Elimination of Unspecific Amplification in the Exponential Amplification Reaction Using Polyethylene Glycol 200 (PEG 200) as a Cosolute

References

• Akram, F., F. I. Shah, R. Ibrar, T. Fatima, I. u Haq, W. Naseem, M. A. Gul, L. Tehreem, and G. Haider. 2023. Bacterial thermophilic DNA polymerases: A focus on prominent biotechnological applications. Analytical Biochemistry 671 (2023):115150. doi:10.1016/j.ab.2023.115150.
   PubMedGoogle Scholar
• Blandamer, M. J., J. B. F. N. Engberts, P. T. Gleeson, and J. C. R. Reis. 2005. Activity of water in aqueous systems: A frequently neglected property. Chemical Society Reviews 34 (5):440–58. doi:10.1039/b400473f.
   PubMed Web of Science ®Google Scholar
• Carter, J. G., L. O. Iturbe, J. Duprey, I. R. Carter, C. D. Southern, M. Rana, C. M. Whalley, A. Bosworth, A. D. Beggs, M. R. Hicks, et al. 2021. Ultrarapid detection of SARS-CoV-2 RNA using a reverse transcription-free exponential amplification reaction, RTF-EXPAR. Proceedings of the National Academy of Sciences of the United States of America 118 (35):e2100347118. doi:10.1073/pnas.2100347118.
   PubMed Web of Science ®Google Scholar
• Chang, F., Y. Sun, D. Yang, W. Yang, Y. Sun, C. Liu, and Z. Li. 2019. Specific detection of RNA mutation at single-base resolution by coupling the isothermal exponential amplification reaction (EXPAR) with chimeric DNA probe-aided precise RNA disconnection at the mutation site. Chemical Communications (Cambridge, England)55 (48):6934–7. doi:10.1039/c9cc02700a.
   PubMed Web of Science ®Google Scholar
• Chen, J., X. Q. Zhou, Y. J. Ma, X. L. Lin, Z. Dai, and X. Y. Zou. 2016. Asymmetric exponential amplification reaction on a toehold/biotin featured template: An ultrasensitive and specific strategy for isothermal microRNAs analysis. Nucleic Acids Research 44 (15):e130. doi:10.1093/nar/gkw504.
   PubMed Web of Science ®Google Scholar
• Chen, Y. J., C. Qian, C. Z. Liu, H. Shen, Z. J. Wang, J. F. Ping, J. Wu, and H. Chen. 2020. Nucleic acid amplification free biosensors for pathogen detection. Biosensors & Bioelectronics 153 (2020):112049. doi:10.1016/j.bios.2020.112049.
   PubMedGoogle Scholar
• Dames, S., R. L. Margraf, D. C. Pattison, C. T. Wittwer, and K. V. Voelkerding. 2007. Characterization of aberrant melting peaks in unlabeled probe assays. The Journal of Molecular Diagnostics: JMD 9 (3):290–6. doi:10.2353/jmoldx.2007.060139.
   PubMed Web of Science ®Google Scholar
• Deng, H. M., and Z. Q. Gao. 2015. Bioanalytical applications of isothermal nucleic acid amplification techniques. Analytica Chimica Acta 853 (2015):30–45. doi:10.1016/j.aca.2014.09.037.
   PubMedGoogle Scholar
• Emaus, M. N., and J. L. Anderson. 2021. Magnetic ionic liquids as microRNA extraction solvents and additives for the exponential amplification reaction. Analytica Chimica Acta 1181 (2021):338900. doi:10.1016/j.aca.2021.338900.
   PubMedGoogle Scholar
• Gao, R. R., R. Y. Ji, and W. Dong. 2023. Catalytic hairpin assembly-assisted dual-signal amplification platform for ultrasensitive detection of tumor markers and intelligent diagnosis of gastric cancer. Talanta 265 (2023):124812. doi:10.1016/j.talanta.2023.124812.
   PubMedGoogle Scholar
• Ghosh, S., S. Takahashi, T. Endoh, H. Tateishi-Karimata, S. Hazra, and N. Sugimoto. 2019. Validation of the nearest-neighbor model for Watson-Crick self-complementary DNA duplexes in molecular crowding condition. Nucleic Acids Research 47 (7):3284–94. doi:10.1093/nar/gkz071.
