ISSN 2410-7751 (Print)
ISSN 2410-776X (Online)
Biotechnologia Acta Т. 14, No. 5 , 2021
P. 5-20, Bibliography 45, Engl.
UDC: 576.522; 576.523; 576.385.5; 571.27; 616-006
https://doi.org/10.15407/biotech14.05.005
DEOXYRIBOZYMES IN DETECTION OF PATHOGENIC BACTERIA
K. A. P. Gaminda 1, I. B. K. Thomas 1, D. T. Abeysinghe 1, C. D. Jayasinghe 2 , R. Senthilnithy 1
1 Department of Chemistry, The Open University of Sri Lanka, Nugegoda
2 Department of Zoology, The Open University of Sri Lanka, Nugegoda
The purpose of the review was to analyze the use of DNAzyme biosensors for the detection of pathogens. In the recent years, deoxyribozymes (DNAzymes) have a significant impact as biosensors in diverse fields, from detection of metal ions in the environment to theranostic applications and detection of microorganisms. Although routinely used sophisticated instrumental methods are available to detect pathogenic bacterial contamination, they involve time-consuming, complicated sample pre-treatment and expensive instruments. As an alternative, pathogen-specific DNAzymes have demonstrated a series of advantages: a non-destructive rapid analysis technique with in situ and real-time detection of bacteria with high sensitivity and selectivity. A wide range of pathogen-specific DNAzymes has been developed using colorimetric and fluorescence-based detections for pathogenic bacterial contamination in various samples. The current review summarizes the in vitro selection of pathogen-specific DNAzymes, various strategies utilized in the sensor designs, and their potential use in theranostic applications.
Key words: Pathogen, DNAzyme, Biosensors, peroxidase mimicking DNAzyme.
© Palladin Institute of Biochemistry of National Academy of Sciences of Ukraine, 2021
References
1. Palumbo J. D., Borucki M. K., Mandrell R. E., Gorski L. Serotyping of Listeria monocytogenes by enzyme-linked immunosorbent assay and identification of mixed-serotype cultures by colony immunoblotting. J. Clin. Microbiol. 2003, 41 (2), 564–571. https://doi.org/10.1128/JCM.41.2.564-571.2003
2. J?rvinen A. K., Laakso S., Piiparinen P., Aittakorpi A., Lindfors M., Huopaniemi L., M?ki M. Rapid identification of bacterial pathogens using a PCR- and microarray-based assay. BMC Microbiol. 2009, 9 (1). 1–16. https://doi.org/10.1186/1471-2180-9-161
3. Ali M. M., Aguirre S. D., Lazim H., Li Y. Fluorogenic DNAzyme Probes as Bacterial Indicators. Angew. Chemie. 2011, 123 (16), 3835–3838. https://doi.org/10.1002/anie.201100477
4. Breaker R. R., Joyce G. F. A DNA enzyme that cleaves RNA. Chem. Biol. 1994, 1 (4), 223–229. https://doi.org/10.1016/1074-5521(94)90014-0
5. Santoro S. W., Joyce G. F. A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA. 1997, 94 (9), 4262–4266. https://doi.org/10.1073/pnas.94.9.4262
6. Brown A. K., Liu J., He Y., Lu Y. Biochemical characterization of a uranyl ion-specific DNAzyme. Chem. BioChem. 2009, 10 (3), 486–492. https://doi.org/10.1002/cbic.200800632
7. Huang P. J. J., Liu J. Rational evolution of Cd2+-specific DNAzymes with phosphorothioate modified cleavage junction and Cd2+ sensing. Nucleic Acids Res. 2015, 43 (12), 6125–6133. https://doi.org/10.1093/nar/gkv519
8. Huang P. J. J., Lin J., Cao J., Vazin M., Liu J. Ultrasensitive DNAzyme beacon for lanthanides and metal speciation. Anal. Chem. 2014, 86 (3), 1816–1821. https://doi.org/10.1021/ac403762s
