Ligase-mediated synthesis of Cu<sup>II</sup>-responsive allosteric DNAzyme with bifacial 5-carboxyuracil nucleobases

Takezawa, Yusuke; Zhang, Hanci; Mori, Keita; Hu, Lingyun; Shionoya, Mitsuhiko

doi:10.1039/d3sc05042d

Cited by 4 publications

(1 citation statement)

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“…(i) Template-dependent synthesis using sugar and phosphate-modified nucleotides and the KOD polymerase; (ii) endonuclease V cleaves the second phosphodiester linkage 3'-downstream of a deoxyinosine moiety present in the template and generates the modified sequence (in red); (iii) after endonucleasecleavage, the template is available for subsequent rounds of catalytic synthesis. https://doi.org/10.1038/s42004-024-01216-0 nucleobase [124][125][126] , but also on the sugar moiety of oligonucleotides 127 . This rather high permissiveness can be exploited to generate longer, chemically modified oligonucleotides by joining together carefully designed precursor fragments.…”

Section: Ligase-based Strategiesmentioning

confidence: 99%

Controlled enzymatic synthesis of oligonucleotides

Pichon,

Hollenstein

2024

Commun Chem

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Oligonucleotides are advancing as essential materials for the development of new therapeutics, artificial genes, or in storage of information applications. Hitherto, our capacity to write (i.e., synthesize) oligonucleotides is not as efficient as that to read (i.e., sequencing) DNA/RNA. Alternative, biocatalytic methods for the de novo synthesis of natural or modified oligonucleotides are in dire need to circumvent the limitations of traditional synthetic approaches. This Perspective article summarizes recent progress made in controlled enzymatic synthesis, where temporary blocked nucleotides are incorporated into immobilized primers by polymerases. While robust protocols have been established for DNA, RNA or XNA synthesis is more challenging. Nevertheless, using a suitable combination of protected nucleotides and polymerase has shown promises to produce RNA oligonucleotides even though the production of long DNA/RNA/XNA sequences (>1000 nt) remains challenging. We surmise that merging ligase- and polymerase-based synthesis would help to circumvent the current shortcomings of controlled enzymatic synthesis.

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Section: Ligase-based Strategiesmentioning

confidence: 99%

Controlled enzymatic synthesis of oligonucleotides

Pichon,

Hollenstein

2024

Commun Chem

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Mg2+- dependent six-jawed trap-mediated SERS biosensor for ratiometric detection of microRNA with use of the highly ordered Au NCs as substrate

Man,

Zhang,

Zhou

et al. 2025

Sensors and Actuators B: Chemical

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Functional Nucleic Acid Enzymes: Nucleic Acid-Based Catalytic Factories

Yang,

Xie,

Zhu

et al. 2024

ACS Catal.

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Biocatalysis plays a vital role in the operations of all living organisms, which is usually thought to be mediated by protein enzymes. However, the pioneering discovery of self-splicing intronsplicing RNA ribozyme demonstrated that nucleic acids can also promote catalysis, with efficiency comparable to that of proteases. The discovery of deoxyribozyme (DNAzymes) further broadened the understanding of the catalytic function of nucleic acids. Since then, nucleic acids with various catalytic functions have been gradually discovered and significant efforts have been devoted to the applications studies of nucleic acid catalyst. Consequently, a systematically and comprehensive review is needed to summarize all the advancements in the FNAzymes field. In this review, we propose the concept of functional nucleic acid enzymes (FNAzymes). FNAzymes are nucleic acids or nucleic acid complexes with special structure and catalytic functions. Then FNAzymes are divided into four groups based on the components that make them up: ribozymes, DNAzymes, modified FNAzymes, and functional nucleic acid nanozymes (FNA nanozymes). In addition, the catalytic function, structure, and catalytic mechanism of each FNAzymes are introduced. The applications of FNAzymes in biosensing, bioimaging, and biotherapy of are summarized. Finally, future development trends and application prospects of functional nucleases are discussed.

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Ligase-mediated synthesis of Cu^II-responsive allosteric DNAzyme with bifacial 5-carboxyuracil nucleobases

Abstract: A CuII-responsive allosteric DNAzyme has been developed by introducing bifacial 5-carboxyuracil (caU) nucleobases, which form both a hydrogen-bonded caU–A and a metal-mediated caU–CuII–caU base pairs. The base sequence was logically...

Cited by 4 publications

References 41 publications

Controlled enzymatic synthesis of oligonucleotides

Controlled enzymatic synthesis of oligonucleotides

Mg2+- dependent six-jawed trap-mediated SERS biosensor for ratiometric detection of microRNA with use of the highly ordered Au NCs as substrate

Functional Nucleic Acid Enzymes: Nucleic Acid-Based Catalytic Factories

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Ligase-mediated synthesis of CuII-responsive allosteric DNAzyme with bifacial 5-carboxyuracil nucleobases

Abstract: A CuII-responsive allosteric DNAzyme has been developed by introducing bifacial 5-carboxyuracil (caU) nucleobases, which form both a hydrogen-bonded caU–A and a metal-mediated caU–CuII–caU base pairs. The base sequence was logically...

Cited by 4 publications

References 41 publications

Controlled enzymatic synthesis of oligonucleotides

Controlled enzymatic synthesis of oligonucleotides

Mg2+- dependent six-jawed trap-mediated SERS biosensor for ratiometric detection of microRNA with use of the highly ordered Au NCs as substrate

Functional Nucleic Acid Enzymes: Nucleic Acid-Based Catalytic Factories

Contact Info

Product

Resources

About

Ligase-mediated synthesis of Cu^II-responsive allosteric DNAzyme with bifacial 5-carboxyuracil nucleobases