 20, pp. 176–183. https://doi.org/10.1006/geno.1994.1151

Zong, C., Lu, S., Chapman, A. R., & Xie, X. S. (2012). Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science, 338(6114), 1622–1626. https://doi.org/10.1126/science.1229164

Zuo, Z., & Jabbar, K. J. (2016). COLD-PCR: Applications and advantages. Methods in Molecular Biology, 1392, 17–25. https://doi.org/10.1007/978-1-4939-3360-0_2

How to Cite
Giri Putra, L., Yonathan, C., Niedhatrata, N., Rizka Firdaus, M., & Yoewono, J. (2020). A review of the development of Polymerase Chain Reaction technique and its uses in Scientific field. Stannum : Jurnal Sains Dan Terapan Kimia, 2(1), 14-30. https://doi.org/10.33019/jstk.v2i1.1619
Abstract viewed = 5633 times
PDF (ENGLISH) downloaded = 3233 times