Rolling Circle and Loop Mediated Isothermal Amplification Strategy for Ultrasensitive miRNA Detection
Abstract
:1. Introduction
2. Materials and Methods
2.1. Apparatus
2.2. Materials and Reagents
2.3. Preparation of Solution
2.4. RC-LAMP Assay Procedures
2.5. Cell Lysis and RNA Preparation
2.6. Detection of miRNA in Cell and Serum
3. Results and Discussion
3.1. Design Principle of RC-LAMP Assay
3.2. Optimization of Reaction Parameters
3.3. Selectivity
3.4. Quantification of miRNA
3.5. Real Sample Detection
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Friedman, R.C.; Farh, K.K.-H.; Burge, C.B.; Bartel, D.P. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009, 19, 92–105. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Farooqi, A.A.; Qureshi, M.Z.; Coskunpinar, E.; Naqvi, S.K.-U.-H.; Yaylim, I.; Ismail, M. miR-421, miR-155 and miR-650: Emerging trends of regulation of cancer and apoptosis. Asian Pac. J. Cancer Prev. 2014, 15, 1909–1912. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Iqbal, M.A.; Arora, S.; Prakasam, G.; Calin, G.A.; Syed, M.A. MicroRNA in lung cancer: Role, mechanisms, pathways and therapeutic relevance. Mol. Asp. Med. 2019, 70, 3–20. [Google Scholar] [CrossRef]
- Lu, T.X.; Rothenberg, M.E. MicroRNA. J. Allergy Clin. Immunol. 2018, 141, 1202–1207. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Huang, Y.; Huang, Y.; Zou, Q.; Zou, Q.; Wang, S.P.; Wang, S.P.; Tang, S.M.; Tang, S.M.; Zhang, G.Z.; Zhang, G.Z.; et al. The discovery approaches and detection methods of microRNAs. Mol. Biol. Rep. 2011, 38, 4125–4135. [Google Scholar] [CrossRef] [PubMed]
- Cai, S.; Cao, Z.J.; Lau, C.W.; Lu, J.Z. Label-free technology for the amplified detection of microRNA based on the allosteric hairpin DNA switch and hybridization chain reaction. Analyst 2014, 139, 6022–6027. [Google Scholar] [CrossRef] [PubMed]
- Deng, R.J.; Tang, L.H.; Tian, Q.Q.; Wang, Y.; Lin, L.; Li, J.H. Toehold-initiated Rolling Circle Amplification for Visualizing Individual MicroRNAs In Situ in Single Cells. Angew. Chem. 2014, 53, 2389–2393. [Google Scholar] [CrossRef]
- Huang, J.F.; Zhao, N.; Xu, H.Q.; Xia, H.; Wei, K.; Fu, W.L.; Huang, Q. Sensitive and specific detection of miRNA using an isothermal exponential amplification method using fluorescence-labeled LNA/DNA chimera primers. Anal. Bioanal. Chem. 2016, 408, 7437–7446. [Google Scholar] [CrossRef]
- Jia, H.; Bu, Y.; Zou, B.; Wang, J.; Kumar, S.; Pitman, J.L.; Zhou, G.; Song, Q. Signal amplification of microRNAs with modified strand displacement-based cycling probe technology. Analyst 2016, 141, 6297–6302. [Google Scholar] [CrossRef]
- Miao, J.; Wang, J.S.; Guo, J.Y.; Gao, H.G.; Han, K.; Jiang, C.M.; Miao, P. A plasmonic colorimetric strategy for visual miRNA detection based on hybridization chain reaction. Sci. Rep. 2016, 6, 32219. [Google Scholar] [CrossRef]
- Schwarzkopf, M.; Pierce, N.A. Multiplexed miRNA northern blots via hybridization chain reaction. Nucleic Acids Res. 2016, 44, e129. [Google Scholar] [CrossRef] [Green Version]
- Xu, Y.J.; Li, D.D.; Cheng, W.; Hu, R.; Sang, Y.; Yin, Y.B.; Ding, S.J.; Ju, H.X. Chemiluminescence imaging for microRNA detection based on cascade exponential isothermal amplification machinery. Anal. Chim. Acta 2016, 936, 229–235. [Google Scholar] [CrossRef] [PubMed]
- Yang, J.R.; Tang, M.; Diao, W.; Cheng, W.B.; Zhang, Y.; Yan, Y.R. Electrochemical strategy for ultrasensitive detection of microRNA based on MNAzyme-mediated rolling circle amplification on a gold electrode. Microchim. Acta 2016, 183, 3061–3067. [Google Scholar] [CrossRef]
