One-step isothermal amplification strategy for microRNA specific and ultrasensitive detection based on nicking-assisted entropy-driven DNA circuit triggered exponential amplification reaction

Abstract

Sensitive and specific detection of microRNAs (miRNAs) is of critical significance for early diagnosis of cancers such as pancreatic cancer with atypical initial symptoms and high mortality. Despite exponential amplification reaction (EXPAR) is an attractive isothermal amplification method for detecting miRNAs, it faces the problems of the dependence difference and low specificity. To address such challenges, herein, a nicking-assisted entropy-driven DNA circuit triggered exponential amplification reaction (NAED-EXPAR) was firstly employed for ultrasensitive and specific detection of miRNA in "one-pot" manner at constant temperature. Nicking-assisted entropy-driven DNA circuit can specifically recognize the target miRNA, leading to continuous disassembly of DNA substrates via intramolecular toehold-mediated branch migration. During the reaction, the catalytic circuit can consume excess fuel DNA strands to produce a large number of primers. Then the newly formed primers can trigger EXPAR for highly efficient signal amplification. Mechanism analysis shows that the amplification efficiency of NAED-EXPAR is superior than that of single EXPAR. For miR-21, the detection limit of NAED-EXPAR can reach 100 aM, which is at least five orders of magnitude higher than the standard EXPAR that directly uses the target as primer. NAED-EXPAR shows improved specificity for identifying single nucleotide variations and enables sensitive and accurate analysis of miR-21 in human cancer cell lines. This method is expected to offer a new approach for the reliable quantification of miRNAs in complex biological matrices and provide valuable information for early cancer diagnosis.

Keywords: Exponential amplification reaction; Fluorescence; Isothermal amplification; MicroRNA; Nicking-assisted entropy-driven reaction.