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Principle of Emulsion PCR and Its Applications in Biotechnology

  • Chai, Changhoon (Department of Applied Animal Science, Kangwon National University)
  • Received : 2019.11.20
  • Accepted : 2019.12.11
  • Published : 2019.12.31

Abstract

Emulsion polymerase chain reaction (PCR) is performed on compartmentalized DNA, allowing a large number of PCR reactions to be carried out in parallel. Emulsion PCR has unique advantages in DNA amplification. It can be applied in many molecular biological assays, especially those requiring highly sensitive and specific DNA amplification. This review discusses the principle of emulsion PCR and its applications in biotechnology. Related technologies are also discussed.

Keywords

References

  1. Bayat P, Nosrati R, Alibolandi M, Rafatpanah H, Abnous K, Khedri M, Ramezani M. 2018. SELEX methods on the road to protein targeting with nucleic acid aptamers. Biochimie. 154:132-155. https://doi.org/10.1016/j.biochi.2018.09.001
  2. BioRad. QX200 droplet digital PCR system. https://www.bio-rad.com/ko-kr/product/qx200-droplet-digital-pcrsystem?ID=MPOQQE4VY. Accessed Oct. 31 2019.
  3. Blind M and Blank M. 2015. Aptamer selection technology and recent advances. Mol Ther Nucleic Acids. 4:e223. https://doi.org/10.1038/mtna.2014.74
  4. Byrnes SA, Chang TC, Huynh T, Astashkina A, Weigl BH, Nichols KP. 2018. Simple polydisperse droplet emulsion polymerase chain reaction with statistical volumetric correction compared with microfluidic droplet digital polymerase chain reaction. Anal Chem. 90:9374-9380. https://doi.org/10.1021/acs.analchem.8b01988
  5. Chai C and Oh S-W. 2015. Emulsion PCR to improve sensitivity of PCR-based E. coli O157:H7 ATCC 35150 detection. Food Sci Biotechnol. 24:1559-1563. https://doi.org/10.1007/s10068-015-0201-1
  6. Chiu CY and Miller SA. 2019. Clinical metagenomics. Nat Rev Genet. 20:341-355. https://doi.org/10.1038/s41576-019-0113-7
  7. Demuth C, Spindler K-LG, Johansen JS, Pallisgaard N, Nielsen D, Hogdall E, Vittrup B, Sorensen BS. 2018. Measuring KRAS mutations in circulating tumor DNA by droplet digital PCR and next-generation sequencing. Transl Oncol. 11:1220-1224. https://doi.org/10.1016/j.tranon.2018.07.013
  8. Diehl F, Li M, He Y, Kinzler KW, Vogelstein B, Dressman D. 2006. BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions. Nat Methods. 3:551-559. https://doi.org/10.1038/nmeth898
  9. Du Y, Zhao X, Zhao B, Xu Y, Shi W, Ren F, Wu Y, Hu R, Fan X, Zhang Q, Zhang X, Zhang W, Wu W, Shi B, Zhao H, Zhao K. 2019. A novel emulsion PCR method coupled with fluorescence spectrophotometry for simultaneous qualitative, quantitative and high-throughput detection of multiple DNA targets. Sci Rep. 9:184. https://doi.org/10.1038/s41598-018-36981-1
  10. Ehrlich DJ, McKenna BK, Evans JG, Belkina AC, Denis GV, Sherr DH, Cheung MC. 2011. Parallel imaging microfluidic cytometer. In: Z. Darzynkiewicz, E. Holden, A. Orfao, W. Telford and D. Wlodkowic (eds.) Methods in cell biology. Academic Press. p 49-75.
  11. Hayat MA. 2008. Methods of cancer diagnosis, Therapy and prognosis: breast carcinoma. Springer, Heidelberg.
  12. Heredia NJ and Makarewicz AJ. 2016. Methods and compositions for using oils for analysis and detection of molecules. US9427737B2. U.S. Patent and Trademark Office.
