Defining the substrate scope of DNAzyme catalysis for reductive amination with aliphatic amines

Yang, Sen; Silverman, Scott

doi:10.1039/d3ob00070b

Org. Biomol. Chem.

2023

DOI: 10.1039/d3ob00070b

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Defining the substrate scope of DNAzyme catalysis for reductive amination with aliphatic amines

Sen Yang

Scott Silverman

Abstract: Amines can be alkylated using various reactions, such as reductive amination of aldehydes. In this study, we sought DNAzymes as catalytic DNA sequences that promote reductive amination with aliphatic amines,...

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2024

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Cited by 3 publications

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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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Functional Nucleic Acid Enzymes: Nucleic Acid-Based Catalytic Factories

Yang,

Xie,

Zhu

et al. 2024

ACS Catal.

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Site-specific N-alkylation of DNA oligonucleotide nucleobases by DNAzyme-catalyzed reductive amination

Boyd,

Kennebeck,

Miranda

et al. 2024

Nucleic Acids Research

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DNA and RNA nucleobase modifications are biologically relevant and valuable in fundamental biochemical and biophysical investigations of nucleic acids. However, directly introducing site-specific nucleobase modifications into long unprotected oligonucleotides is a substantial challenge. In this study, we used in vitro selection to identify DNAzymes that site-specifically N-alkylate the exocyclic nucleobase amines of particular cytidine, guanosine, and adenosine (C, G and A) nucleotides in DNA substrates, by reductive amination using a 5′-benzaldehyde oligonucleotide as the reaction partner. The new DNAzymes each require one or more of Mg2+, Mn2+, and Zn2+ as metal ion cofactors and have kobs from 0.04 to 0.3 h–1, with rate enhancement as high as ∼104 above the splinted background reaction. Several of the new DNAzymes are catalytically active when an RNA substrate is provided in place of DNA. Similarly, several new DNAzymes function when a small-molecule benzaldehyde compound replaces the 5′-benzaldehyde oligonucleotide. These findings expand the scope of DNAzyme catalysis to include nucleobase N-alkylation by reductive amination. Further development of this new class of DNAzymes is anticipated to facilitate practical covalent modification and labeling of DNA and RNA substrates.

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DNA Catalysis: Design, Function, and Optimization

Stratton,

Pokhrel,

Smith

et al. 2024

Molecules

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Catalytic DNA has gained significant attention in recent decades as a highly efficient and tunable catalyst, thanks to its flexible structures, exceptional specificity, and ease of optimization. Despite being composed of just four monomers, DNA’s complex conformational intricacies enable a wide range of nuanced functions, including scaffolding, electrocatalysis, enantioselectivity, and mechano-electro spin coupling. DNA catalysts, ranging from traditional DNAzymes to innovative DNAzyme hybrids, highlight the remarkable potential of DNA in catalysis. Recent advancements in spectroscopic techniques have deepened our mechanistic understanding of catalytic DNA, paving the way for rational structural optimization. This review will summarize the latest studies on the performance and optimization of traditional DNAzymes and provide an in-depth analysis of DNAzyme hybrid catalysts and their unique and promising properties.

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Defining the substrate scope of DNAzyme catalysis for reductive amination with aliphatic amines

Abstract: Amines can be alkylated using various reactions, such as reductive amination of aldehydes. In this study, we sought DNAzymes as catalytic DNA sequences that promote reductive amination with aliphatic amines,...

Cited by 3 publications

References 38 publications

Functional Nucleic Acid Enzymes: Nucleic Acid-Based Catalytic Factories

Functional Nucleic Acid Enzymes: Nucleic Acid-Based Catalytic Factories

Site-specific N-alkylation of DNA oligonucleotide nucleobases by DNAzyme-catalyzed reductive amination

DNA Catalysis: Design, Function, and Optimization

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