Selenium atom on phosphate enhances specificity and sensitivity of DNA polymerization and detection

Luo, Guangcheng; Zhang, Jun; Yang, Mei; He, Hongfei; Huang, Zhen

doi:10.1039/d1tb00428j

Cited by 7 publications

(10 citation statements)

References 28 publications

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“…These results indicated that the improvement by the dNTPαSe substrates was not caused by increasing the substrate concentrations, which was consistent with our previous studies. 29,32…”

Section: Resultsmentioning

confidence: 99%

“…Though these reagents are often used as commercial optimizers and kit enhancers for polymerase chain reactions, their effect via the buffer improvement is limited. Nevertheless, the supplementary dNTPαSe significantly enhanced the polymerase reaction accuracy, 29,32 thereby greatly improving the specificity and sensitivity of PCR detection. Clearly, our simple and convenient Se-atom strategy has great potential in nucleic acid amplification and detection.…”

Section: Discussionmentioning

confidence: 99%

“…was not caused by increasing the substrate concentrations, which was consistent with our previous studies. 29,32…”

Section: Supplementary Dntpαse Improved Detection Sensitivitymentioning

confidence: 99%

“…Besides, enhancing the accuracy and sensitivity of DNA polymerization via the use of Se-atom-modified nucleotide substrates (dNTPαSe and 2-Se-TTP) has been explored recently. 27–29 This enhancement may be attributed to the reduced T m of the Se-DNA duplexes. To detect the Covid-19 virus accurately, we further developed our strategy by studying clinical samples with supplementary dNTPαSe, and we were able to reduce the false-negative rate significantly.…”

Section: Introductionmentioning

confidence: 99%

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Reducing COVID-19 diagnostic errors with dNTPαSe supplementation

Zhang

Tang

Liu

et al. 2023

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“…These results indicated that the improvement by the dNTPαSe substrates was not caused by increasing the substrate concentrations, which was consistent with our previous studies. 29,32…”

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…was not caused by increasing the substrate concentrations, which was consistent with our previous studies. 29,32…”

Section: Supplementary Dntpαse Improved Detection Sensitivitymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Reducing COVID-19 diagnostic errors with dNTPαSe supplementation

Zhang

Tang

Liu

et al. 2023

Analyst

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“…In order to investigate the mechanism of the de novo DNA synthesis, we have explored the polymerization with the modified dNTPs (Figure ). − We have discovered that the de novo synthesis with polymerases (Pol I, Bst, and Taq functioning under 37, 63, and 72 °C, respectively) can be inhibited by the modified dNTPs (such as dNTPαSe; Figure B). Furthermore, we have found that although the polymerase generates byproduct DNAs more and faster in the presence of the nickase than its absence, dNTPαSe can inhibit the byproduct polymerization as well (Figure D).…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2022

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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.

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Atom‐Modified gDNA Enhances Cleavage Activity of TtAgo Enabling Ultra‐Sensitive Nucleic Acid Testing

Zhang,

Chen,

Jiang

et al. 2024

Advanced Science

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The DNA‐guided (gDNA) Argonaute from Thermus thermophilus (TtAgo) has little potential for nucleic acid detection and gene editing due to its poor dsDNA cleavage activity at relatively low temperature. Herein, the dsDNA cleavage activity of TtAgo is enhanced by using 2′‐fluorine (2′F)‐modified gDNA and developes a novel nucleic acid testing strategy. This study finds that the gDNA with 2′F‐nucleotides at the 3′‐end (2′F‐gDNA) can promote the assembly of the TtAgo‐guide‐target ternary complex significantly by increasing its intermolecular force to target DNA and TtAgo, thereby providing ≈40‐fold activity enhancement and decreasing minimum reaction temperature from 65 to 60°C. Based on this outstanding advance, a novel nucleic acid testing strategy is proposed, termed FAST, which is performed by using the 2′F‐gDNA/TtAgo for target recognition and combining it with Bst DNA polymerase for nucleic acid amplification. By integrating G‐quadruplex and Thioflavin T, the FAST assay achieves one‐pot real‐time fluorescence analysis with ultra‐sensitivity, providing a limit of detection up to 5 copies (20 µL reaction mixture) for miR‐21 detection. In summary, an atom‐modification‐based strategy has been developed for enhancing the cleavage activity of TtAgo efficiently, thereby improving its practicability and establishing a TtAgo‐based nucleic acid testing technology with ultra‐sensitivity and high‐specificity.

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Selenium atom on phosphate enhances specificity and sensitivity of DNA polymerization and detection

Abstract: DNA polymerization is of high specificity in vivo. However, its specificity is much lower in vitro, which limits the advanced applications of DNA polymerization in ultrasensitive nucleic acid detection. Herein...

Cited by 7 publications

References 28 publications

Reducing COVID-19 diagnostic errors with dNTPαSe supplementation

Reducing COVID-19 diagnostic errors with dNTPαSe supplementation

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

Atom‐Modified gDNA Enhances Cleavage Activity of TtAgo Enabling Ultra‐Sensitive Nucleic Acid Testing

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