- Hong, C.; Baek, A.; Hah, S.S.; Jung, W.; Kim, D.E. Fluorometric Detection of MicroRNA Using Isothermal Gene Amplification and Graphene Oxide. Anal. Chem. 2016, 88, 2999–3003. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ge, J.; Zhang, L.L.; Liu, S.J.; Yu, R.Q.; Chu, X. A highly sensitive target-primed rolling circle amplification (TPRCA) method for fluorescent in situ hybridization detection of microRNA in tumor cells. Anal. Chem. 2014, 86, 1808–1815. [Google Scholar] [CrossRef]
- Cui, L.; Zhu, Z.; Lin, N.; Zhang, H.; Guan, Z.; Yang, C.J. A T7 exonuclease-assisted cyclic enzymatic amplification method coupled with rolling circle amplification: A dual-amplification strategy for sensitive and selective microRNA detection. Chem. Commun. 2014, 50, 1576–1578. [Google Scholar] [CrossRef] [Green Version]
- Gao, Z.; Wu, C.; Lv, S.; Wang, C.; Zhang, N.; Xiao, S.; Han, Y.; Xu, H.; Zhang, Y.; Li, F.; et al. Nicking-enhanced rolling circle amplification for sensitive fluorescent detection of cancer-related microRNAs. Anal. Bioanal. Chem. 2018, 410, 6819–6826. [Google Scholar] [CrossRef]
- Liu, S.; Fang, H.; Sun, C.; Wang, N.; Li, J. Highly sensitive and multiplexed miRNA analysis based on digitally encoded silica microparticles coupled with RCA-based cascade amplification. Analyst 2018, 143, 5137–5144. [Google Scholar] [CrossRef]
- Wang, R.; Zhao, X.; Chen, X.; Qiu, X.; Qing, G.; Zhang, H.; Zhang, L.; Hu, X.; He, Z.; Zhong, D.; et al. Rolling Circular Amplification (RCA)-Assisted CRISPR/Cas9 Cleavage (RACE) for Highly Specific Detection of Multiple Extracellular Vesicle MicroRNAs. Anal. Chem. 2020, 92, 2176–2185. [Google Scholar] [CrossRef]
- Zhang, J.; He, M.; Nie, C.; He, M.; Pan, Q.; Liu, C.; Hu, Y.; Yi, J.; Chen, T.; Chu, X. Biomineralized Metal-Organic Framework Nanoparticles Enable Enzymatic Rolling Circle Amplification in Living Cells for Ultrasensitive MicroRNA Imaging. Anal. Chem. 2019, 91, 9049–9057. [Google Scholar] [CrossRef]
- Zhang, C.; Li, D.; Li, D.; Wen, K.; Yang, X.; Zhu, Y. Rolling circle amplification-mediated in situ synthesis of palladium nanoparticles for the ultrasensitive electrochemical detection of microRNA. Analyst 2019, 144, 3817–3825. [Google Scholar] [CrossRef]
- Zhao, B.; Song, J.; Guan, Y. Discriminative identification of miRNA let-7 family members with high specificity and sensitivity using rolling circle amplification. Acta Biochim. Biophys. Sin. 2015, 47, 130–136. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- He, Y.; Yang, X.; Yuan, R.; Chai, Y. “Off” to “On” Surface-Enhanced Raman Spectroscopy Platform with Padlock Probe-Based Exponential Rolling Circle Amplification for Ultrasensitive Detection of MicroRNA 155. Anal. Chem. 2017, 89, 2866–2872. [Google Scholar] [CrossRef] [PubMed]
- Li, R.; Wang, Y.; Wang, P.; Lu, J. A dual discrimination mode for improved specificity towards let-7a detection via a single-base mutated padlock probe-based exponential rolling circle amplification. Lumin. J. Biol. Chem. Lumin. 2017, 32, 1574–1581. [Google Scholar] [CrossRef] [PubMed]
- Tian, W.; Li, P.; He, W.; Liu, C.; Li, Z. Rolling circle extension-actuated loop-mediated isothermal amplification (RCA-LAMP) for ultrasensitive detection of microRNAs. Biosens. Bioelectron. 2018, 128, 17–22. [Google Scholar] [CrossRef] [PubMed]
- Xu, H.; Wu, D.; Zhang, Y.F.; Shi, H.M.; Ouyang, C.H.; Li, F.; Jia, L.; Yu, S.H.; Wu, Z.S. RCA-enhanced multifunctional molecule beacon-based strand-displacement amplification for sensitive microRNA detection. Sens. Actuators B 2018, 258, 470–477. [Google Scholar] [CrossRef]
- Xu, H.; Zhang, Y.; Zhang, S.; Sun, M.; Li, W.; Jiang, Y.; Wu, Z.S. Ultrasensitive assay based on a combined cascade amplification by nicking-mediated rolling circle amplification and symmetric strand-displacement amplification. Anal. Chim. Acta 2019, 1047, 172–178. [Google Scholar] [CrossRef]
