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A new method for the detection of FEN1, a cancer marker

Flap endonuclease 1 (FEN1), a potential biomarker in oncological investigations, can help determine the location, diagnosis, and prognosis of cancers. Yet, there has been limited progress toward the development of analytical techniques to detect FEN1. According to a study led by researchers at Nanjing Normal University, a sensing system for the detection of FEN1 was developed and this investigation increased the sensitivity of FEN1 detection to the femtomolar level.

The researchers reported in the journal Analytical Chemistry Feb.2 that flap endonuclease 1 (FEN1), an endogenous nuclease with the ability to cleave the 5′ overhang of branched dsDNA, is a potential biomarker in oncological investigations. High FEN1 levels correlated with aggressive breast cancer, poor survival, and epithelial ovarian cancer. Therefore, FEN1 has the potential for use as a cancer marker for determining the location, diagnosis, and prognosis of cancers.

However, few analytical methods targeting FEN1 with high sensitivity and simplicity have been developed. Thus, researchers developed a signal-amplified detection of FEN1 based on the cleavage-induced ligation of a dumbbell DNA probe and rolling circle amplification (RCA). A flapped dumbbell DNA probe (FDP) was rationally designed with a FEN1 cleavable flap at the 5′ end. The cleavage generated a nick site with juxtaposed 5′ phosphate and 3′ hydroxyl ends, which were linkable by T4 DNA ligase to form a closed dumbbell DNA probe (CDP) with a circular conformation. The CDP functioned as a template for RCA, which produced abundant DNA that could be probed using SYBR Green I. The highly sensitive detection of FEN1 with a limit of detection of 15 fM was achieved, and this method showed high specificity, which enabled the quantification of FEN1 in real samples. The inhibitory effects of chemicals on FEN1 were also evaluated. This study represents the first attempt to develop an FEN1 assay that involves signal amplification, and the novel biosensor method enriches the tools for FEN1-based diagnostics.

Bingzhi Li (First Author) worked with co-corresponding authors Xing Zhang and He Huang from School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Anqi Xia, Siying Xie, Zhirun Ji, and Tiying Suo from School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, and Lei Lin from School of Environment, Nanjing Normal University.

The study, “Signal-Amplified Detection of the Tumor Biomarker FEN1 Based on Cleavage-Induced Ligation of a Dumbbell DNA Probe and Rolling Circle Amplification” was published in the journal Analytical Chemistry Feb.2.
 

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