Abstract
Circulating tumor DNA (ctDNA), originating directly from the tumor or circulating tumor cells, may reflect the entire tumor genom and has gained considerable attention for its potential clinical diagnosis and prognosis throughout the treatment regimen. However, the reliable and robust ctDNA detection remains a key challenge. Here, this work designs a pair of DNA clutch separation probes and an ideal discrimination probes based on toehold-mediated strand displacement reaction (TSDR) to specifically recognize ctDNA. First, the ctDNAs were denatured to form ssDNAs, the pair of DNA clutch separation probes [one of which modified onto the magnetic nanoparticles (MNPs)] are used to recognize and hybridize with the complemental chains and prevent reassociation of denatured ssDNAs. The complemental chains are removed in magnetic field and left the wild and mutant ssDNA chains in the supernatant. Then, the TSDR specificity recognizes the target mutant sequence to ensure only the mutated strands to be detection. The proposed assay exhibited good sensitivity and selectivity without any signal amplification. The proposed assay displayed a linear range from 2 to100 nM with a limit of detection (LOD) of 0.85 nM, and it was useful for ctDNA biomedical analysis and clinic theranostic.
Highlights
In recent years, many advanced analytical methods have been established to quantify DNAs and RNAs (Schwarzenbach et al, 2011; Si et al, 2014; Li et al, 2015; Wang et al, 2018), among them, liquid biopsy has increasingly attracted intense attention due to its rapid, cost-effective and non-invasive properties
This work designs a pair of DNA clutch separation probes and an ideal discrimination probes based on toehold-mediated strand displacement reaction (TSDR) to recognize mutant Circulating tumor DNA (ctDNA) (Figure 1)
These results suggested the successful modification of DNA on the surface of magnetic nanoparticles (MNPs)
Summary
Many advanced analytical methods have been established to quantify DNAs and RNAs (Schwarzenbach et al, 2011; Si et al, 2014; Li et al, 2015; Wang et al, 2018), among them, liquid biopsy has increasingly attracted intense attention due to its rapid, cost-effective and non-invasive properties. Circulating tumor DNA (ctDNA), originating directly from the tumor or circulating tumor cells, is an effective diagnostic biomarker existing as a single or double strand in peripheral blood (Zou et al, 2017). It is potential surrogate for the entire tumor genome and has gained considerable attention for cancer diagnosis and prognosis (Das et al, 2016). It was reported that ctDNA was detected in 82 and 47% for patients with stage IV and I disease, respectively (Bettegowda et al, 2014). The detection of specific cancer-related sequences in ctDNA is very important in clinical application
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