- Wang, Z.-Y.; Li, F.; Zhang, Y.; Zhao, H.; Xu, H.; Wu, Z.-S.; Lyu, J.-X.; Shen, Z.-F. Sensitive detection of cancer gene based on a nicking-mediated RCA of circular DNA nanomachine. Sens. Actuators B 2017, 251, 692–698. [Google Scholar] [CrossRef]
- Zhou, Y.T.; Huang, Q.; Gao, J.M.; Lu, J.X.; Shen, X.Z.; Fan, C.H. A dumbbell probe-mediated rolling circle amplification strategy for highly sensitive microRNA detection. Nucleic Acids Res. 2010, 38, e156. [Google Scholar] [CrossRef] [Green Version]
- Xu, M.; Ye, J.; Yang, D.; Al-Maskri, A.A.A.; Hu, H.; Jung, C.; Cai, S.; Zeng, S. Ultrasensitive detection of miRNA via one-step rolling circle-quantitative PCR (RC-qPCR). Anal. Chim. Acta 2019, 1077, 208–215. [Google Scholar] [CrossRef]
- Li, C.; Li, Z.; Jia, H.; Yan, J. One-step ultrasensitive detection of microRNAs with loop-mediated isothermal amplification (LAMP). Chem. Commun. 2011, 47, 2595–2597. [Google Scholar] [CrossRef] [PubMed]
- Sun, Y.; Tian, H.; Liu, C.; Sun, Y.; Li, Z. One-step detection of microRNA with high sensitivity and specificity via target-triggered loop-mediated isothermal amplification (TT-LAMP). Chem. Commun. 2017, 53, 11040–11043. [Google Scholar] [CrossRef] [PubMed]
- Du, W.; Lv, M.; Li, J.; Yu, R.; Jiang, J. A ligation-based loop-mediated isothermal amplification (ligation-LAMP) strategy for highly selective microRNA detection. Chem. Commun. 2016, 52, 12721–12724. [Google Scholar] [CrossRef]
- Hashimoto, K.; Inada, M.; Ito, K. Multiplex Real-Time Loop-Mediated Isothermal Amplification Using an Electrochemical DNA Chip Consisting of a Single Liquid-Flow Channel. Anal. Chem. 2019, 91, 3227–3232. [Google Scholar] [CrossRef] [PubMed]
- Kalea, A.Z.; Hoteit, R.; Suvan, J.; Lovering, R.C.; Palmen, J.; Cooper, J.A.; Khodiyar, V.K.; Harrington, Z.; Humphries, S.E.; D’Aiuto, F. Upregulation of Gingival Tissue miR-200b in Obese Periodontitis Subjects. J. Dent. Res. 2015, 94, 59s–69s. [Google Scholar] [CrossRef] [Green Version]
- Kawakubo-Yasukochi, T.; Morioka, M.; Hazekawa, M.; Yasukochi, A.; Nishinakagawa, T.; Ono, K.; Kawano, S.; Nakamura, S.; Nakashima, M. miR-200c-3p spreads invasive capacity in human oral squamous cell carcinoma microenvironment. Mol. Carcinog. 2018, 57, 295–302. [Google Scholar] [CrossRef] [PubMed]
Name | Sequence (5′–3′) |
---|---|
miR-200a-3p (miR-200a) | UAACACUGUCUGGUAACGAUGU |
miR-200a-5p | CAUCUUACCGGACAGUGCUGGA |
miR-200b | UAAUACUGCCUGGUAAUGAUGA |
miR-200c | UAAUACUGCCGGGUAAUGAUGGA |
miR-429 | UAAUACUGUCUGGUAAAACCGU |
let-7a | UGAGGUAGUAGGUUGUAUAGUU |
Padlock probe | AGACAGTGTTATTCCTCTTCACCCTCCCACTCATTGGCACAGTTTAGAGGTGAAAAGTAGAGCTGTCAAGCCCAAGGGCTTAGCTTTAGGGCTCCTCCTGAGTTCGGCCCACAGTAGACATCGTTACC |
F3 | CACTCATTGGCACAGT |
FIP | AGGAGCCCTAAAGCTAAGTTAGAGGTGAAAAGTAGAGC |
BIP | GAGTTCGGCCCACAGTAGGGAGGGTGAAGAGGAA |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Cao, Z.; Jiang, X.; Xiao, G.; Xu, M.; Liu, H.; Cai, S. Rolling Circle and Loop Mediated Isothermal Amplification Strategy for Ultrasensitive miRNA Detection. Separations 2021, 8, 166. https://doi.org/10.3390/separations8100166
Cao Z, Jiang X, Xiao G, Xu M, Liu H, Cai S. Rolling Circle and Loop Mediated Isothermal Amplification Strategy for Ultrasensitive miRNA Detection. Separations. 2021; 8(10):166. https://doi.org/10.3390/separations8100166
Chicago/Turabian StyleCao, Zheng, Xianfeng Jiang, Guizhou Xiao, Mingcheng Xu, Hui Liu, and Sheng Cai. 2021. "Rolling Circle and Loop Mediated Isothermal Amplification Strategy for Ultrasensitive miRNA Detection" Separations 8, no. 10: 166. https://doi.org/10.3390/separations8100166
APA StyleCao, Z., Jiang, X., Xiao, G., Xu, M., Liu, H., & Cai, S. (2021). Rolling Circle and Loop Mediated Isothermal Amplification Strategy for Ultrasensitive miRNA Detection. Separations, 8(10), 166. https://doi.org/10.3390/separations8100166