A comprehensive system for detecting rare single nucleotide variants based on competitive DNA probe and duplex-specific nuclease

Magnetic Covalent Organic Framework Composites for Wastewater Remediation

Covalent organic frameworks (COFs) with high specific surface area, tailored structure, easy functionalization, and excellent chemical stability have been extensively exploited as fantastic materials in various fields. However, in most cases, COFs prepared in powder form suffer from the disadvantages of tedious operation, strong tendency to agglomerate, and poor recyclability, greatly limiting their practical application in environmental remediation. To tackle these issues, the fabrication of magnetic COFs (MCOFs) has attracted tremendous attention. In this review, several reliable strategies for the fabrication of MCOFs are summarized. In addition, the recent application of MCOFs as outstanding adsorbents for the removal of contaminants including toxic metal ions, dyes, pharmaceuticals and personal care products, and other organic pollutants is discussed. Moreover, in-depth discussions regarding the structural parameters affecting the practical potential of MCOFs are highlighted in detail. Finally, the current challenges and future prospects of MCOFs in this field are provided with the expectation to boost their practical application.

Molecular dynamics simulation‐guided toehold mediated strand displacement probe for single‐nucleotide variants detection

Single nucleotide variant (SNV) has become an emerging biomarker for various diseases such as cancers and infectious diseases. Toehold‐mediated strand displacement (TMSD), the core reaction of DNA nanotechnology, has been widely leveraged to identify SNVs. However, inappropriate choice of mismatch location results in poor discrimination ability. Here, we comprehensively investigate the effect of mismatch location on TMSD kinetics by molecular dynamic simulation tool oxDNA through umbrella sampling and forward flux sampling disclosing that mismatches at the border of the toehold and branch migration domain yield the lowest TMSD reaction rate. Nine disease‐related SNVs (SARS‐CoV‐2‐D614G, EGFR‐L858R, EGFR‐T790M, KRAS‐G12R, etc.) were tested experimentally showing a good agreement with simulation. The best choice of mismatch location enables high discrimination factor with a median of 124 for SNV and wild type. Coupling with a probe‐sink system, a low variant allele frequency of 0.1% was detected with 3 S/N. We successfully used the probes to detect SNVs with high confidence in the PCR clones of constructed plasmids. This work provides mechanistic insights into TMSD process at the single‐nucleotide level and can be a guidance for the design of TMSD system with fine‐tuning kinetics for various applications in biosensors and nanotechnology.

Signaling probe design for amplification-free detection of bacterial genes using DNA microarray

DNA microarrays are useful to detect microorganisms for various purposes including clinical testing and food safety. However, conventional DNA microarrays need complicated operations such as amplification, fluorescence labeling, and washing steps. To address this issue, we previously developed the signaling probe-based DNA microarray system that can eliminate these steps, and demonstrated a direct detection of bacterial genes. Nonetheless, this system requires well-designed probe sets due to the fluorescence resonance energy transfer (FRET)-based mode of action. Up to date, the probe design was highly dependent on the trial-and-error processes. In this study, we propose a strategy to rationally design the sequences of signaling probes based on the thermodynamic analysis. This analysis aided to improve the probe performance approximately 2.8 times, without experiments, by suppressing the secondary structure formation of the probes. We successfully demonstrated the specific and amplification-free detection of 5S rRNA from total RNA extracted from Escherichia coli within 30 min.