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)

References 41 publications

(27 reference statements)

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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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