Rational redesign of high-activity G-quadruplex DNAzyme through flanking and looping of nucleobases

1. Liu, R., Li, J., Salena, B. J. & Li, Y. Aptamer and DNAzyme based colorimetric biosensors for pathogen detection. Angew. Chem. Int. Ed. 64 (4), e202418725. (2025).

2. Adeoye, R. I. et al. Catalytic activities of multimeric G-quadruplex dnazymes. Catalysts 9 (7), 613 (2019).

   Google Scholar 

3. Sahayasheela, V. J. & Sugiyama, H. RNA G-quadruplex in functional regulation of noncoding RNA: challenges and emerging opportunities. Cell. Chem. Biology. 31 (1), 53–70 (2024).

   Google Scholar 

4. Wang, Y. et al. A self-assembled G-quadruplex/hemin DNAzyme-driven DNA walker strategy for sensitive and rapid detection of lead ions based on rolling circle amplification. Biosensors 13 (8), 761 (2023).

   Google Scholar 

5. Kong, D. M., Xu, J. & Shen, H. X. Positive effects of ATP on G-quadruplex-hemin DNAzyme-mediated reactions. Anal. Chem. 82 (14), 6148–6153 (2010).

   Google Scholar 

6. Qi, C. et al. Activity enhancement of G-quadruplex/hemin DNAzyme by spermine. RSC Adv. 4 (3), 1441–1448 (2014).

   Google Scholar 

7. Adeoye, R. I. et al. Spermine enhances the peroxidase activities of multimeric antiparallel G-quadruplex dnazymes. Biosensors 15 (1), 12 (2025).

   Google Scholar 

8. Stefan, L., Denat, F. & Monchaud, D. Deciphering the DNAzyme activity of multimeric quadruplexes: insights into their actual role in the telomerase activity evaluation assay. J. Am. Chem. Soc. 133 (50), 20405–20415 (2011).

   Google Scholar 

9. Cheng, Y. et al. The noncovalent dimerization of a G-quadruplex/hemin DNAzyme improves its biocatalytic properties. Chem. Sci. 11 (33), 8846–8853 (2020).

   Google Scholar 

10. Zhang, Y. et al. Design of a high-sensitivity dimeric G-quadruplex/hemin DNAzyme biosensor for Norovirus detection. Molecules 26 (23), 7352 (2021).

    Google Scholar 

11. Kosman, J., Żukowski, K. & Juskowiak, B. Comparison of characteristics and DNAzyme activity of G4–Hemin conjugates obtained via two Hemin attachment methods. Molecules 23 (6), 1400 (2018).

    Google Scholar 

12. Li, J. et al. Zippered G-quadruplex/hemin dnazyme: exceptional catalyst for universal bioanalytical applications. Nucleic Acids Res. 49 (22), 13031–13044 (2021).

    Google Scholar 

13. Virgilio, A., Esposito, V., Lejault, P., Monchaud, D. & Galeone, A. Improved performances of catalytic G-quadruplexes (G4-DNAzymes) via the chemical modifications of the DNA backbone to provide G-quadruplexes with double 3′-external G-quartets. Int. J. Biol. Macromol. 151, 976–983 (2020).

    Google Scholar 

14. Chang, T. et al. Activity enhancement of G-Quadruplex/Hemin DNAzyme by flanking d (CCC). Chemistry–A Eur. J. 22 (12), 4015–4021 (2016).

    Google Scholar 

15. Guo, Y. et al. A thermophilic tetramolecular G-Quadruplex/Hemin DNAzyme. Angew. Chem. Int. Ed. 56 (52), 16636–16640 (2017).

    Google Scholar 

16. Zhu, L. et al. In vitro selection of highly efficient G-quadruplex-based dnazymes. Anal. Chem. 84 (19), 8383–8390 (2012).

    Google Scholar 

17. Bhuyan, S. K. et al. Directed evolution of a G-quadruplex peroxidase DNAzyme and application in proteomic DNAzyme–aptamer proximity labeling. J. Am. Chem. Soc. 145 (23), 12726–12736 (2023).

    Google Scholar 

18. Yang, X. et al. Characterization of G-quadruplex/hemin peroxidase: substrate specificity and inactivation kinetics. Chemistry–A Eur. J. 17 (51), 14475–14484 (2011).