   PubMed Web of Science ®Google Scholar
• Ghosh, S., S. Takahashi, T. Ohyama, T. Endoh, H. Tateishi-Karimata, and N. Sugimoto. 2020. Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions. Proceedings of the National Academy of Sciences of the United States of America 117 (25):14194–201. doi:10.1073/pnas.1920886117.
   PubMed Web of Science ®Google Scholar
• Hoser, M. J., H. K. Mansukoski, S. W. Morrical, and K. E. Eboigbodin. 2014. Strand invasion based amplification (SIBA®): A novel isothermal DNA amplification technology demonstrating high specificity and sensitivity for a single molecule of target analyte. PLoS One 9 (11):e112656. doi:10.1371/journal.pone.0112656.
   PubMed Web of Science ®Google Scholar
• Huang, M. Q., X. M. Zhou, H. Y. Wang, and D. Xing. 2018. Clustered regularly interspaced short palindromic repeats/Cas9 triggered isothermal amplification for site-specific nucleic acid detection. Analytical Chemistry 90 (3):2193–200. doi:10.1021/acs.analchem.7b04542.
   PubMed Web of Science ®Google Scholar
• Jia, H. X., Z. P. Li, C. H. Liu, and Y. Q. Cheng. 2010. Ultrasensitive detection of microRNAs by exponential isothermal amplification. Angewandte Chemie (International ed. in English)49 (32):5498–501. doi:10.1002/anie.201001375.
   PubMed Web of Science ®Google Scholar
• Kao, M. C., and R. A. Durst. 2010. Detection of using nucleic acid sequence-based amplification and oligonucleotide probes for 16s ribosomal RNA. Analytical Letters 43 (10-11):1756–69. doi:10.1080/00032711003654005.
   Web of Science ®Google Scholar
• Knowles, D. B., A. S. LaCroix, N. F. Deines, I. Shkel, and M. T. Record. 2011. Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability. Proceedings of the National Academy of Sciences of the United States of America 108 (31):12699–704. doi:10.1073/pnas.1103382108.
   PubMed Web of Science ®Google Scholar
• Li, R. D., B. C. Yin, and B. C. Ye. 2016. Ultrasensitive, colorimetric detection of microRNAs based on isothermal exponential amplification reaction-assisted gold nanoparticle amplification. Biosensors & Bioelectronics 86 (2016):1011–6. doi:10.1016/j.bios.2016.07.042.
   PubMedGoogle Scholar
• Liang, X. G., K. Jensen, and M. D. Frank-Kamenetskii. 2004. Very efficient template/primer-independent DNA synthesis by thermophilic DNA polymerase in the presence of a thermophilic restriction endonuclease. Biochemistry 43 (42):13459–66. doi:10.1021/bi0489614.
   PubMed Web of Science ®Google Scholar
• Ma, C. P., H. Jing, P. S. Zhang, L. Z. Han, M. L. Zhang, F. X. Wang, S. Y. Niu, and C. Shi. 2018. An ultrafast one-step assay for the visual detection of RNA virus. Chemical Communications (Cambridge, England)54 (25):3118–21. doi:10.1039/c8cc00150b.
   PubMed Web of Science ®Google Scholar
• Ma, J., X. Li, C. Lou, X. Lin, Z. Zhang, D. Chen, and S. Yang. 2023. Utility of CRISPR/CAS mediated electrochemical biosensors. Analytical Methods: Advancing Methods and Applications 15 (31):3785–801. doi:10.1039/d3ay00903c.
   PubMed Web of Science ®Google Scholar
• Mao, J. K., S. Y. Tang, S. J. Liang, W. F. Pan, Y. L. Kang, J. B. Cheng, D. D. Yu, J. Chen, J. A. Lou, H. Zhao, et al. 2021. A new self-passivating template with the phosphorothioate strategy to effectively improve the detection limit and applicability of exponential amplification reaction. Analytical Methods: Advancing Methods and Applications 13 (35):3947–53. doi:10.1039/d1ay00520k.
