Enhanced DNA Entropy-Driven Circuit by Locked Nucleic Acids and Simulation-Guided Localization

Abstract

Signal amplification methods based on DNA molecular interactions are promising tools for detecting various biomarkers in low abundance. The entropy-driven circuit (EDC), as an enzyme-free signal amplification method, has been used in detecting and imaging a variety of biomarkers. The localization strategy can effectively increase the local concentration of the DNA reaction modules to improve the signal amplification effect. However, the localization strategy may also amplify the leak reaction of the EDC, and effective signal amplification can be limited by the unclear structure−function relationship. Herein, we utilized locked nucleic acid (LNA) modification to enhance the stability of the localized entropy-driven circuit (LEDC), which suppressed a 94.6% leak signal. The coarse-grained model molecular simulation was used to guide the structure design of the LEDC, and the influence of critical factors such as the localized distance and spacer length was analyzed at the molecular level to obtain the best reaction performance. The sensitivities of miR-21 and miR-141 detected by a simulation-guided optimal LEDC probe were 17.45 and 65 pM, 1345 and 521 times higher than free-EDC, respectively. The LEDC was further employed for the fluorescence imaging of miRNA in cancer cells, showing excellent specificity and sensitivity. This work utilizes LNA and molecular simulations to comprehensively improve the performance of a localized DNA signal amplification circuit, providing an advanced DNA probe design strategy for biosensing and imaging as well as valuable information for the designers of DNA-based probes.

Flexible-Arranged Biomimetic Array Integrated with Parallel Entropy-Driven Circuits for Ultrasensitive, Multiple, and Reliable Detection of Cancer-Related MicroRNAs

“…Compared with lane 3 (R/P/Q), lane 6 (the mixture of R/P/Q and F) shows a few fuzzy bands, indicating a degree of background leakage in EDC. This leakage may be because of the “breathing” phenomenon of the base pairs at the end of the DNA double strand, which still required research to further minimize (e.g., by introducing the locked nucleic acid). , Fortunately, thanks to the efficient amplification ability of EDC, the existing leakage can obtain remission to a certain degree. Meanwhile, the fluorescence analysis was performed.…”

Importance of DNA nanotechnology for DNA methyltransferases in biosensing assays

“…DNA nanotechnology 103 specializes in exploiting the molecular property (e.g., self-assembling property) of DNA to construct new types of nanoscale structure that can be manipulated, and the assembly of DNA nanostructure has the advantages of programmability, 104 ease of modification and ease of synthesis. 105,106 In these technologies, DNA is not used as genetic material, but is used as a template for guiding other molecules in the direction or position of their movement, or for fabricating DNA nanospatial structures that are themselves functional, and so on.…”

“…DNA nanotechnology 103 specializes in exploiting the molecular property ( e.g. , self-assembling property) of DNA to construct new types of nanoscale structure that can be manipulated, and the assembly of DNA nanostructure has the advantages of programmability, 104 ease of modification and ease of synthesis.…”