Quantification of miRNAs by mass spectrometry based on DNase I-assisted amplification with the aid of a chemometric model

Abstract

Herein, the hydrolysis patterns of DNase I against a DNA probe in both single-strand form and DNA/miRNA heteroduplex were experimentally investigated in detail by mass spectrometric technique. Based on the knowledge obtained in the experiments, DNase I-assisted signal amplification strategy was proposed and used to design a mass spectrometric platform for miRNA detection. As a proof of concept, the performance of the proposed platform was evaluated for the detection of miRNA-122 in cell lysate samples. An advanced calibration model was explicitly derived to model the relationships between the concentration of miRNA-122 and the mass spectral signals of mass spectrometrically detected fragments of the DNA probe produced in the DNase I-assisted signal amplification process. With the aid of the advanced calibration model, the proposed mass spectrometric platform achieved quite accurate quantification results for miRNA-122 in cell lysate samples of Huh-7 and HepG-2 ​cell lines with recovery rates ranging from 98% to 104%. It is noteworthy that the proposed mass spectrometric platform can differentiate the target miRNA from other non-target ones based on their mass spectral response patterns instead of mass spectral intensities, and hence possesses high specificity for the target miRNA. It is reasonable to expect that the combination of mass spectrometry based on DNase I-assisted signal amplification with the advanced chemometric model provides a competitive alternative for designing cost-effective and label-free miRNA detection methods.