ArticleNucleic acids research2024
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline.
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 7 papers.
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Who cites it
7 citing papers in PubMed, 9 citations in OpenAlex.
- Alternative probe chemistries for single-molecule analysis of long noncoding RNA.The Journal of biological chemistry · 2026Article
- Are we there yet with XNA aptamers?RSC advances · 2026Review
- Alternative probe chemistries for single-molecule analysis of long non-coding RNA.bioRxiv : the preprint server for biology · 2026Article
- Omega Nucleic Acids (ΩNA), Ultimate Nucleic Acids for Future Technology.Molecules (Basel, Switzerland) · 2026Review
- Tuning i-motif folding and stability with acyclic phosphonate-linked (ZNA) cytidine residues.RSC advances · 2025Article
- The pucke.rs toolkit to facilitate sampling the conformational space of biomolecular monomers.Journal of cheminformatics · 2025Article
- modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields.Journal of chemical theory and computation · 2024Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
The field of synthetic nucleic acids with novel backbone structures [xenobiotic nucleic acids (XNAs)] has flourished due to the increased importance of XNA antisense oligonucleotides and aptamers in medicine, as well as the development of XNA processing enzymes and new XNA genetic materials. Molecular modeling on XNA structures can accelerate rational design in the field of XNAs as it contributes in understanding and predicting how changes in the sugar-phosphate backbone impact on the complementation properties of the nucleic acids. To support the development of novel XNA polymers, we present a first-in-class open-source program (Ducque) to build duplexes of nucleic acid analogs with customizable chemistry. A detailed procedure is described to extend the Ducque library with new user-defined XNA fragments using quantum mechanics (QM) and to generate QM-based force field parameters for molecular dynamics simulations within standard packages such as AMBER. The tool was used within a molecular modeling workflow to accurately reproduce a selection of experimental structures for nucleic acid duplexes with ribose-based as well as non-ribose-based nucleosides. Additionally, it was challenged to build duplexes of morpholino nucleic acids bound to complementary RNA sequences.
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Registered trials
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