Reliable breast cancer miRNAs detection with enhanced silicon nanowire biosensor by PNA probe and optical calibration

MicroRNAs (miRNAs) have attracted significant attention in the field of cancer research as a promising class of biomarkers. However, precise, sensitive, and specific detection of miRNAs still confronts challenges due to their dynamic expression, low abundance, and high sequence similarity among families. The highly sensitive silicon nanowires (SiNWs) biosensors are limited by little interface discrepancy within the SiNWs, which has the potential to affect the final output results. In this study, the calibration of the SiNWs biosensor was initially suggested to be conducted through photo response. This approach successfully mitigated the impact of preparation and modification procedures, resulting in an enhanced correlation between the biosensor and q-PCR for the identification of breast cancer miRNA. Specifically, the correlation coefficient was raised from below 0.5 to above 0.8. Furthermore, the uncharged peptide nucleic acid (PNA) was used for device modification in order to address the issue of detecting miRNAs with a total length in below 0.01xPBS buffer. It was shown that the PNA probe exhibited greater sensitivity compared to the DNA probe in 0.001xPBS buffer. Significantly, the improved biosensor exhibited favorable selectivity and was capable of identifying single base mismatch. The sensor exhibited a high level of sensitivity in detecting miRNA within a concentration range of 1 fM to 10 pM when applied to actual human blood samples. The biosensor exhibited an excellent level of reproducibility in the analysis of spiked samples, achieving a recovery rate of 91 %, without requiring RNA extraction or amplification procedures. The biosensor has the capability to directly detect miRNA in authentic clinical samples, hence demonstrating significant promise for the timely diagnosis of cancer via the use of miRNA as biomarkers.

Automated summary

miRNAs have emerged as promising biomarkers in cancer research, but their detection remains challenging. In this study, a photo response calibration method was proposed to enhance the correlation between a silicon nanowire biosensor and q-PCR for the identification of breast cancer miRNA. The use of an uncharged peptide nucleic acid (PNA) for device modification improved the sensor's sensitivity in detecting low concentration miRNA. The improved biosensor demonstrated favorable selectivity and the ability to detect miRNA directly in authentic clinical samples.