ArticleNucleic acids research2019
Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Crystal structure of a closed ternary complex of a HNA Reverse Transcriptase in complex with a HNA/DNA duplex.PloS one · 2026Article
- From liquid-phase synthesis to chemical ligation: preparation of oligonucleotides and their backbone analogs in solution.Nucleic acids research · 2025Review
- The XNA alphabet.Nucleic acids research · 2025Review
- Nucleic acid joining enzymes: biological functions and synthetic applications beyond DNA.The Biochemical journal · 2025Review
- Template-dependent DNA ligation for the synthesis of modified oligonucleotides.Nature communications · 2024Article
- Controlled enzymatic synthesis of oligonucleotides.Communications chemistry · 2024Review
- Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline.Nucleic acids research · 2024Article
- Nucleic acid nanostructures forApplied physics reviews · 2023Review
- Enzymatic Conjugation of Modified RNA Fragments by Ancestral RNA Ligase AncT4_2.Applied and environmental microbiology · 2022Article
- Discovery of Rift Valley fever virus natural pan-inhibitors by targeting its multiple key proteins through computational approaches.Scientific reports · 2022Article
- Evaluation of 3'-phosphate as a transient protecting group for controlled enzymatic synthesis of DNA and XNA oligonucleotides.Communications chemistry · 2022Article
- Structural Elucidation of Rift Valley Fever Virus L Protein towards the Discovery of Its Potential Inhibitors.Pharmaceuticals (Basel, Switzerland) · 2022Article
- Bacterial Cell Display as a Robust and Versatile Platform for Engineering Low-Affinity Ligands and Enzymes.Chembiochem : a European journal of chemical biology · 2020Article
- Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds.Nucleic acids research · 2020Review
- Review
Corrections and comments
- Erratum issued
Authors and funding
11 authors.
Funding
Abstract
Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.