Phenol/Chloroform-Free TiO2-Based miRNA Extraction from Cell Lysate
Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
CZ.02.1.01/0.0/0.0/17_048/0007421
Ministry of Education Youth and Sports
PubMed
36012112
PubMed Central
PMC9407779
DOI
10.3390/ijms23168848
PII: ijms23168848
Knihovny.cz E-zdroje
- Klíčová slova
- TiO2, miRNA isolation, phenol/chloroform-free, short RNA extraction,
- MeSH
- chloroform chemie MeSH
- fenol * chemie MeSH
- fenoly MeSH
- mikro RNA * genetika MeSH
- titan MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- chloroform MeSH
- fenol * MeSH
- fenoly MeSH
- mikro RNA * MeSH
- titan MeSH
- titanium dioxide MeSH Prohlížeč
While microRNAs are considered as excellent biomarkers of various diseases, there are still several remaining challenges regarding their isolation. In this study, we aimed to design a novel RNA isolation method that would help to overcome those challenges. Therefore, we present a novel phenol/chloroform-free, low-cost method for miRNA extraction. Within this method, RNA is extracted from cell lysate with an isopropanol/water/NaCl system, followed by solid-phase extraction using TiO2 microspheres to effectively separate short RNAs from long RNA molecules. We also demonstrated the pH-dependent selectivity of TiO2 microspheres towards different sizes of RNA. We were able to regulate the size range of extracted RNAs with simple adjustments in binding conditions used during the solid-phase extraction.
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Bartel D.P. MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell. 2004;116:281–297. doi: 10.1016/S0092-8674(04)00045-5. PubMed DOI
Calin G.A., Sevignani C., Dumitru C.D., Hyslop T., Noch E., Yendamuri S., Shimizu M., Rattan S., Bullrich F., Negrini M., et al. Human MicroRNA Genes Are Frequently Located at Fragile Sites and Genomic Regions Involved in Cancers. Proc. Natl. Acad. Sci. USA. 2004;101:2999–3004. doi: 10.1073/pnas.0307323101. PubMed DOI PMC
Lu J., Getz G., Miska E.A., Alvarez-Saavedra E., Lamb J., Peck D., Sweet-Cordero A., Ebert B.L., Mak R.H., Ferrando A.A., et al. MicroRNA Expression Profiles Classify Human Cancers. Nature. 2005;435:834–838. doi: 10.1038/nature03702. PubMed DOI
Barad O., Meiri E., Avniel A., Aharonov R., Barzilai A., Bentwich I., Einav U., Gilad S., Hurban P., Karov Y., et al. MicroRNA Expression Detected by Oligonucleotide Microarrays: System Establishment and Expression Profiling in Human Tissues. Genome Res. 2004;14:2486–2494. doi: 10.1101/gr.2845604. PubMed DOI PMC
Calin G.A., Liu C.-G., Sevignani C., Ferracin M., Felli N., Dumitru C.D., Shimizu M., Cimmino A., Zupo S., Dono M., et al. MicroRNA Profiling Reveals Distinct Signatures in B Cell Chronic Lymphocytic Leukemias. Proc. Natl. Acad. Sci. USA. 2004;101:11755–11760. doi: 10.1073/pnas.0404432101. PubMed DOI PMC
Weber J.A., Baxter D.H., Zhang S., Huang D.Y., Huang K.H., Lee M.J., Galas D.J., Wang K. The MicroRNA Spectrum in 12 Body Fluids. Clin. Chem. 2010;56:1733–1741. doi: 10.1373/clinchem.2010.147405. PubMed DOI PMC
Brunet-Vega A., Pericay C., Quílez M.E., Ramírez-Lázaro M.J., Calvet X., Lario S. Variability in MicroRNA Recovery from Plasma: Comparison of Five Commercial Kits. Anal. Biochem. 2015;488:28–35. doi: 10.1016/j.ab.2015.07.018. PubMed DOI
Ntelios D., Georgiou E., Alexouda S., Malousi A., Efthimiadis G., Tzimagiorgis G. A Critical Approach for Successful Use of Circulating MicroRNAs as Biomarkers in Cardiovascular Diseases: The Case of Hypertrophic Cardiomyopathy. Heart Fail. Rev. 2022;27:281–294. doi: 10.1007/s10741-021-10084-y. PubMed DOI
Dong H., Lei J., Ding L., Wen Y., Ju H., Zhang X. MicroRNA: Function, Detection, and Bioanalysis. Chem. Rev. 2013;113:6207–6233. doi: 10.1021/cr300362f. PubMed DOI