9. Ma L. A New Na(+)-specific DNAzyme Mutant from in Vitro Selection. University of Waterloo. 2017.
10. Sambrook J., Russell D. W. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. 2001.
11. Proudnikov D., Mirzabekov A. Chemical methods of DNA and RNA fluorescent labeling. Nucleic Acids Res. 1996, 24 (22), 4535–4542. https://doi.org/10.1093/nar/24.22.4535
12. Liu J., Cao Z., Lu Y. Functional nucleic acid sensors. Chem. Rev. 2009, 109 (5), 1948–1998. https://doi.org/10.1021/cr030183i
13. Thomas I. B. K., Gaminda K. A. P., Jayasinghe C. D., Abeysinghe D. T., Senthilnithy R. DNAzymes, Novel Therapeutic Agents in Cancer Therapy: A Review of Concepts to Applications. Basu A., editor. J. Nucleic Acids. 2021, V. 2021, P. 1–21. https://doi.org/10.1155/2021/9365081
14. Zhou W., Ding J., Liu J. Theranostic dnazymes. Theranostics. 2017, 7 (4), 1010–1025. https://doi.org/10.7150/thno.17736
15. Zhao W., Ali M. M., Brook M. A., Li Y. Rolling circle amplification: Applications in nanotechnology and biodetection with functional nucleic acids. V. 47, Angewandte Chemie ? International Edition. Angew. Chem. Int. Ed. Engl. 2008, P. 6330–6337.https://doi.org/10.1002/anie.200705982
16. Liu Z., Yao C., Wang Y., Yang C. A G-quadruplex DNAzyme-based LAMP biosensing platform for a novel colorimetric detection of: Listeria monocytogenes. Anal. Methods. 2018, 10 (8), 848–854. https://doi.org/10.1039/C7AY02908J
17. Li B., Du Y., Li T., Dong S. Investigation of 3,3?,5,5?-tetramethylbenzidine as colorimetric substrate for a peroxidatic DNAzyme. Anal. Chim. Acta. 2009, 651 (2), 234–240. https://doi.org/10.1016/j.aca.2009.09.009
18. Gu L., Yan W., Wu H., Fan S., Ren W., Wang S., Lyu M., Liu J. Selection of DNAzymes for Sensing Aquatic Bacteria: Vibrio Anguillarum. Anal. Chem. 2019, 91 (12), 7887–7893. https://doi.org/10.1021/acs.analchem.9b01707
19. Ali M. M., Wolfe M., Tram K., Gu J., Filipe C. D. M., Li Y., Brennan J. D. A DNAzyme-Based Colorimetric Paper Sensor for Helicobacter pylori. Angew. Chem. ? Int. Ed. 2019, 58 (29), 9907–9911. https://doi.org/10.1002/anie.201901873
20. Ali M. M., Slepenkin A., Peterson E., Zhao W. A Simple DNAzyme-Based Fluorescent Assay for Klebsiella pneumoniae. Chem. BioChem. 2019, 20 (7), 906–910.https://doi.org/10.1002/cbic.201800701
21. Rothenbroker M., McConnell E. M., Gu J., Urbanus M. L., Samani S. E., Ensminger A. W. Selection and Characterization of an RNA?Cleaving DNAzyme Activated by Legionella pneumophila. Angew. Chem. 2021, 133 (9), 4832–4838. https://doi.org/10.1002/anie.202012444
22. Ma X., Wang C., Qin M., Tian X., Fan S., Zu H., Lyu M., Wang S. Rapid detection of Aeromonas hydrophila with a DNAzyme-based sensor. Food Control. 2021, V. 123, P. 107829. https://doi.org/10.1016/j.foodcont.2020.107829
23. Aguirre S. D., Monsur Ali M., Kanda P., Li Y. Detection of bacteria using fluorogenic DNAzymes. J. Vis. Exp. 2012, V. 63, P. 1–8. https://doi.org/10.3791/3961
24. Aguirre S. D., Ali M. M., Salena B. J., Li Y. A sensitive DNA enzyme-based fluorescent assay for bacterial detection. Biomolecules. 2013, 3 (3), 563–577. https://doi.org/10.3390/biom3030563
25. Cao T., Wang Y., Zhao L. L., Wang Y., Tao Y., Heyman J. A. A simple mix-and-read bacteria detection system based on a DNAzyme and a molecular beacon. Chem. Commun. 2019, 55 (51), 7358–7361. https://doi.org/10.1039/C9CC03746B
26. Tram K., Kanda P., Salena B. J., Huan S., Li Y. Translating bacterial detection by DNAzymes into a litmus test. Angew. Chem. ? Int. Ed. 2014, 53 (47), 12799–12802. https://doi.org/10.1002/anie.201407021
27. Liu M., Zhang Q., Brennan J. D., Li Y. Graphene-DNAzyme-based fluorescent biosensor for Escherichia coli detection. MRS Commun. 2018, 8 (3), 687–694. https://doi.org/10.1557/mrc.2018.97
28. Zheng L., Qi P., Zhang D. DNA-templated fluorescent silver nanoclusters for sensitive detection of pathogenic bacteria based on MNP-DNAzyme-AChE complex. Sensors Actuators, B Chem. 2018, V. 276, P. 42–47. https://doi.org/10.1016/j.snb.2018.08.078
