Metal-dependent activity control of a compact-sized 8–17 DNAzyme based on metal-mediated unnatural base pairing

Takezawa, Yusuke; Hu, Lingyun; Nakama, Takahiro; Shionoya, Mitsuhiko

doi:10.1039/d3cc05520e

Cited by 4 publications

(1 citation statement)

References 49 publications

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“…Metal-responsive DNAzymes have been developed previously by incorporating metal-mediated base pairs such as Cu II -mediated hydroxypyridone base pairs (H–Cu II –H). 9 The bifacial caU bases used in this study not only form hydrogen-bonded caU–A base pairs, but also Cu II -mediated caU–Cu II –caU base pairs with high metal selectivity. 6 The caU–Cu II –caU base pairing significantly stabilizes the DNA duplexes (Δ T m = +30.7 °C for a duplex with three caU–Cu II –caU pairs), whereas the caU–A base pairs are destabilized by the addition of Cu II ions (Δ T m = −7.3 °C for a duplex with three caU–A pairs by using 6 equiv.…”

Section: Introductionmentioning

confidence: 99%

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

Takezawa,

Zhang,

Mori

et al. 2024

Chem. Sci.

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Section: Introductionmentioning

confidence: 99%

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

Takezawa,

Zhang,

Mori

et al. 2024

Chem. Sci.

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Rational design of metal-responsive functional DNA supramolecules

Takezawa

2024

J Incl Phenom Macrocycl Chem

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DNA molecules have excellent molecular recognition abilities through the complementary hydrogen-bonded base pairing. Since the hybridization of oligonucleotides can be programmed based on the sequences of the nucleobases, a great number of DNA supramolecular architectures have been constructed via self-assembly processes. The development of stimuli-responsive DNA supramolecules has attracted increasing interests because it will contribute to the construction of dynamic molecular systems such as molecular machines. Metal ions are considered as useful chemical stimuli, but the construction of metal-responsive DNA systems is still in the early stage. This review article describes current progress on the development of DNA supramolecules whose structure and function can be regulated in response to metal ions, with mainly focusing on our recent studies. The basic strategy is the introduction of unnatural metal ligands that form interstrand metal complexes in DNA structures. For example, artificial metal-mediated base pairs, formed through complexation between ligand-type nucleobase analogs and a bridging metal ion, were incorporated into known DNAzymes (catalytic DNA) to allosterically regulate their activity in a metal-responsive manner. Novel ligand-type nucleobases that form both metal-mediated and hydrogen-bonded base pairs have been recently devised as metal-responsive building blocks, and were used to construct a simple prototype of DNA molecular machines. Branched DNA structures bearing metal ligands at the junction core were also synthesized as novel structural motifs, with which metal-mediated structure transformation was demonstrated. These metal-responsive DNA supramolecules are expected to expand the toolbox of DNA-based supramolecular chemistry and nanotechnology.

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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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Metal-dependent activity control of a compact-sized 8–17 DNAzyme based on metal-mediated unnatural base pairing

Abstract: A compactly-folded 8–17 DNAzyme was reshaped into a metal-responsive allosteric DNAzyme by introducing a CuII-meditated unnatural base pair.

Cited by 4 publications

References 49 publications

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

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

Rational design of metal-responsive functional DNA supramolecules

Functional Nucleic Acid Enzymes: Nucleic Acid-Based Catalytic Factories

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Metal-dependent activity control of a compact-sized 8–17 DNAzyme based on metal-mediated unnatural base pairing

Abstract: A compactly-folded 8–17 DNAzyme was reshaped into a metal-responsive allosteric DNAzyme by introducing a CuII-meditated unnatural base pair.

Cited by 4 publications

References 49 publications

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

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

Rational design of metal-responsive functional DNA supramolecules

Functional Nucleic Acid Enzymes: Nucleic Acid-Based Catalytic Factories

Contact Info

Product

Resources

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

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