Ratiometric SERS biosensor for sensitive and reproducible detection of microRNA based on mismatched catalytic hairpin assembly

MicroRNAs (miRNAs) serve as significant regulators in a variety of diseases and have been emerging as a class of promising biomarkers for early cancer diagnosis. Herein, an enzyme-free surface-enhanced Raman scattering (SERS) platform was proposed for sensitive and reliable detection of target miRNA-21 using a corrective internal standard (IS)-based ratiometric SERS probe coupled with mismatched catalytic hairpin assembly (CHA) amplification. The 4-aminothiophenol (4-ATP) was used as IS molecule and modified on the surface of silver nanoparticles decorated silicon wafer. In principle, the presence of miRNA-21 could cyclically trigger the allosteric effects of mismatched CHA amplification and the 3'-R6G labeled hairpin probe 1 (H1) was opened. Then, the hairpin probe 2 (H2) hybridized with H1 to form H1-H2 complex and the released miRNA-21 was free to participate in the next cycle of CHA reaction. Meanwhile, the H1-H2 complex could hybridize with the capture DNA on the SERS chip, making the Raman tag of R6G close to the surface of SERS substrate, and the intensity of SERS signal from R6G labels increase while that from 4-ATP remain relatively unchanged. Benefiting from outstanding performances of the ratiometric SERS strategy and enzyme-free CHA amplification system, this platform exhibits sensitivity toward miRNA-21 with a limit of detection of 3.5 fM and a broad dynamic range from 10 fM to 100 nM, More importantly, this proposed method presents an excellent reliable SERS analysis with the correction of IS. The developed strategy holds a potential alternative tool for miRNA detection in biomedical research and early clinical diagnosis.