BRIEF RESEARCH REPORT article
Front. Mol. Biosci.
Sec. Biological Modeling and Simulation
Volume 12 - 2025 | doi: 10.3389/fmolb.2025.1646428
Modelling the melting of DNA oligomers with non-inert dangling ends
Provisionally accepted
- 1Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- 2Istituto Italiano di Tecnologia, Genoa, Italy
- 3Universita degli Studi di Padova, Padua, Italy
- 4Istituto Nazionale di Fisica Nucleare Sezione di Padova, Padua, Italy
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In this work, we investigate the dependence of the melting temperature of lowvalency DNA constructs on the length of non-inert dangling ends, controlling their sequence composition. We compare two computational models to evaluate their effectiveness and limitations in predicting the melting behaviour of DNA oligomers (bivalent linkers) and more complex structures (trivalent nanostars), benchmarking the results against experimental spectroscopic data. Our results suggest that the length of non-inert dangling ends has minimal impact on the melting point of the DNA duplex for the duplexes we studied, informing the future design of DNA supramolecular constructs.
Keywords: DNA nanotechnology, Melting curves, oxDNA, NUPACK, molecular dynamics, umbrella sampling
Received: 13 Jun 2025; Accepted: 28 Jul 2025.
Copyright: © 2025 Soto, Mambretti, Locatelli and Stoev. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Iliya D. Stoev, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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