    Google Scholar 

19. Li, W. et al. Insight into G-quadruplex-hemin DNAzyme/RNAzyme: adjacent adenine as the intramolecular species for remarkable enhancement of enzymatic activity. Nucleic Acids Res. 44 (15), 7373–7384 (2016).

    Google Scholar 

20. Chen, J., Guo, Y., Zhou, J. & Ju, H. The effect of adenine repeats on G-quadruplex/hemin peroxidase mimicking DNAzyme activity. Chemistry–A Eur. J. 23 (17), 4210–4215 (2017).

    Google Scholar 

21. Chen, J. et al. How proximal nucleobases regulate the catalytic activity of G-quadruplex/hemin dnazymes. ACS Catal. 8 (12), 11352–11361 (2018).

    Google Scholar 

22. Qiu, D. et al. Effect of distance from catalytic synergy group to iron porphyrin center on activity of G-quadruplex/hemin DNAzyme. Molecules 25 (15), 3425 (2020).

    Google Scholar 

23. Cao, Y. et al. Investigation and improvement of catalytic activity of G-quadruplex/hemin dnazymes using designed terminal G-tetrads with deoxyadenosine caps. Chem. Sci. 11 (26), 6896–6906 (2020).

    Google Scholar 

24. Connelly, R. P., Fonseca, V. & Gerasimova, Y. V. Peroxidase-like activity of G-Quadruplex/Hemin complexes for colorimetric nucleic acid analysis: loop and flanking sequences affect signal intensity. DNA 5 (1), 12 (2025).

    Google Scholar 

25. Kong, D. M., Wu, J., Wang, N., Yang, W. & Shen, H. X. Peroxidase activity–structure relationship of the intermolecular four-stranded G-quadruplex–hemin complexes and their application in Hg2 + ion detection. Talanta 80 (2), 459–465 (2009).

    Google Scholar 

26. Udomprasert, A., Chimasungkanun, S. & Kangsamaksin, T. Kinetic analysis of catalytic activity of G-quadruplex/hemin DNAzyme with flanking adenine nucleotides. Scientific Reports, 15(1), p.40260. (2025).

27. Bagheri, Z. et al. Spectral properties and thermal stability of AS1411 G-quadruplex. Int. J. Biol. Macromol. 72, 806–811 (2015).

    Google Scholar 

28. Vazquez-Duhalt, R. Cytochrome c as a biocatalyst. J. Mol. Catal. B: Enzymatic. 7 (1–4), 241–249 (1999).

    Google Scholar 

29. Valderrama, B., Ayala, M. & Vazquez-Duhalt, R. Suicide inactivation of peroxidases and the challenge of engineering more robust enzymes. Chem. Biol. 9 (5), 555–565 (2002).

    Google Scholar 

30. Monte Carlo, A. R. III & Fu, J. Inactivation kinetics of G-Quadruplex/Hemin complex and optimization for more reliable catalysis. ChemPlusChem. 87 (7), e202200090. (2022).

31. Li, J. et al. Self-contained G-quadruplex/hemin dnazyme: a superior ready-made catalyst for in situ imaging analysis. Nucleic Acids Res. 53 (6), gkaf227 (2025).

    Google Scholar 

32. Liu, B. et al. Arginine-Modified Hemin enhances G-Quadruplex DNAzyme peroxidase activity for high sensitivity detection. Anal. Chem. 96 (36), 14590–14597 (2024).

    Google Scholar 

33. Cheng, Y. et al. Highly selective detection of K + based on a dimerized G-quadruplex DNAzyme. Anal. Chem. 93 (18), 6907–6912 (2021).

    Google Scholar 

34. Regelsberger, G. et al. Effect of distal cavity mutations on the formation of compound I in catalase-peroxidases. J. Biol. Chem. 275 (30), 22854–22861 (2000).

    Google Scholar 

35. Rodríguez-López, J. N. et al. Mechanism of reaction of hydrogen peroxide with horseradish peroxidase: identification of intermediates in the catalytic cycle. J. Am. Chem. Soc. 123 (48), 11838–11847 (2001).

    Google Scholar 

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