Design of guide RNA for CRISPR-Cas12-based detection of Salmonella typhimurium

Authors

Department of Biological Sciences, Faculty of Passive Defense, Malek Ashtar University of Technology, Tehran, Iran.

Keywords

Subjects


1. Wang, J. Y., & Doudna, J. A. (2023). CRISPR technology: A decade of genome editing is only the beginning. Science, 379(6629), eadd8643.
2. Isaacson, W. (2021). The code breaker: Jennifer Doudna, gene editing, and the future of the human race. Simon and Schuster.
3. Zhu, H., & Liang, C. (2019). CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity. Bioinformatics, 35(16), 2783-2789.
4. Yang, Y., Wang, D., Lü, P., Ma, S., & Chen, K. (2023). Research progress on nucleic acid detection and genome editing of CRISPR/Cas12 system. Molecular Biology Reports, 50(4), 3723-3738.
5. Leung, R. K. K., Cheng, Q. X., Wu, Z. L., Khan, G., Liu, Y., Xia, H. Y., & Wang, J. (2022). CRISPR-Cas12-based nucleic acids detection systems. Methods, 203, 276-281.
6. Hillary, V.E., Ceasar, S.A. (2023) A review on the mechanism and applications of CRISPR/Cas9/Cas12/Cas13/Cas14 proteins utilized for genome engineering. Molecular Biotechnology. 65(3), 311-325.
7. Jiang, H., Wu, Q., Zhao, Q., Liu, K., Bo, Q., Qin, X., ... & Qin, P. (2023). Using dCas9 as an intermediate bridge of loop-mediated isothermal amplification-based lateral flow colorimetric biosensor for point-of-care Salmonella detection. Sensors and Actuators B: Chemical, 396, 134581.
8. El-Tholoth, M., Bau, H.H., Song, J. (2021) A single and two-stage, closed-tube, molecular test for the 2019 novel coronavirus (COVID-19) at home, clinic, and points of entry. ChemRxiv [Preprint]. Analytical Chemistry. 93(38),13063-13071.
9. Shoushtari, M., Zeinoddini, M., Fathi, J., Alikhani, H. K., & Shiekhi, F. (2024). One-step and Rapid Identification of SARS-CoV-2 using Real-Time Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP). Avicenna Journal of Medical Biotechnology, 16(1), 3.
10. Ownagh, A., Etemadi, N., Khademi, P., Tajik, H. (2023) Identification of Salmonella carriers by amplification of FimA, Stn and InvA genes and bacterial culture methods in fecal samples of buffalo. Veterinary Research Forum. 14(1),21-28.
11. Zeinoddini, M. (2021). Genome-based Detection of Novel Coronavirus: An Overview Study. Journal of Inflammatory Diseases, 25(1), 51-60.
12. Lee, S. Y., & Oh, S. W. (2023). Lateral flow biosensor based on LAMP-CRISPR/Cas12a for sensitive and visualized detection of Salmonella spp. Food Control, 145, 109494.
13. Fulga, T.A., Knapp, D.J.H.F., Ferry, Q.R.V. CRISPR quide RNA design: Methods and protocols, Springer, 2021.
14. Sheikhi, F., Zeinoddini, M., Jalili, S. (2023) Optimization for Rapid Detection of Staphylococcus aureus using Real-time LAMP. Journal of Applied Biotechnology Reports, 10(2), 984-991.
15. Mousavi, S. M., Zeinoddini, M., Saeeidinia, A. R., & Xodadadi, N. (2020). Specific and Rapid Detection of Zonula Occludens Toxin-producing Vibrio Cholerae Using LAMP. Biomacromolecular Journal, 6(2), 139-146.
16. Aman, R., Marsic, T., Sivakrishna Rao, G., Mahas, A., Ali, Z., Alsanea, M., ... & Mahfouz, M. (2022). iSCAN-V2: A one-pot RT-RPA–CRISPR/Cas12b assay for point-of-care SARS-CoV-2 detection. Frontiers in Bioengineering and Biotechnology, 9, 800104.
17. Ali, Z., Aman, R., Mahas, A., Rao, G. S., Tehseen, M., Marsic, T., ... & Mahfouz, M. M. (2020). iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2. Virus Research, 288, 198129.
18. Atçeken, N., Yigci, D., Ozdalgic, B., & Tasoglu, S. (2022). CRISPR-Cas-Integrated LAMP. Biosensors, 12(11), 1035.
19. Lee, S., Nam, D., Park, J. S., Kim, S., Lee, E. S., Cha, B. S., & Park, K. S. (2022). Highly efficient DNA reporter for CRISPR/Cas12a-based specific and sensitive biosensor. BioChip Journal, 16(4), 463-470.
20. Zhang, G., Zhang, L., Tong, J., Zhao, X., & Ren, J. (2020). CRISPR-Cas12a enhanced rolling circle amplification method for ultrasensitive miRNA detection. Microchemical Journal, 158, 105239.
21. Zeinoddini, M., Monazah, A., & Saeedinia, A. R. (2017). Comparison between RT-PCR, NASBA and RT-LAMP methods for detection of Coxsackievirus B3. Biomacromolecular Journal, 3(2), 100-106.
22. Augustine, R., Hasan, A., Das, S., Ahmed, R., Mori, Y., Notomi, T., ... & Thakor, A. S. (2020). Loop-mediated isothermal amplification (LAMP): a rapid, sensitive, specific, and cost-effective point-of-care test for coronaviruses in the context of COVID-19 pandemic. Biology, 9(8), 182.
23. Moehling, T. J., Choi, G., Dugan, L. C., Salit, M., & Meagher, R. J. (2021). LAMP diagnostics at the point-of-care: emerging trends and perspectives for the developer community. Expert Review of Molecular Diagnostics, 21(1), 43-61.
24. Rezaei, M., Razavi Bazaz, S., Morshedi Rad, D., Shimoni, O., Jin, D., Rawlinson, W., & Ebrahimi Warkiani, M. (2021). A portable RT-LAMP/CRISPR machine for rapid COVID-19 screening. Biosensors, 11(10), 369.
25. An, B., Zhang, H., Su, X., Guo, Y., Wu, T., Ge, Y., ... & Cui, L. (2021). Rapid and sensitive detection of salmonella spp. using CRISPR-Cas13a combined with recombinase polymerase amplification. Frontiers in Microbiology, 12, 732426.
26. Awang, M. S., Bustami, Y., Hamzah, H. H., Zambry, N. S., Najib, M. A., Khalid, M. F., ... & Abd Manaf, A. (2021). Advancement in Salmonella detection methods: From conventional to electrochemical-based sensing detection. Biosensors, 11(9), 346.
27. Shao, N., Han, X., Song, Y., Zhang, P., & Qin, L. (2019). CRISPR-Cas12a coupled with platinum nanoreporter for visual quantification of SNVs on a volumetric bar-chart chip. Analytical chemistry, 91(19), 12384-12391.
28. Sun, H., Wan, Y., Du, P., & Bai, L. (2020). The epidemiology of monophasic Salmonella Typhimurium. Foodborne Pathogens and Disease, 17(2), 87-97.
29. Crone, M. A., MacDonald, J. T., Freemont, P. S., & Siciliano, V. (2022). gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells. NPJ Systems Biology and Applications, 8(1), 34.