Detection of specific RNA targets by multimerization

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Abstract

Detection of specific RNA targets via amplification-mediated techniques is widely used in fundamental studies and medicine due to an essential role of RNA in realization of genetic information and diseases development. Here, we report on an approach for detection of RNA targets based on a particular type of isothermal amplification, namely, reaction of nucleic acid multimerization. The proposed technique requires only a single DNA polymerase possessing reverse transcriptase, DNA-dependent DNA polymerase and strand-displacement activities. Reaction conditions that lead to efficient detection of the target RNAs through multimerization mechanism were determined. The approach was approved using genetic material of SARS-CoV-2 coronavirus as a model viral RNA. Reaction of multimerization allowed to differentiate SARS-CoV-2 RNA-positive samples from SARS-CoV-2 negative samples with high reliability. The proposed technique determines detection of RNA even in samples, which undergone multiple freezing.

About the authors

A. R Sakhabutdinova

Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences

Email: garafutdinovr@gmail.com
450054 Ufa, Bashkortostan, Russia

A. V Chemeris

Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences

Email: garafutdinovr@gmail.com
450054 Ufa, Bashkortostan, Russia

R. R Garafutdinov

Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences

Email: garafutdinovr@gmail.com
450054 Ufa, Bashkortostan, Russia

References

  1. Palazzo, A. F., and Lee, E. S. (2015) Non-coding RNA: what is functional and what is junk? Front. Genet., 6, 2, doi: 10.3389/fgene.2015.00002.
  2. Bukasov, R., Dossym, D., and Filchakova, O. (2021) Detection of RNA viruses from influenza and HIV to Ebola and SARS-CoV-2: a review, Anal. Methods, 13, 34-55, doi: 10.1039/d0ay01886d.
  3. Vindeirinho, J. M., Pinho, E., Azevedo, N. F., and Almeida, C. (2022) SARS-CoV-2 diagnostics based on nucleic acids amplification: from fundamental concepts to applications and beyond, Front. Cell. Infect. Microbiol., 12, 799678, doi: 10.3389/fcimb.2022.799678.
  4. Verna, R., Alallon, W., Murakami, M., Hayward, C. P. M., Harrath, A. H., Alwasel, S. H., Sumita, N. M., Alatas, O., Fedeli, V., Sharma, P., Fuso, A., Capuano, D. M., Capalbo, M., Angeloni, A., and Bizzarri, M. (2021) Analytical performance of COVID-19 detection methods (RT-PCR): scientific and societal concerns, Life (Basel), 11, 660, doi: 10.3390/life11070660.
  5. Thapa, S., Singh, K. R., Verma, R., Singh, J., and Singh, R. P. (2022) State-of-the-art smart and intelligent nanobiosensors for SARS-CoV-2 diagnosis, Biosensors (Basel), 12, 637, doi: 10.3390/bios12080637.
  6. Yin, B., Wan, X., Sohan, A. S. M. M. F., and Lin, X. (2022) Microfluidics-based POCT for SARS-CoV-2 diagnostics, Micromachines (Basel), 13, 1238, doi: 10.3390/mi13081238.
  7. Zhang, L., Jiang, H., Zhu, Z., Liu, J., and Li, B. (2022) Integrating CRISPR/Cas within isothermal amplification for point-of-care assay of nucleic acid, Talanta, 243, 123388, doi: 10.1016/j.talanta.2022.123388.
  8. Islam, M. M., and Koirala, D. (2022) Toward a next-generation diagnostic tool: a review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses, Anal. Chim. Acta, 1209, 339338, doi: 10.1016/j.aca.2021.339338.
