A designed locked nucleic acid-based nanopore for discriminating ctDNA and its coexisting analogue ncDNA

In this work, we designed a LNA probe for the α-HL nanopore to simultaneously discriminate ctDNA and ncDNA with single-base difference. The LNA probe greatly improved the discrimination capability of single-base mismatch up to ˜12.3 times. [Display omitted] Circulating tumor DNA (ctDNA), carrying tumor-specific sequence mutations, is a promising biomarker for classification, diagnosis and prognosis of cancers. However, there is still a great challenge in discriminating single-base difference between ctDNA and its coexisting analogue (normal circulating DNA, ncDNA) at a serum sample. A locked nucleic acid (LNA) probe combined with α-HL nanopore sensor was designed, which achieved a high signal-to-background ratio (SBR) of ∼8.34 × 103, as well as a significant discrimination capability (∼12.3 times) of single-base difference. The accurate discrimination strategy is label-free, convenient, selective and sensitive, which has great potential in the early diagnosis of diseases and biomedical research fields.