Modelling one-electron oxidation potentials and hole delocalization in double-stranded DNA by multilayer and dynamic approaches
The number of innovative applications for DNA nowadays is growingquickly. Its use as a nanowire or electrochemical biosensor leads to the need for a deepunderstanding of the charge-transfer process along the strand, as well as its redoxproperties. These features are computationally simulated and ana...
| Autores: | , , |
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| Tipo de recurso: | artículo |
| Fecha de publicación: | 2024 |
| País: | España |
| Institución: | Universidad Autónoma de Madrid |
| Repositorio: | Biblos-e Archivo. Repositorio Institucional de la UAM |
| Idioma: | inglés |
| OAI Identifier: | oai:repositorio.uam.es:10486/713291 |
| Acceso en línea: | http://hdl.handle.net/10486/713291 https://dx.doi.org/10.1021/acs.jcim.4c00528 |
| Access Level: | acceso abierto |
| Palabra clave: | DNA Electrons Molecular Dynamics Simulation Nucleic Acid Conformation Oxidation Reduction Química |
| Sumario: | The number of innovative applications for DNA nowadays is growingquickly. Its use as a nanowire or electrochemical biosensor leads to the need for a deepunderstanding of the charge-transfer process along the strand, as well as its redoxproperties. These features are computationally simulated and analyzed in detailthroughout this work by combining molecular dynamics, multilayer schemes, and theMarcus theory. One-electron oxidation potential and hole delocalization have beenanalyzed for six DNA double strands that cover all possible binary combinations ofnucleotides. The results have revealed that the one-electron oxidation potentialdecreases with respect to the single-stranded DNA, giving evidence that the greaterrigidity of a double helix induces an increase in the capacity of storing the positivecharge generated upon oxidation. In addition, the hole is mainly stored in nucleobaseswith large reducer character, i.e., purines, especially when those are arranged in astacked configuration in the same strand. From the computational point of view, thesampling needed to describe biological systems implies a significant computational cost. Here, we show that a small number ofrepresentative conformations generated by clustering analysis provides accurate results when compared with those obtained fromsampling, reducing considerably the computational cost |
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