  9. Maiti, B., Anupama, K. P., Rai, P., Karunasagar, I., and Karunasagar, I. (2022) Isothermal amplification-based assays for rapid and sensitive detection of severe acute respiratory syndrome coronavirus 2: opportunities and recent developments, Rev. Med. Virol., 32, e2274, doi: 10.1002/rmv.2274.
  10. Chaouch, M. (2021) Loop-mediated isothermal amplification (LAMP): an effective molecular point-of-care technique for the rapid diagnosis of coronavirus SARS-CoV-2, Rev. Med. Virol., 31, e2215, doi: 10.1002/rmv.2215.
  11. Bi, S., Yue, S., and Zhang, S. (2017) Hybridization chain reaction: a versatile molecular tool for biosensing, bioimaging, and biomedicine, Chem. Soc. Rev., 46, 4281-4298, doi: 10.1039/c7cs00055c.
  12. Yue, S., Li, Y., Qiao, Z., Song, W., and Bi, S. (2021) Rolling circle replication for biosensing, bioimaging, and biomedicine, Trends Biotechnol., 39, 1160-1172, doi: 10.1016/j.tibtech.2021.02.007.
  13. Garafutdinov, R. R., Sakhabutdinova, A. R., Gilvanov, A. R., and Chemeris, A. V. (2021) Rolling circle amplification as a universal method for the analysis of a wide range of biological targets, Russ. J. Bioorg. Chem., 47, 1172-1189, doi: 10.1134/S1068162021060078.
  14. Bodulev, O. L., and Sakharov, I. Y. (2020) Isothermal nucleic acid amplification techniques and their use in bioanalysis, Biochemistry (Moscow), 85, 147-166, doi: 10.1134/S0006297920020030.
  15. Hafner, G. J., Yang, I. C., Wolter, L. C., Stafford, M. R., and Giffard, P. M. (2001) Isothermal amplification and multimerization of DNA by Bst DNA polymerase, BioTechniques, 30, 852-856, doi: 10.2144/01304rr03.
  16. Garafutdinov, R. R., Burkhanova, G. F., Maksimov, I. V., and Sakhabutdinova, A. R. (2023) New method for microRNA detection based on multimerization, Anal. Biochem., 664, 115049, doi: 10.1016/j.ab.2023.115049.
  17. Wang, G., Ding, X., Hu, J., Wu, W., Sun, J., and Mu, Y. (2017) Unusual isothermal multimerization and amplification by the strand-displacing DNA polymerases with reverse transcription activities, Sci. Rep., 7, 13928, doi: 10.1038/s41598-017-13324-0.
  18. Sakhabutdinova, A. R., Kamalov, M. I., Salakhieva, D. V., Mavzyutov, A. R., and Garafutdinov, R. R. (2021) Inhibition of nonspecific polymerase activity using poly(aspartic) acid as a model anionic polyelectrolyte, Anal. Biochem., 628, 114267, doi: 10.1016/j.ab.2021.114267.
  19. Garafutdinov, R. R., Gilvanov, A. R., and Sakhabutdinova, A. R. (2020) The influence of reaction conditions on DNA multimerization during isothermal amplification with Bst DNA polymerase, Appl. Biochem. Biotechnol., 190, 758-771, doi: 10.1007/s12010-019-03127-6.
  20. Garafutdinov, R. R., Gilvanov, A. R., Kupova, O. Y., and Sakhabutdinova, A. R. (2020) Effect of metal ions on isothermal amplification with Bst exo- DNA polymerase, Int. J. Biol. Macromol., 161, 1447-1455, doi: 10.1016/j.ijbiomac.2020.08.028.
  21. Garafutdinov, R. R., Sakhabutdinova, A. R., Kupryushkin, M. S., and Pyshnyi, D. V. (2020) Prevention of DNA multimerization during isothermal amplification with Bst exo- DNA polymerase, Biochimie, 168, 259-267, doi: 10.1016/j.biochi.2019.11.013.
  22. Sakhabutdinova, A. R., Mirsaeva, L. R., Garafutdinov, R. R., Oscorbin, I. P., and Filipenko, M. L. (2020) Elimination of DNA multimerization arising from isothermal amplification in the presence of Bst exo- DNA polymerase, Russ. J. Bioorg. Chem., 46, 52-59, doi: 10.1134/s1068162020010082.