  13. Holtze C, Rowat AC, Agresti JJ, Hutchison JB, Angile FE, Schmitz CHJ, Koster S, Duan H, Humphry KJ, Scanga RA, Johnson JS, Pisignano D, Weitz DA. 2008. Biocompatible surfactants for water-in-fluorocarbon emulsions. Lab Chip. 8:1632-1639. https://doi.org/10.1039/b806706f
  14. Illumina. 2013. 16s metagenomic sequencing library preparation. https://support.illumina.com/documents/documentation/chemistry_documentation/16s/16s-metagenomiclibrary-prep-guide-15044223-b.pdf. Accessed 2019-10-17.
  15. Kanagal-Shamanna R. 2016. Emulsion PCR: Techniques and applications. In: R. Luthra, R. R. Singh and K. P. Patel (eds.) Clinical Applications of PCR. Springer. p 33-42.
  16. Kang D-K, Ali MM, Zhang K, Huang SS, Peterson E, Digman MA, Gratton E, Zhao W. 2014. Rapid detection of single bacteria in unprocessed blood using integrated comprehensive droplet digital detection. Nat Commun. 5:5427. https://doi.org/10.1038/ncomms6427
  17. Kihana M, Mizuno F, Sawafuji R, Wang L, Ueda S. 2013. Emulsion PCR-coupled target enrichment: An effective fishing method for high-throughput sequencing of poorly preserved ancient DNA. Gene. 528:347-351. https://doi.org/10.1016/j.gene.2013.07.040
  18. Kralik P and Ricchi M. 2017. A basic guide to real time pcr in microbial diagnostics: Definitions, parameters, and everything. Front Microbiol. 8.
  19. Linderholm AE. 2019. DNA: Next generation sequencing. In: S. L. L. Varela (ed.) The encyclopedia of archaeological sciences. Wiley. p 1-3.
  20. Ma Y-D, Luo K, Chang W-H, Lee G-B. 2018. A microfluidic chip capable of generating and trapping emulsion droplets for digital loop-mediated isothermal amplification analysis. Lab Chip. 18:296-303. https://doi.org/10.1039/C7LC01004D
  21. Martinez-Hernandez F, Garcia-Heredia I, Lluesma Gomez M, Maestre-Carballa L, Martinez Martinez J, Martinez-Garcia M. 2019. Droplet digital PCR for estimating absolute abundances of widespread pelagibacter viruses. Front Microbiol. 10.
  22. Mu D, Yan L, Tang H, Liao Y. 2015. A sensitive and accurate quantification method for the detection of hepatitis B virus covalently closed circular DNA by the application of a droplet digital polymerase chain reaction amplification system. Biotechnol Lett. 37:2063-2073. https://doi.org/10.1007/s10529-015-1890-5
  23. Myerski A, Siegel A, Engstrom J, McGowan I, Brand RM. 2019. The use of droplet digital PCR to quantify HIV-1 replication in the colorectal explant model. AIDS Res Hum Retroviruses. 35:326-334. https://doi.org/10.1089/aid.2018.0227
  24. Pekin D, Skhiri Y, Baret J, Le Corre D, Mazutis L, Salem CB, Griffiths A, Laurent-Puig P, Taly V. 2010. Droplet-based microfluidics for the quantitative detection of rare mutations. In: Proceedings of MicroTAS. p 58-60.
  25. Pelt-Verkuil Ev, Belkum Av, Hays JP. 2008. Principles and technical aspects of PCR amplification. Springer, Heidelberg.
  26. Perkins G, Lu H, Garlan F, Taly V. 2017. Droplet-based digital PCR: Application in cancer research. In: G. S. Makowski (ed.) Advances in Clinical Chemistry. Elsevier. p 43-91.
  27. Quince C, Walker AW, Simpson JT, Loman NJ, Segata N. 2017. Shotgun metagenomics, from sampling to analysis. Nat Biotechnol. 35:833. https://doi.org/10.1038/nbt.3935