Brown R.A.M., Epis M.R., Horsham J.L., Kabir T.D., Richardson K.L., Leedman P.J. Total RNA Extraction from Tissues for MicroRNA and Target Gene Expression Analysis: Not All Kits Are Created Equal. BMC Biotechnol. 2018;18:16. doi: 10.1186/s12896-018-0421-6. PubMed DOI PMC
Zaporozhchenko I.A., Morozkin E.S., Skvortsova T.E., Bryzgunova O.E., Bondar A.A., Loseva E.M., Vlassov V.V., Laktionov P.P. A Phenol-Free Method for Isolation of MicroRNA from Biological Fluids. Anal. Biochem. 2015;479:43–47. doi: 10.1016/j.ab.2015.03.028. PubMed DOI
Toni L.S., Garcia A.M., Jeffrey D.A., Jiang X., Stauffer B.L., Miyamoto S.D., Sucharov C.C. Optimization of Phenol-Chloroform RNA Extraction. MethodsX. 2018;5:599–608. doi: 10.1016/j.mex.2018.05.011. PubMed DOI PMC
Ali N., Rampazzo R.d.C.P., Costa A.D.T., Krieger M.A. Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics. Biomed Res. Int. 2017;2017:9306564. doi: 10.1155/2017/9306564. PubMed DOI PMC
Boom R., Sol C.J., Salimans M.M., Jansen C.L., Dillen P.M.W., Noordaa J.v.d. Rapid and Simple Method for Purification of Nucleic Acids. J. Clin. Microbiol. 1990;28:495–503. doi: 10.1128/jcm.28.3.495-503.1990. PubMed DOI PMC
Hashemi E., Akhavan O., Shamsara M., Rahighi R., Esfandiar A., Tayefeh A.R. Cyto and Genotoxicities of Graphene Oxide and Reduced Graphene Oxide Sheets on Spermatozoa. RSC Adv. 2014;4:27213–27223. doi: 10.1039/c4ra01047g. DOI
Park J.S., Goo N.-I., Kim D.-E. Mechanism of DNA Adsorption and Desorption on Graphene Oxide. Langmuir. 2014;30:12587–12595. doi: 10.1021/la503401d. PubMed DOI
Saha S., Sarkar P. Understanding the Interaction of DNA–RNA Nucleobases with Different ZnO Nanomaterials. Phys. Chem. Chem. Phys. 2014;16:15355–15366. doi: 10.1039/c4cp01041h. PubMed DOI
Nandy B., Santosh M., Maiti P.K. Interaction of Nucleic Acids with Carbon Nanotubes and Dendrimers. J. Biosci. 2012;37:457–474. doi: 10.1007/s12038-012-9220-8. PubMed DOI
Saiyed Z.M., Bochiwal C., Gorasia H., Telang S.D., Ramchand C.N. Application of Magnetic Particles (Fe3O4) for Isolation of Genomic DNA from Mammalian Cells. Anal. Biochem. 2006;356:306–308. doi: 10.1016/j.ab.2006.06.027. PubMed DOI
Kupcik R., Macak J.M., Rehulkova H., Sopha H., Fabrik I., Anitha V.C., Klimentova J., Murasova P., Bilkova Z., Rehulka P. Amorphous TiO2 Nanotubes as a Platform for Highly Selective Phosphopeptide Enrichment. ACS Omega. 2019;4:12156–12166. doi: 10.1021/acsomega.9b00571. PubMed DOI PMC
Amano T., Toyooka T., Ibuki Y. Preparation of DNA-Adsorbed TiO2 Particles—Augmentation of Performance for Environmental Purification by Increasing DNA Adsorption by External PH Regulation. Sci. Total Environ. 2010;408:480–485. doi: 10.1016/j.scitotenv.2009.10.037. PubMed DOI
Jimenez L.A., Gionet-Gonzales M.A., Sedano S., Carballo J.G., Mendez Y., Zhong W. Extraction of MicroRNAs from Biological Matrices with Titanium Dioxide Nanofibers. Anal. Bioanal. Chem. 2018;410:1053–1060. doi: 10.1007/s00216-017-0649-3. PubMed DOI PMC
Laemmli U.K. Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4. Nature. 1970;227:680–685. doi: 10.1038/227680a0. PubMed DOI
Oakley B.R., Kirsch D.R., Morris N.R. A Simplified Ultrasensitive Silver Stain for Detecting Proteins in Polyacrylamide Gels. Anal. Biochem. 1980;105:361–363. doi: 10.1016/0003-2697(80)90470-4. PubMed DOI
Aryal U.K., Ross A.R.S. Enrichment and Analysis of Phosphopeptides under Different Experimental Conditions Using Titanium Dioxide Affinity Chromatography and Mass Spectrometry. Rapid Commun. Mass Spectrom. 2010;24:219–231. doi: 10.1002/rcm.4377. PubMed DOI
Wu T., Xu T., Chen Y., Yang Y., Xu L.-P., Zhang X., Wang S. Renewable Superwettable Biochip for MiRNA Detection. Sens. Actuators B Chem. 2018;258:715–721. doi: 10.1016/j.snb.2017.11.109. DOI
Molina-Reyes J., Romero-Morán A., Sánchez-Salas J.L. Enhanced Photocatalytic Bacterial Inactivation of Atomic-Layer Deposited Anatase-TiO2 Thin Films on Rutile-TiO2 Nanotubes. Photochem. Photobiol. Sci. 2020;19:399–405. doi: 10.1039/C9PP00348G. PubMed DOI