title: Detection of bacterial 16S rRNA using a molecular beacon-based X sensor.
abstract: We demonstrate how a long structurally constrained RNA can be analyzed in homogeneous solution at ambient temperatures with high specificity using a sophisticated biosensor. The sensor consists of a molecular beacon probe as a signal reporter and two DNA adaptor strands, which have fragments complementary to the reporter and to the analyzed RNA. One adaptor strand uses its long RNA-binding arm to unwind the RNA secondary structure. Second adaptor strand with a short RNA-binding arm hybridizes only to a completely complementary site, thus providing high recognition specificity. Overall the three-component sensor and the target RNA form a four-stranded DNA crossover (X) structure. Using this sensor, Escherichia coli16S rRNA was detected in real time with the detection limit of ~0.17 nM. The high specificity of the analysis was proven by differentiating Bacillus subtilis from E. coli 16S rRNA sequences. The sensor responds to the presence of the analyte within seconds.
authors.affiliation: Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA. yugeras@gmail.com
authors.forename: Yulia V
authors.initials: YV
authors.lastname: Gerasimova
authors.forename: Dmitry M
authors.initials: DM
authors.lastname: Kolpashchikov
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics* / Q000302:isolation & purification*; D015374:Biosensing Techniques / Q000295:instrumentation; D004247:DNA / Q000235:genetics*; D004867:Equipment Design; D019544:Equipment Failure Analysis; D004926:Escherichia coli / Q000235:genetics* / Q000302:isolation & purification*; D015336:Molecular Probe Techniques / Q000295:instrumentation; D012336:RNA, Ribosomal, 16S / Q000032:analysis / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013050:Spectrometry, Fluorescence / Q000295:instrumentation*
chemical_list: D012336:RNA, Ribosomal, 16S; D004247:DNA