ArticleScientific reports2022
Quantification of synthetic errors during chemical synthesis of DNA and its suppression by non-canonical nucleosides.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 41 citations in OpenAlex.
- Engineered eMutS based magnetic separation system for high-fidelity DNA synthesis.Synthetic and systems biotechnology · 2026Article
- Polus: a context-aware enhancement framework for DNA storage via transformer-based soft-decision decoding.Bioinformatics (Oxford, England) · 2026Article
- Oligonucleotide Synthesis Errors Are a Source of Untoward Variation in HDR-Mediated Gene Editing.Genes · 2026Article
- GuanineOrganic & biomolecular chemistry · 2026Article
- Chemically synthesized high-fidelity oligos ≤ 600 nt as building blocks to accelerate complex gene construction in synthetic biology.Synthetic biology (Oxford, England) · 2026Article
- The Influence of the Capping Step During Solid-Phase Phosphoramidite Synthesis of Oligonucleotides on Synthetic Errors in Oligonucleotides.Molecules (Basel, Switzerland) · 2025Article
- Novel enzymatic DNA produced from a text file achieves comparable immune responses as plasmid vaccine.NPJ vaccines · 2025Article
- CRISPR-Cas9 HDR optimization: RAD52, denatured, and 5'-modified DNA templates in knock-in mice generation.iScience · 2025Article
- Guidelines in the Preparation of Fully Synthetic, Human Single-Domain Antibody Phage Display Libraries.Antibodies (Basel, Switzerland) · 2025Article
- Long oligos: direct chemical synthesis of genes with up to 1728 nucleotides.Chemical science · 2025Article
- Enhancing single-cell transcriptomics using interposed anchor oligonucleotide sequences.Communications biology · 2025Article
- De Novo Synthesis of Error-Free Long Oligos.Current protocols · 2024Article
- Amplified DNA Heterogeneity Assessment with Oxford Nanopore Sequencing Applied to Cell Free Expression Templates.bioRxiv : the preprint server for biology · 2024Article
- In vitro generation of genetic diversity for directed evolution by error-prone artificial DNA synthesis.Communications biology · 2024Article
- Nonaqueous Oxidation in DNA Microarray Synthesis Improves the Oligonucleotide Quality and Preserves Surface Integrity on Gold and Indium Tin Oxide Substrates.Analytical chemistry · 2024Article
- Advancing microbiota therapeutics: the role of synthetic biology in engineering microbial communities for precision medicine.Frontiers in bioengineering and biotechnology · 2024Review
- Amplified DNA heterogeneity assessment with Oxford Nanopore sequencing applied to cell free expression templates.PloS one · 2024Article
- Highly Accurate Sequence- and Position-Independent Error Profiling of DNA Synthesis and Sequencing.ACS synthetic biology · 2023Article
- Long oligodeoxynucleotides: chemical synthesis, isolation via catching-by-polymerization, verification via sequencing, and gene expression demonstration.Beilstein journal of organic chemistry · 2023Article
- Towards the controlled enzymatic synthesis of LNA containing oligonucleotides.Frontiers in chemistry · 2023Article
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Authors and funding
3 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Substitutions, insertions, and deletions derived from synthetic oligonucleotides are the hurdles for the synthesis of long DNA such as genomes. We quantified these synthetic errors by next-generation sequencing and revealed that the quality of the enzymatically amplified final combined product depends on the conditions of the preceding solid phase chemical synthesis, which generates the initial pre-amplified fragments. Among all possible substitutions, the G-to-A substitution was the most prominently observed substitution followed by G-to-T, C-to-T, T-to-C, and A-to-G substitutions. The observed error rate for G-to-A substitution was influenced by capping conditions, suggesting that the capping step played a major role in the generation of G-to-A substitution. Because substitutions observed in long DNA were derived from the generation of non-canonical nucleosides during chemical synthesis, non-canonical nucleosides resistant to side reactions could be used as error-proof nucleosides. As an example of such error-proof nucleosides, we evaluated 7-deaza-2´-deoxyguanosine and 8-aza-7-deaza-2´-deoxyguanosine and showed 50-fold decrease in the error rate of G-to-A substitution when phenoxyacetic anhydride was used as capping reagents. This result is the first example that improves the quality of synthesized sequences by using non-canonical nucleosides as error-proof nucleosides. Our results would contribute to the development of highly accurate template DNA synthesis technologies.
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