Single-Atom-Directed Inhibition of De Novo DNA Synthesis in Isothermal Amplifications

• Published in: Analytical chemistry (Washington) 2022-11, Vol.94 (45), p.15763-15771
• Main Authors: Zhang, Shun, Tang, Ling, Zhang, Jun, Sun, Wen, Liu, Dan, Chen, Jiuyi, Hu, Bei, Huang, Zhen
• Format: Article
• Language: English
• Subjects: Amplification; Biotechnology; Byproducts; Chemical synthesis; Chemistry; Deoxyribonuclease I - metabolism; Deoxyribonucleic acid; Disease detection; DNA; DNA - genetics; DNA biosynthesis; DNA polymerase; DNA Primers; DNA Replication; DNA-directed DNA polymerase; DNA-Directed DNA Polymerase - metabolism; Molecular biology; Nucleotide sequence; Nucleotides; Nucleotides - metabolism; Selenium
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/acs.analchem.2c03489

The template-dependent DNA synthesis, with DNA polymerases, templates, and primers, is essential for disease detection, molecular biology, and biotechnology. However, DNA polymerases can also initiate de novo DNA synthesis without templates and primers, forming byproduct DNAs with random sequences. Herein, we report the mechanisms of the de novo DNA synthesis in the absence or presence of nickase by discovering the reduced bindings between the polymerases and modified dNTPs and between the nickases and the modified DNAs and finding the reduced polymerase synthesis and nickase cleavage. Furthermore, via sequencing, we have identified the mechanism of the de novo synthesis in the nickase-based isothermal amplifications, generating the random DNAs as the major byproducts. Fortunately, we have discovered a novel strategy to inhibit the undesired synthesis with the single-atom-modified nucleotides and achieved the accurate and sensitive detection of clinic samples in the isothermal amplifications. In general, we have revealed the suppression mechanisms on the de novo synthesis and demonstrated that this selenium-atom strategy can allow more accurate and sensitive detection of pathogens via the isothermal amplifications.