Construction of a Structure-Switchable Toehold Dumbbell Probe for Sensitive and Label-Free Measurement of MicroRNA in Cancer Cells and Tissues

MicroRNAs (miRNAs) play multiple crucial roles in post-transcriptional regulating gene expression, and the abnormal expression may induce various human diseases. Herein, we demonstrate the construction of a structure-switchable toehold dumbbell probe for sensitive and label-free measurement of microRNA in cancer cells and tissues on the basis of integrating exponential-rolling circle amplification (EXP-RCA) with linear-rolling circle amplification (LRCA). We designed a structure-switchable toehold dumbbell probe with annular and symmetric structure whose either side can hybridize with target miRNA to initiate EXP-RCA, greatly improving the detection sensitivity. Moreover, the dumbbell probe is designed with an appropriate standard free energy (G), and it cannot be activated by mismatched miRNAs, endowing this assay with good specificity. When target miRNA is present, it interacts with the dumbbell probe to activate EXP-RCA via toehold-mediated stand displacement, generating abundant triggers. The resulting triggers and target miRNA can function as primers to initiate LRCA, producing abundant long tandem repeats that can generate a distinct fluorescence signal using SYBR Gold as the indicator. This assay can be carried out homogeneously and isothermally without the requirement for either sophisticated modification/separation steps or any extra primers. It displays ultrahigh sensitivity with a limit of detection of 8.45 x 10(-17) M and excellent specificity, and it can differentiate let-7a from its homologous analogues. Moreover, this method can accurately quantify let-7a expression at a single-cell level and can even distinguish the let-7a expression between non-small cell lung cancer patient tissues and healthy person tissues.

Automated summary

In this study, a structure-switchable toehold dumbbell probe was designed for sensitive and label-free measurement of microRNA in cancer cells and tissues. The probe integrates exponential-rolling circle amplification (EXP-RCA) with linear-rolling circle amplification (LRCA) to improve detection sensitivity. This assay exhibits ultrahigh sensitivity and excellent specificity, allowing for accurate quantification of microRNA expression at a single-cell level and differentiation of expression differences in different tissues.