ArticleJournal of chemical theory and computation2020
Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet.
Article in Journal of chemical theory and computation, 2020. 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, 36 citations in OpenAlex.
- Quantifying replication fidelity of unnatural base pairs using nanopore sequencing.Nature communications · 2026Article
- Sequencing a DNA analog composed of artificial bases.Nature communications · 2025Article
- The QDπ dataset, training data for drug-like molecules and biopolymer fragments and their interactions.Scientific data · 2025Article
- Excited-state proton transfer in the rare isoguanine-isocytosine base pair in water solution.Journal of molecular modeling · 2025Article
- Cancer cell target discovery: comparing laboratory evolution of expanded DNA six-nucleotide alphabets with standard four-nucleotide alphabets.Nucleic acids research · 2025Article
- Nucleic acid joining enzymes: biological functions and synthetic applications beyond DNA.The Biochemical journal · 2025Review
- Solvent-Controlled Separation of Integratively Self-Sorted PdAngewandte Chemie (International ed. in English) · 2025Article
- Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials.Molecules (Basel, Switzerland) · 2024Article
- Investigation of dynamical flexibility of D5SIC-DNAM inside DNA duplex in aqueous solution: a systematic classical MD approach.Physical chemistry chemical physics : PCCP · 2024Article
- Investigation of the stability of D5SIC-DNAM-incorporated DNA duplex inPhysical chemistry chemical physics : PCCP · 2024Article
- A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase.Nature communications · 2023Article
- Tautomeric equilibrium and spectroscopic properties of 8-azaguanine revealed by quantum chemistry methods.European biophysics journal : EBJ · 2023Article
- How proton transfer impacts hachimoji DNA.RSC advances · 2023Article
- Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states.The Journal of chemical physics · 2023Article
- QDπ: A Quantum Deep Potential Interaction Model for Drug Discovery.Journal of chemical theory and computation · 2023Article
- Rethinking nucleic acids from their origins to their applications.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Review
- Investigations Into Chemically Stabilized Four-Letter DNA for DNA-Encoded Chemistry.Frontiers in chemistry · 2022Article
- Interaction of Thymine DNA Glycosylase with Oxidised 5-Methyl-cytosines in Their Amino- and Imino-Forms.Molecules (Basel, Switzerland) · 2021Article
- Chemically Stabilized DNA Barcodes for DNA-Encoded Chemistry.Angewandte Chemie (International ed. in English) · 2021Article
- Quantum-mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges?Journal of computer-aided molecular design · 2021Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 3 countries.
Funding
Abstract
Evolution has yielded biopolymers that are constructed from exactly four building blocks and are able to support Darwinian evolution. Synthetic biology aims to extend this alphabet, and we recently showed that 8-letter (hachimoji) DNA can support rule-based information encoding. One source of replicative error in non-natural DNA-like systems, however, is the occurrence of alternative tautomeric forms, which pair differently. Unfortunately, little is known about how structural modifications impact free-energy differences between tautomers of the non-natural nucleobases used in the hachimoji expanded genetic alphabet. Determining experimental tautomer ratios is technically difficult, and so, strategies for improving hachimoji DNA replication efficiency will benefit from accurate computational predictions of equilibrium tautomeric ratios. We now report that high-level quantum-chemical calculations in aqueous solution by the embedded cluster reference interaction site model, benchmarked against free-energy molecular simulations for solvation thermodynamics, provide useful quantitative information on the tautomer ratios of both Watson-Crick and hachimoji nucleobases. In agreement with previous computational studies, all four Watson-Crick nucleobases adopt essentially only one tautomer in water. This is not the case, however, for non-natural nucleobases and their analogues. For example, although the enols of isoguanine and a series of related purines are not populated in water, these heterocycles possess N
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