29. Zhou Z., Zhang Y., Guo M., Huang K., Xu W. Ultrasensitive magnetic DNAzyme-copper nanoclusters fluorescent biosensor with triple amplification for the visual detection of E. coli O157:H7. Biosens Bioelectron. 2020, 167 (17), 112475.https://doi.org/10.1016/j.bios.2020.112475
30. Liu M., Zhang Q., Chang D., Gu J., Brennan J. D., Li Y. A DNAzyme Feedback Amplification Strategy for Biosensing. Angew. Chem. ? Int. Ed. 2017, 56 (22), 6142–6146. https://doi.org/10.1002/anie.201700054
31. Sun Y., Chang Y., Zhang Q., Liu M. An origami paper-based device printed with DNAzyme-containing DNA superstructures for Escherichia Coli detection. Micromachines. 2019, 10 (8), 531. https://doi.org/10.3390/mi10080531
32. Liu M., Zhang Q., Kannan B., Botton G. A., Yang J., Soleymani L., Brennan J. D., Li Y. Self-Assembled Functional DNA Superstructures as High-Density and Versatile Recognition Elements for Printed Paper Sensors. Angew. Chem. 2018, 130 (38), 12620–12623. https://doi.org/10.1002/anie.201806489
33. Zhou Z., Brennan J. D., Li Y. A Multi-component All-DNA Biosensing System Controlled by a DNAzyme. Angew. Chem. ? Int. Ed. 2020, 59 (26), 10401–10405. https://doi.org/10.1002/anie.202002019
34. Kusters J. G., Van Vliet A. H. M., Kuipers E. J. Pathogenesis of Helicobacter pylori infection. Clin. Microbiol. Rev. 2006, 19 (3), 449–490. https://doi.org/10.1128/CMR.00054-05
35. Suerbaum S., Michetti P. Helicobacter pylori Infection. N Engl. J. Med. 2002, 347 (15), 1175–1186. https://doi.org/10.1056/NEJMra020542
36. Liu Z., Yuan Y., Wu X., Ning Q., Wu S., Fu L. A turn-off colorimetric DNAzyme-aptasensor for ultra-high sensitive detection of viable Cronobacter sakazakii. Sensors Actuators: B Chem. 2020, V. 322, P. 128646. https://doi.org/10.1016/j.snb.2020.128646
37. Li S. T., Zhang Y., Tian J. J., Xu W. T. Luminescent DNAzyme and universal blocking linker Super Polymerase Chain Reaction visual biosensor for the detection of Salmonella. Food Chem. 2020, V. 324, P. 126859. https://doi.org/10.1016/j.foodchem.2020.126859
38. Ding X., Li H., Deng L., Peng Z., Chen H., Wang D. A novel homogenous detection method based on the self-assembled DNAzyme labeled DNA probes with SWNT conjugates and its application in detecting pathogen. Biosens Bioelectron. 2011, 26 (11), 4596–4600. https://doi.org/10.1016/j.bios.2011.04.041
39. Seok Y., Byun J. Y., Mun H., Kim M. G. Colorimetric detection of PCR products of DNA from pathogenic bacterial targets based on a simultaneously amplified DNAzyme. Microchim. Acta. 2014, 181 (15–16), 1965–1971. https://doi.org/10.1007/s00604-014-1297-3
40. Ning Y., Li W., Duan Y., Yang M., Deng L. High Specific DNAzyme-Aptamer Sensor for Salmonella paratyphi A Using Single-Walled Nanotubes–Based Dual Fluorescence-Spectrophotometric Methods. 2014, 19 (7), 1099–1106. https://doi.org/10.1177/1087057114528538
41. Hui C. Y., Liu M., Li Y., Brennan J. D. A Paper Sensor Printed with Multifunctional Bio/Nano Materials. Angew Chem. ? Int. Ed. 2018, 57 (17), 4549–4553.https://doi.org/10.1002/anie.201712903
42. Sun Y., Duan N., Ma P., Liang Y., Zhu X., Wang Z. Colorimetric Aptasensor Based on Truncated Aptamer and Trivalent DNAzyme for Vibrio parahemolyticus Determination. J. Agric. Food Chem. 2019, 67 (8), 2313–2320. https://doi.org/10.1021/acs.jafc.8b06893
43. Qin M., Ma X., Fan S., Wu H., Yan W., Tian X., Lu J., Lyu M., Wang S. Rapid detection of Pseudomonas aeruginosa using a DNAzyme-based sensor. Food Sci. Nutr. 2021, 9 (7), 3873–3884. https://doi.org/10.1002/fsn3.2367
44. Wu C. S., Khaing O. M. K., Fan X. Highly sensitive multiplexed heavy metal detection using quantum-dot-labeled DNAzymes. ACS Nano. 2010, 4 (10), 5897–5904. https://doi.org/10.1021/nn1021988
45. Zhou Z., Zhang Y., Guo M., Huang K., Xu W. Ultrasensitive magnetic DNAzyme-copper nanoclusters fluorescent biosensor with triple amplification for the visual detection of E. coli O157:H7. Biosens. Bioelectron. 2020, V. 167, P. 112475. https://doi.org/10.1016/j.bios.2020.112475