The Efficiency of Various DNA Polymerases for Amplification of Long Sequences from Genomic DNA and cDNA of Cultivated Potato

Мұқаба

Дәйексөз келтіру

Толық мәтін

Ашық рұқсат Ашық рұқсат
Рұқсат жабық Рұқсат берілді
Рұқсат жабық Тек жазылушылар үшін

Аннотация

Amplification of long fragments from complex templates, such as eukaryotic genomic DNA, is considered a difficult task for most DNA polymerases. In this research, 6 variants of DNA polymerases were used to amplify full-length sequences from the genomic DNA of Solanum tuberosum genes encoding translation initiation factors of the eIF4E family, as well as for the synthesis of fragments of the potato Y virus genome from cDNA of potato plants infected by this virus. It was found that the efficiency of amplification by various DNA polymerases generally decreased with increasing length of the amplicons. LongAmp and Platinum SuperFi II polymerases demonstrated the highest efficiency in the synthesis of long fragments, which made it possible to synthesize PCR products with a length of more than 10,000 base pairs with high efficiency. The lowest efficiency was demonstrated by Encyclo polymerase. None of the DNA polymerases provided efficient amplification of all the studied DNA fragments. At the same time, any of the studied DNA fragments could be effectively amplified using at least one DNA polymerase variant. Thus, the choice of DNA polymerase was of key importance for the efficiency of the synthesis of a desired PCR product.

Авторлар туралы

A. Antipov

All-Russia Research Institute of Agricultural Biotechnology

Email: stresslab@yandex.ru
Russia, 127550, Moscow, Timiryazevskaya, 42

N. Zlobin

All-Russia Research Institute of Agricultural Biotechnology

Хат алмасуға жауапты Автор.
Email: stresslab@yandex.ru
Russia, 127550, Moscow, Timiryazevskaya, 42

