Isothermal amplification based on specific signal extraction and output for fluorescence and colorimetric detection of nucleic acids

Due to the complexity of compositions and low abundance of target in clinical sample, nucleic acids detection often suffers from false positives caused by nonspecific amplification. In in vitro diagnosis (IVD), PCR usually employ TaqMan probe to report specific signals and block false positive signals. However, nucleic acid isothermal amplifications, such as loop-mediated isothermal amplification (LAMP), lack of mature specific signal output mechanism, which prevents them from being used for IVD and point-of-care testing (POCT). In this work, we constructed a specific signal extract-to-output isothermal detection system (SSEI). SSEI contains a well-designed DNA probe for specific signal extraction and output in LAMP. This probe is a double-stranded DNA with an overhang sequence and named as extract-to-output probe (ETO probe). ETO probe can recognize the target -specific intermediate products in LAMP and release another signal-output probe (OP) to report the target -specific signals. With these unique properties, SSEI can detect as low as 10 copies of target DNA per reaction either by fluorescence detector or naked eyes. Moreover, due to the excellent performance against background nucleic acids interference, this biosensing platform had been successfully used for hepatitis B virus (HBV) clinical samples detection.

Automated summary

Due to the complexity of detecting nucleic acids in clinical samples and the low abundance of the target, false positives caused by nonspecific amplification are common. This study presents a specific signal extract-to-output isothermal detection system (SSEI) that can detect as low as 10 copies of target DNA per reaction, overcoming the limitations of other nucleic acid isothermal amplification techniques.