DNA Nanomachine (DNM) Biplex Assay for Differentiating Bacillus cereus Species

• Published in: International journal of molecular sciences 2023-02, Vol.24 (5), p.4473
• Main Authors: Ateiah, Muhannad, Gandalipov, Erik R, Rubel, Aleksandr A, Rubel, Maria S, Kolpashchikov, Dmitry M
• Format: Article
• Language: English
• Subjects: 10–23 DNAzyme; 16S rRNA; Acids; amplification-free detection; Assaying; B. cereus; Bacillus - genetics; Bacillus cereus; Bacillus cereus - genetics; binary probes; Binding; Deoxyribonucleic acid; Design; detection of folded RNA; DNA; DNA, Bacterial; DNA, Ribosomal - genetics; Environmental monitoring; Fluorescein; Fluorescence; Nucleic acids; Nucleotides; Pathogens; RNA, Ribosomal, 16S - genetics; rRNA 16S; Selectivity; Sensors
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms24054473

Conventional methods for the detection and differentiation of group species have drawbacks mostly due to the complexity of genetic discrimination between the species. Here, we describe a simple and straightforward assay based on the detected unamplified bacterial 16S rRNA by DNA nanomachine (DNM). The assay uses a universal fluorescent reporter and four all-DNA binding fragments, three of which are responsible for "opening up" the folded rRNA while the fourth stand is responsible for detecting single nucleotide variation (SNV) with high selectivity. Binding of the DNM to 16S rRNA results in the formation of the 10-23 deoxyribozyme catalytic core that cleaves the fluorescent reporter and produces a signal, which is amplified over time due to catalytic turnover. This developed biplex assay enables the detection of 16S rRNA at fluorescein and at Cy5 channels with a limit of detection of 30 × 10 and 35 × 10 CFU/mL, respectively, after 1.5 h with a hands-on time of ~10 min. The new assay may simplify the analysis of biological RNA samples and might be useful for environmental monitoring as a simple and inexpensive alternative to amplification-based nucleic acid analysis. The DNM proposed here may become an advantageous tool for detecting SNV in clinically significant DNA or RNA samples and can easily differentiate SNV under broadly variable experimental conditions and without prior amplification.