Әдебиет тізімі

  1. Karunanathie H., Kee P.S., Ng S.F., Kennedy M.A., Chua E.W. // Biochimie. 2022. V. 197. P. 130–143. https://doi.org/10.1016/j.biochi.2022.02.009
  2. Knierim E., Lucke B., Schwarz J.M., Schuelke M., Seelow D. // PloS One. 2011. V. 6. № 11. P. e28240. https://doi.org/10.1371/journal.pone.0028240
  3. Qiao W., Yang Y., Sebra R., Mendiratta G., Gaedigk A., Desnick R.J., Scott S.A. // Hum. Mutat. 2016. V. 37. № 3. P. 315–323. https://doi.org/10.1002/humu.22936
  4. Martijn J., Lind A.E., Schön M.E., Spiertz I., Juzokaite L., Bunikis I. et al. // Environ. Microbiol. 2019. V. 21. № 7. P. 2485–2498. https://doi.org/10.1111/1462-2920.14636
  5. Karst S.M., Ziels R.M., Kirkegaard R.H., Sørensen E.A., McDonald D., Zhu Q., Knight R., Albertsen, M. // Nat. Methods. 2021. V. 18. № 2. P. 165–169. https://doi.org/10.1038/s41592-020-01041-y
  6. Brait N., Külekçi B., Goerzer I. // BMC Genomics. 2022. V. 23. № 1. P. 1–16. https://doi.org/10.1186/s12864-021-08272-z
  7. Briscoe A.G., Goodacre S., Masta S.E., Taylor M.I., Arnedo M.A., Penney D., Kenny J., Creer S. // PLoS One. 2013. V. 8. № 5. P. e62404. https://doi.org/10.1371/journal.pone.0062404
  8. Jia H., Guo Y., Zhao W., Wang K. // Sci. Rep. 2014. V. 4. № 1. P. 1–8. https://doi.org/10.1038/srep05737
  9. Ozaki Y., Suzuki S., Shigenari A., Okudaira Y., Kikkawa E., Oka A. et al. // Tissue Antigens. 2014. V. 83. № 1. P. 10–16. https://doi.org/10.1111/tan.12258
  10. Deiner K., Renshaw M.A., Li Y., Olds B.P., Lodge D.M., Pfrender M.E. // Methods Ecol. Evol. 2017. V. 8. № 12. P. 1888–1898. https://doi.org/10.1111/2041-210X.12836
  11. Togi S., Ura H., Niida Y. Optimization and Validation of Multimodular // J. Mol. Diagn. 2021. V. 23. № 4. P. 424–446. https://doi.org/10.1016/j.jmoldx.2020.12.009
  12. Günther S., Sommer G., Von Breunig F., Iwanska A., Kalinina T., Sterneck M., Will H. // J. Clin. Microbiol. 1998. V. 36. № 2. P. 531–538. https://doi.org/10.1128/JCM.36.2.531-538.1998
  13. Trémeaux P., Caporossi A., Ramière C., Santoni E., Tarbouriech N., Thélu M.A. et al. // Clin. Microbiol. Infect. 2016. V. 22. № 5. P. 460-e1. https://doi.org/10.1016/j.cmi.2016.01.015
  14. Joffret M.L., Polston P.M., Razafindratsimandresy R., Bessaud M., Heraud J.M., Delpeyroux F. // Front. Microbiol. 2018. V. 9. P. 2339. https://doi.org/10.3389/fmicb.2018.02339
  15. Isaacs S.R., Kim K.W., Cheng J.X., Bull R.A., Stelzer-Braid S., Luciani F. et al. // Sci. Rep. 2018. V. 8. № 1. P. 1–9. https://doi.org/10.1038/s41598-018-30322-y
  16. Shagin D.A., Lukyanov K.A., Vagner L.L., Matz M.V. // Nucleic Acids Res. 1999. V. 27. № 18. P. e23-i. https://doi.org/10.1093/nar/27.18.e23-i
  17. Zhao Z., Xie X., Liu W., Huang J., Tan J., Yu H., Zong W. et al. // Mol. Plant. 2022. V. 15. № 4. P. 620–629. https://doi.org/10.1016/j.molp.2021.12.018
  18. Ignatov K.B., Kramarov V.M. //Biochemistry (Moscow). 2009. V. 74. № 5. P. 557–561. https://doi.org/10.1134/S0006297909050113
  19. Cheng S., Fockler C., Barnes W.M., Higuchi R. // PNAS. 1994. V. 91. № 12. P. 5695–5699. https://doi.org/10.1073/pnas.91.12.5695
  20. Waggott W. // Humana Press. 1998. V. 16. P. 81–91. https://doi.org/10.1385/0-89603-499-2:81
  21. Kasajima I. // Trends Res. 2018. V. 1. P. 1–2. https://doi.org/10.15761/TR.1000115
  22. Singh R.P., Singh M., King R.R. // J. Virol. Methods. 1998. V. 74. № 2. P. 231–235. https://doi.org/10.1016/S0166-0934(98)00092-5
  23. Singh R.P., Nie X., Singh M., Coffin R., Duplessis P. // J. Virol. Methods. 2002. V. 99. № 1–2. P. 123–131. https://doi.org/10.1016/S0166-0934(01)00391-3
  24. Valcarcel J., Reilly K., Gaffney M., O’Brien N.M. // Potato Res. 2015. V. 58. № 3. P. 221–244. https://doi.org/10.1007/s11540-015-9299-z
  25. Анисимова И.Н., Алпатьева Н.В., Абдуллаев Р.А., Карабицина Ю.И., Кузнецова Е.Б. Скрининг генетических ресурсов растений с использованием ДНК-маркеров: основные принципы, выделение ДНК, постановка ПЦР, электрофорез в агарозном геле. / Ред. Радченко Е.Е.: Методические указания ВИР. СПб: ВИР, 2018. 47 с. https://doi.org/10.30901/978-5-905954-81-8
  26. Moury B., Charron C., Janzac B., Simon V., Gallois J.L., Palloix A., Caranta C. // Infect. Genet. Evol. 2014. V. 27. P. 472–480. https://doi.org/10.1016/j.meegid.2013.11.024
  27. Lucioli A., Tavazza R., Baima S., Fatyol K., Burgyan J., Tavazza M. // Front. Microbiol. 2022. V. 13. https://doi.org/10.3389/fmicb.2022.873930
  28. Quenouille J., Vassilakos N., Moury B. // Plant Pathol. 2013. V. 14. № 5. P. 439–452. https://doi.org/10.1111/mpp.12024
  29. Suzuki Y., Sugano S. // Genomics Protocols. 2001. V. 175. P. 143–153. https://doi.org/10.1385/1-59259-235-X:143
  30. Ling A.K., Munro M., Chaudhary N., Li C., Berru M., Wu B., Durocher D., Martin A. // EMBO Rep. 2020. V. 21. № 8. P. e49823. https://doi.org/10.15252/embr.201949823
  31. Xie X., Muruato A., Lokugamage K.G., Narayanan K., Zhang X., Zou J., Liu J. et al. // Cell Host Microbe. 2020. V. 27. № 5. P. 841–848. https://doi.org/10.1016/j.chom.2020.04.004
  32. Sannier G., Dube M., Dufour C., Richard C., Brassard N., Delgado G.G., Pagliuzza A., Baxter A.E., Niessl J., Brunet-Ratnasingham E., Charlebois R., Routy B., Routy J.P., Fromentin R., Chomont N., Kaufmann D.E. // Cell Rep. 2021. V. 36. № 9. https://doi.org/10.1016/j.celrep.2021.109643
  33. Keraite I., Becker P., Canevazzi D., Frias-López C., Dabad M., Tonda-Hernandez R., Paramonov I., Ingham M.J., Brun-Heath I., Leno J., Abulí A., Garcia-Arumí E., Heath S.C., Gut M., Gut I.G. // Nat. Commun. 2022. V. 13. № 1. P. 1–12. https://doi.org/10.1038/s41467-022-33530-3
  34. Maniego J., Pesko B., Habershon-Butcher J., Hincks P., Taylor P., Tozaki T., Ohnuma A., Stewart G., Proudman C., Ryder E. // Drug Testing and Analysis. 2022. V. 14. № 8. P. 1429–1437. https://doi.org/10.1002/dta.3267
  35. Tasca F., Brescia M., Wang Q., Liu J., Janssen J.M., Szuhai K., Gonçalves M.A. // Nucleic Acids Res. 2022. V. 50. № 13. P. 7761–7782. https://doi.org/10.1093/nar/gkac567
  36. Vincendeau E., Wei W., Zhang X., Planchais C., Yu W., Lenden-Hasse H., Cokelaer T., da Fonseca J.P., Mouquet H., Adams D.J., Alt F.W., Jackson S.P., Balmus G., Lescale C., Deriano L. // Nat. Commun. 2022. V. 13. № 1. P. 1–16. https://doi.org/10.1038/s41467-022-31287-3

Қосымша файлдар

Қосымша файлдар
Әрекет
1. JATS XML
Жүктеу
2.

Жүктеу (672KB)
Метадеректер
3.

Жүктеу (601KB)
Метадеректер

© А.Д. Антипов, Н.Е. Злобин, 2023