Single-Molecule Sensor for High-Confidence Detection of miRNA

MicroRNAs (miRNAs) play a crucial role in regulating gene expression and have been linked to many diseases. Therefore, sensitive andaccurate detection of disease-linked miRNAs is vital to the emergingrevolution in early diagnosis of diseases. While the detection of miRNAs is achallenge due to their intrinsic properties such as small size, high sequencesimilarity among miRNAs and low abundance in biologicalfluids, themajority of miRNA-detection strategies involve either target/signalamplification or involve complex sensing designs. In this study, we havedeveloped and tested a DNA-basedfluorescence resonance energy transfer(FRET) sensor that enables ultrasensitive detection of a miRNA biomarker(miRNA-342-3p) expressed by triple-negative breast cancer (TNBC) cells. The sensor shows a relatively low FRET state in theabsence of a target but it undergoes continuous FRET transitions between low- and high-FRET states in the presence of the target.The sensor is highly specific, has a detection limit down to low femtomolar (fM) without having to amplify the target, and has a largedynamic range (3 orders of magnitude) extending to 300 000 fM. Using this strategy, we demonstrated that the sensor allowsdetection of miRNA-342-3p in the miRNA-extracts from cancer cell lines and TNBC patient-derived xenografts. Given the simple-to-design hybridization-based detection, the sensing platform developed here can be used to detect a wide range of miRNAs enabling early diagnosis and screening of other genetic disorders.

Automated summary

A DNA-based FRET sensor has been developed for ultrasensitive detection of miRNAs, enabling early diagnosis of diseases.