   PubMed Web of Science ®Google Scholar
• Miyoshi, D., H. Karimata, and N. Sugimoto. 2006. Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions. Journal of the American Chemical Society 128 (24):7957–63. doi:10.1021/ja061267m.
   PubMed Web of Science ®Google Scholar
• Mok, E., E. Wee, Y. L. Wang, and M. Trau. 2016. Comprehensive evaluation of molecular enhancers of the isothermal exponential amplification reaction. Scientific Reports 6 (1):37837. doi:10.1038/srep37837.
   PubMedGoogle Scholar
• Mrozowich, T., D. J. Winzor, D. J. Scott, and T. R. Patel. 2019. Use of molecular crowding for the detection of protein self-association by size-exclusion chromatography. Analytical Biochemistry 584 (2019):113392. doi:10.1016/j.ab.2019.113392.
   PubMedGoogle Scholar
• Nakano, S., D. Yamaguchi, H. Tateishi-Karimata, D. Miyoshi, and N. Sugimoto. 2012. Hydration changes upon DNA folding studied by osmotic stress experiments. Biophysical Journal 102 (12):2808–17. doi:10.1016/j.bpj.2012.05.019.
   PubMed Web of Science ®Google Scholar
• Nakano, S., H. Karimata, T. Ohmichi, J. Kawakami, and N. Sugimoto. 2004. The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability. Journal of the American Chemical Society 126 (44):14330–1. doi:10.1021/ja0463029.
   PubMed Web of Science ®Google Scholar
• Nguyen, H. K., O. Fournier, U. Asseline, D. Dupret, and N. T. Thuong. 1999. Smoothing of the thermal stability of DNA duplexes by using modified nucleosides and chaotropic agents. Nucleic Acids Research 27 (6):1492–8. doi:10.1093/nar/27.6.1492.
   PubMed Web of Science ®Google Scholar
• Niu, C. Q., J. W. Liu, X. H. Xing, and C. Zhang. 2023. CRISPR-Cas12a-assisted elimination of the non-specific signal from non-specific amplification in the exponential amplification reaction. Analytica Chimica Acta 1251 (2023):340998. doi:10.1016/j.aca.2023.340998.
   PubMedGoogle Scholar
• Qian, C., R. Wang, H. Wu, F. Ji, and J. Wu. 2019. Nicking enzyme-assisted amplification (NEAA) technology and its applications: A review. Analytica Chimica Acta 1050 (2019):1–15. doi:10.1016/j.aca.2018.10.054.
   PubMedGoogle Scholar
• Qian, J. F., T. M. Ferguson, D. N. Shinde, A. J. Ramírez-Borrero, A. Hintze, C. Adami, and A. Niemz. 2012. Sequence dependence of isothermal DNA amplification via EXPAR. Nucleic Acids Research 40 (11):e87–e87. doi:10.1093/nar/gks230.
   PubMed Web of Science ®Google Scholar
• Reid, M. S., R. E. Paliwoda, H. Q. Zhang, and X. C. Le. 2018. Reduction of background generated from template-template hybridizations in the exponential amplification reaction. Analytical Chemistry 90 (18):11033–9. doi:10.1021/acs.analchem.8b02788.
   PubMed Web of Science ®Google Scholar
• Shi, C., F. Shang, M. Zhou, P. Zhang, Y. Wang, and C. Ma. 2016. Triggered isothermal PCR by denaturation bubble-mediated strand exchange amplification. Chemical Communications (Cambridge, England)52 (77):11551–4. doi:10.1039/c6cc05906f.
   PubMed Web of Science ®Google Scholar
• Song, J., S. Kim, H. Y. Kim, K. H. Hur, Y. Kim, and H. G. Park. 2021. A novel method to detect mutation in DNA by utilizing exponential amplification reaction triggered by the CRISPR-Cas9 system. Nanoscale 13 (15):7193–201. doi:10.1039/d1nr00438g.
   PubMed Web of Science ®Google Scholar
• Stellwagen, N. C., and E. Stellwagen. 2019. DNA thermal stability depends on solvent viscosity. The Journal of Physical Chemistry. B 123 (17):3649–57. doi:10.1021/acs.jpcb.9b01217.