  23. Qasem, A., Shaw, A. M., Elkamel, E., and Naser, S. A. (2021) Coronavirus disease 2019 (COVID-19) diagnostic tools: a focus on detection technologies and limitations, Curr. Issues Mol. Biol., 43, 728-748, doi: 10.3390/cimb43020053.
  24. Panchali, M. J. L., Oh, H. J., Lee, Y. M., Kim, C. M., Tariq, M., Seo, J. W., Kim, D. Y., Yun, N. R., and Kim, D. M. (2022) Accuracy of real-time polymerase chain reaction in COVID-19 patients, Microbiol. Spectr., 10, e0059121, doi: 10.1128/spectrum.00591-21.
  25. Meena, D. S., Kumar, B., Kachhwaha, A., Kumar, D., Khichar, S., Bohra, G. K., Sharma, A., Kothari, N., Garg, P., Sureka, B., Banerjee, M., Garg, M. K., and Misra, S. (2022) Comparison of clinical characteristics and outcome in RT-PCR positive and false-negative RT-PCR for COVID-19: a retrospective analysis, Infez. Med., 30, 403-411, doi: 10.53854/liim-3003-8.
  26. Jackson, L. N., Chim, N., Shi, C., and Chaput, J. C. (2019) Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase, Nucleic Acids Res., 47, 6973-6983, doi: 10.1093/nar/gkz513.
  27. Sakhabutdinova, A. R., Gazizov, R. R., Chemeris, A. V., and Garafutdinov, R. R. (2022) Reverse transcriptase-free detection of viral RNA using Hemo KlenTaq DNA polymerase, Anal. Biochem., 659, 114960, doi: 10.1016/j.ab.2022.114960.
  28. Silva, A., Azevedo, M., Sampaio-Maia, B., and Sousa-Pinto, B. (2022) The effect of mouthrinses on severe acute respiratory syndrome coronavirus 2 viral load: A systematic review, J. Am. Dent. Assoc., 153, 635-648, doi: 10.1016/j.adaj.2021.12.007.
  29. Hern�ndez-V�squez, A., Barrenechea-Pulache, A., Comand�, D., and Aza�edo, D. (2022) Mouthrinses and SARS-CoV-2 viral load in saliva: a living systematic review, Evid. Based Dent., doi: 10.1038/s41432-022-0253-z.
  30. Tallmadge, R. L., Laverack, M., Cronk, B., Venugopalan, R., Martins, M., Zhang, X., Elvinger, F., Plocharczyk, E., and Diel, D. G. (2022) Viral RNA load and infectivity of SARS-CoV-2 in paired respiratory and oral specimens from symptomatic, asymptomatic, or postsymptomatic individuals, Microbiol. Spectr., 10, e0226421, doi: 10.1128/spectrum.02264-21.
  31. Fujiya, Y., Sato, Y., Katayama, Y., Nirasawa, S., Moriai, M., Saeki, M., Yakuwa, Y., Kitayama, I., Asanuma, K., Kuronuma, K., and Takahashi, S. (2022) Viral load may impact the diagnostic performance of nasal swabs in nucleic acid amplification test and quantitative antigen test for SARS-CoV-2 detection, J. Infect. Chemother., 28, 1590-1593, doi: 10.1016/j.jiac.2022.07.023.
  32. Dutta, D., Naiyer, S., Mansuri, S., Soni, N., Singh, V., Bhat, K. H., Singh, N., Arora, G., and Mansuri, M. S. (2022) COVID-19 diagnosis: a comprehensive review of the RT-qPCR method for detection of SARS-CoV-2, Diagnostics (Basel), 12, 1503, doi: 10.3390/diagnostics12061503.
  33. Ravina, Kumar, A., Manjeet, Twinkle, Subodh, Narang, J., and Mohan, H. (2022) Analytical performances of different diagnostic methods for SARS-CoV-2 virus - a review, Sens. Int., 3, 100197, doi: 10.1016/j.sintl.2022.100197.
  34. Marando, M., Tamburello, A., Gianella, P., Taylor, R., Bernasconi, E., Fusi-Schmidhauser, T. (2022) Diagnostic sensitivity of RT-PCR assays on nasopharyngeal specimens for detection of SARS-CoV-2 infection: a systematic review and meta-analysis, Caspian J. Intern. Med., 13, 139-147, doi: 10.22088/cjim.13.0.139.
  35. Garafutdinov, R. R., Galimova, A. A., and Sakhabutdinova, A. R. (2017) Polymerase chain reaction with nearby primers, Anal. Biochem., 518, 126-133, doi: 10.1016/j.ab.2016.11.017.

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