title: Detection of microRNA by fluorescence amplification based on cation-exchange in nanocrystals.
abstract: Small RNA molecules are effective regulators of gene expression, and the expression signature of one subgroup of small RNA, the microRNA (miRNA), has been linked to disease development and progression. Therefore, detection of small RNA in biological samples will greatly improve the understanding of their functions and render effective tools to researchers for cellular process control and disease prevention. To solve the challenges in detecting the low-abundance and short strand-length of small RNA molecules, we designed a ligation-assisted binding assay and applied the cation exchange-based fluorescence amplification (CXFluoAmp) method developed in our group for detection. Nonfluorescent, ionic nanocrystals (NCs) of CdSe were conjugated to detection probes and immobilized onto the array surface via ligation with the target small RNA, miR21, which bound to the capture probe complimentarily. Each binding event induced by one target miR21 molecule was then amplified by the release of thousands of Cd2+ from one NC. The free Cd2+ immediately turned on the fluorescence of thousands of fluorogenic Rhod-5N molecules. With such a powerful signal amplification strategy, our assay achieved a limit of detection (LOD) of 35 fM and signals were detectable with analyte concentrations spanning over 7 orders of magnitude. We also identified the differential expression of miR21 in total RNA extracts from healthy breast tissue and diseased cells. Furthermore, our detection scheme demonstrated good specificity in small RNA detection, because significant signal intensity could be observed from small RNAs with one or two nucleotides difference in sequences. Thus, our assay has great application potential for disease diagnosis relying on miRNA biomarkers, or in small RNA expression profiling for new target discovery and functional study.
authors.affiliation: Department of Chemistry, University of California, Riverside, California 92521, USA.
authors.forename: Jishan
authors.initials: J
authors.lastname: Li
authors.forename: Samantha
authors.initials: S
authors.lastname: Schachermeyer
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.forename: Yadong
authors.initials: Y
authors.lastname: Yin
authors.forename: Wenwan
authors.initials: W
authors.lastname: Zhong
mesh_terms: D001483:Base Sequence; D019187:Cadmium Compounds / Q000737:chemistry; D045744:Cell Line, Tumor; D015342:DNA Probes / Q000737:chemistry / Q000235:genetics; D005456:Fluorescent Dyes / Q000737:chemistry; D005786:Gene Expression Regulation; D006801:Humans; D057230:Limit of Detection; D008280:Magnetics; D008670:Metals / Q000737:chemistry; D035683:MicroRNAs / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D053758:Nanoparticles / Q000737:chemistry*; D009693:Nucleic Acid Hybridization; D015347:RNA Probes / Q000737:chemistry / Q000235:genetics; D018036:Selenium Compounds / Q000737:chemistry; D013050:Spectrometry, Fluorescence
chemical_list: D019187:Cadmium Compounds; D015342:DNA Probes; D005456:Fluorescent Dyes; D008670:Metals; D035683:MicroRNAs; D015347:RNA Probes; D018036:Selenium Compounds; C058667:cadmium selenide