   PubMed Web of Science ®Google Scholar
• Sun, H. M., S. Y. Zhou, Y. Liu, P. Lu, N. Qi, G. X. Wang, M. Yang, D. Q. Huo, and C. J. Hou. 2023. A fluorescent biosensor based on exponential amplification reaction-initiated CRISPR/Cas12a (EIC) strategy for ultrasensitive DNA methyltransferase detection. Analytica Chimica Acta 1239 (2023):340732. doi:10.1016/j.aca.2022.340732.
   PubMedGoogle Scholar
• Trinh, M. P., J. G. Carballo, G. B. Adkins, K. Z. Guo, and W. W. Zhong. 2020. Physical and chemical template-blocking strategies in the exponential amplification reaction of circulating microRNAs. Analytical and Bioanalytical Chemistry 412 (11):2399–412. doi:10.1007/s00216-020-02496-w.
   PubMed Web of Science ®Google Scholar
• Van Ness, J., L. K. Van Ness, and D. J. Galas. 2003. Isothermal reactions for the amplification of oligonucleotides. Proceedings of the National Academy of Sciences of the United States of America 100 (8):4504–9. doi:10.1073/pnas.0730811100.
   PubMed Web of Science ®Google Scholar
• Verma, P. K., S. Rakshit, R. K. Mitra, and S. K. Pal. 2011. Role of hydration on the functionality of a proteolytic enzyme α-chymotrypsin under crowded environment. Biochimie 93 (9):1424–33. doi:10.1016/j.biochi.2011.04.017.
   PubMed Web of Science ®Google Scholar
• Wang, J. P., B. J. Zou, J. Z. Rui, Q. X. Song, T. Kajiyama, H. Kambara, and G. H. Zhou. 2015. Exponential amplification of DNA with very low background using graphene oxide and single-stranded binding protein to suppress non-specific amplification. Microchimica Acta 182 (5-6):1095–101. doi:10.1007/s00604-014-1426-z.
   Web of Science ®Google Scholar
• Wang, L., C. Qian, H. Wu, W. J. Qian, R. Wang, and J. Wu. 2018. Technical aspects of nicking enzyme assisted amplification. The Analyst 143 (6):1444–53. doi:10.1039/c7an02037f.
   PubMed Web of Science ®Google Scholar
• Yu, Y. Y., Z. G. Chen, L. J. Shi, F. Yang, J. B. Pan, B. B. Zhang, and D. P. Sun. 2014. Ultrasensitive electrochemical detection of microRNA based on an arched probe mediated isothermal exponential amplification. Analytical Chemistry 86 (16):8200–5. doi:10.1021/ac501505a.
   PubMed Web of Science ®Google Scholar
• Zhang, X., Y. Jin, and B. Li. 2018. Copper nanocluster as a fluorescent indicator for label-free and sensitive detection of DNA hybridization assisted with a cascade isothermal exponential amplification reaction. New Journal of Chemistry 42 (7):5178–84. doi:10.1039/C7NJ05130A.
   Web of Science ®Google Scholar
• Zhang, Y. P., Y. X. Cui, X. Y. Li, Y. C. Du, A. N. Tang, and D. M. Kong. 2019. A modified exponential amplification reaction (EXPAR) with an improved signal-to-noise ratio for ultrasensitive detection of polynucleotide kinase. Chemical Communications (Cambridge, England)55 (53):7611–4. doi:10.1039/c9cc03568k.
   PubMed Web of Science ®Google Scholar
• Zhao, Y. M., X. F. Lv, Z. Peng, K. X. Zhao, D. Zhou, and Y. L. Deng. 2023. Microfluidic chip integrated with hydrogel microparticles and CDS cation interfacial exchange for the sensitive determination of miRNA. Analytical Letters 56 (16):2677–91. doi:10.1080/00032719.2023.2180803.
   Web of Science ®Google Scholar
• Zhou, H. X., G. N. Rivas, and A. P. Minton. 2008. Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences. Annual Review of Biophysics 37 (1):375–97. doi:10.1146/annurev.biophys.37.032807.125817.
   PubMedGoogle Scholar