ArticleNucleic acids research2011
Fluorescent xDNA nucleotides as efficient substrates for a template-independent polymerase.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 50 citations in OpenAlex.
- Substrate energetics in non-templated DNA synthesis by terminal deoxynucleotidyl transferase.Nucleic acids research · 2026Article
- Aspergillus fumigatus PolX1 is an early ancestor of vertebrate terminal deoxynucleotidyl transferases.Nucleic acids research · 2026Article
- The Role of Active Site Hydrophobic Interactions in Facilitating Catalysis in Human Terminal Deoxynucleotidyl Transferase.International journal of molecular sciences · 2025Article
- Template-independent enzymatic functionalization of DNA oligonucleotides with environment-sensitive nucleotide probes using terminal deoxynucleotidyl transferase.Nucleic acids research · 2025Article
- Post-translational digital data encoding into the genomes of mammalian cell populations.bioRxiv : the preprint server for biology · 2024Article
- Template-independent synthesis and 3'-end labelling of 2'-modified oligonucleotides with terminal deoxynucleotidyl transferases.Nucleic acids research · 2024Article
- Controlled enzymatic synthesis of oligonucleotides.Communications chemistry · 2024Review
- Substrate Specificity Diversity of Human Terminal Deoxynucleotidyltransferase May Be a Naturally Programmed Feature Facilitating Its Biological Function.International journal of molecular sciences · 2024Article
- Enzymatic Preparation of DNA with an Expanded Genetic Alphabet Using Terminal Deoxynucleotidyl Transferase and Its Applications.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly.Chemical Society reviews · 2021Review
- Sequence Preference and Initiator Promiscuity forACS synthetic biology · 2021Article
- One-step enzymatic modification of RNA 3' termini using polymerase θ.Nucleic acids research · 2019Article
- A versatile method for the UVA-induced cross-linking of acetophenone- or benzophenone-functionalized DNA.Scientific reports · 2018Article
- Template-Independent Enzymatic Oligonucleotide Synthesis (TiEOS): Its History, Prospects, and Challenges.Biochemistry · 2018Review
- Fluorescent nucleobases as tools for studying DNA and RNA.Nature chemistry · 2017Review
- Modified Nucleotides as Substrates of Terminal Deoxynucleotidyl Transferase.Molecules (Basel, Switzerland) · 2017Article
- DNA polymerase θ specializes in incorporating synthetic expanded-size (xDNA) nucleotides.Nucleic acids research · 2016Article
- Computational Evaluation of Nucleotide Insertion Opposite Expanded and Widened DNA by the Translesion Synthesis Polymerase Dpo4.Molecules (Basel, Switzerland) · 2016Article
- The Effects of Magnesium Ions on the Enzymatic Synthesis of Ligand-Bearing Artificial DNA by Template-Independent Polymerase.International journal of molecular sciences · 2016Article
- DNA-multichromophore systems.Chemical reviews · 2012Review
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Template independent polymerases, and terminal deoxynucleotidyl transferase (TdT) in particular, have been widely used in enzymatic labeling of DNA 3'-ends, yielding fluorescently-labeled polymers. The majority of fluorescent nucleotides used as TdT substrates contain tethered fluorophores attached to a natural nucleotide, and can be hindered by undesired fluorescence characteristics such as self-quenching. We previously documented the inherent fluorescence of a set of four benzo-expanded deoxynucleoside analogs (xDNA) that maintain Watson-Crick base pairing and base stacking ability; however, their substrate abilities for standard template-dependent polymerases were hampered by their large size. However, it seemed possible that a template-independent enzyme, due to lowered geometric constraints, might be less restrictive of nucleobase size. Here, we report the synthesis and study of xDNA nucleoside triphosphates, and studies of their substrate abilities with TdT. We find that this polymerase can incorporate each of the four xDNA monomers with kinetic efficiencies that are nearly the same as those of natural nucleotides, as measured by steady-state methods. As many as 30 consecutive monomers could be incorporated. Fluorescence changes over time could be observed in solution during the enzymatic incorporation of expanded adenine (dxATP) and cytosine (dxCTP) analogs, and after incorporation, when attached to a glass solid support. For (dxA)(n) polymers, monomer emission quenching and long-wavelength excimer emission was observed. For (dxC)(n), fluorescence enhancement was observed in the polymer. TdT-mediated synthesis may be a useful approach for creating xDNA labels or tags on DNA, making use of the fluorescence and strong hybridization properties of the xDNA.
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Registered trials
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