ArticleNucleic acids research2024
Site-specific N-alkylation of DNA oligonucleotide nucleobases by DNAzyme-catalyzed reductive amination.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- A metal-DNA biohybrid as enantioselective artificial photoDNAzyme.Nature communications · 2026Article
- Alkyltransferase Ribozyme for Site-Specific NAngewandte Chemie (International ed. in English) · 2026Article
- Site-specific ribozyme-mediated alkylation of DNA substrates.Nucleic acids research · 2026Article
- Advances in DNAzyme Selection, Molecular Engineering and Biomedical Applications.International journal of molecular sciences · 2026Review
- Chemically modified DNA aptamers and DNAzymes for expanded functional capabilities.Chemical science · 2026Review
- Metal surface-triggered DNAzyme catalysis for efficient DNA cleavage.Communications chemistry · 2026Article
- Derivative-Based Non-Target Identification of DNA-Reactive Impurities with Fragment Ion Filtering.Molecules (Basel, Switzerland) · 2025Article
- Click DNA ligation with deoxyribozyme.Nucleic acids research · 2025Article
- Signal Transduction Strategies for DNAzyme-Based Sensing and Imaging of Metal Ions in Cells andChemical & biomedical imaging · 2025Review
- Ribozyme-Catalyzed Site-Specific Labeling of RNA Using OAngewandte Chemie (International ed. in English) · 2025Article
- Sequence-Dependent Acylation of Peptide Lysine Residues by DNAzymes.Chembiochem : a European journal of chemical biology · 2024Article
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Authors and funding
5 authors.
Funding
Abstract
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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