  28. Schutze T, Rubelt F, Repkow J, Greiner N, Erdmann VA, Lehrach H, Konthur Z, Glokler J. 2011. A streamlined protocol for emulsion polymerase chain reaction and subsequent purification. Anal Biochem. 410:155-157. https://doi.org/10.1016/j.ab.2010.11.029
  29. Shanks ME, Downes SM, Copley RR, Lise S, Broxholme J, Hudspith KAZ, Kwasniewska A, Davies WIL, Hankins MW, Packham ER, Clouston P, Seller A, Wilkie AOM, Taylor JC, Ragoussis J, Nemeth AH. 2012. Next-generation sequencing (NGS) as a diagnostic tool for retinal degeneration reveals a much higher detection rate in early-onset disease. Europ J Hum Genet. 21:274. https://doi.org/10.1038/ejhg.2012.172
  30. Shao K, Ding W, Wang F, Li H, Ma D, Wang H. 2011. Emulsion PCR: A high efficient way of PCR amplification of random DNA libraries in aptamer selection. PLoS One. 6:e24910. https://doi.org/10.1371/journal.pone.0024910
  31. Spangler R, Goddard NL, Thaler DS. 2009. Optimizing Taq polymerase concentration for improved signal-to-noise in the broad range detection of low abundance bacteria. PLoS One. 4:e7010. https://doi.org/10.1371/journal.pone.0007010
  32. Strain MC, Lada SM, Luong T, Rought SE, Gianella S, Terry VH, Spina CA, Woelk CH, Richman DD. 2013. Highly precise measurement of HIV DNA by droplet digital PCR. PLoS One. 8:e55943. https://doi.org/10.1371/journal.pone.0055943
  33. Swami A, Espinosa G, Guillot S, Raspaud E, Boue F, Langevin D. 2008. Confinement of DNA in water-in-oil microemulsions. Langmuir. 24:11828-11833. https://doi.org/10.1021/la802233e
  34. Tuerk C and Gold L. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 249:505-510. https://doi.org/10.1126/science.2200121
  35. Viljoen GJ, Nel LH, Crowther JR. 2005. Molecular diagnostic PCR handbook. Springer, Heidelberg.
  36. Williams R, Peisajovich SG, Miller OJ, Magdassi S, Tawfik DS, Griffiths AD. 2006. Amplification of complex gene libraries by emulsion PCR. Nat Methods. 3:545-550. https://doi.org/10.1038/nmeth896
  37. Witt M, Phung NL, Stalke A, Walter J-G, Stahl F, von Neuhoff N, Scheper T. 2017. Comparing two conventional methods of emulsion PCR and optimizing of Tegosoft-based emulsion PCR. Eng Life Sci. 17:953-958. https://doi.org/10.1002/elsc.201700047
  38. Yang R, Paparini A, Monis P, Ryan U. 2014. Comparison of nextgeneration droplet digital PCR (ddPCR) with quantitative PCR (qPCR) for enumeration of Cryptosporidium oocysts in faecal samples. Int J Parasitol. 44:1105-1113. https://doi.org/10.1016/j.ijpara.2014.08.004
  39. Yufa R, Krylova SM, Bruce C, Bagg EA, Schofield CJ, Krylov SN. 2015. Emulsion PCR significantly improves nonequilibrium capillary electrophoresis of equilibrium mixtures-based aptamer selection: Allowing for efficient and rapid selection of aptamer to unmodified ABH2 protein. Anal Chem. 87:1411-1419. https://doi.org/10.1021/ac5044187
  40. Zhang L, Jing X, Chen W, Bai J, Vasseur L, He W, You M. 2019. Selection of reference genes for expression analysis of plantderived microRNAs in Plutella xylostella using qRT-PCR and ddPCR. PLoS One. 14:e0220475. https://doi.org/10.1371/journal.pone.0220475
  41. Zhu Z, Jenkins G, Zhang W, Zhang M, Guan Z, Yang CJ. 2012. Single-molecule emulsion PCR in microfluidic droplets. Anal Bioanal Chem. 403:2127-2143. https://doi.org/10.1007/s00216-012-5914-x