2026-04-28T14:24:41Zhttps://riubu.ubu.es/oai/request

oai:riubu.ubu.es:10259/57192024-07-25T07:24:10Zcom_10259_9476com_10259.4_106com_10259_2604col_10259_9477

Marty Roda, Marta 350 600 0000-0002-5440-1454 Dahlen, Oda 0b638929-7b71-4ae3-b4b3-1806f6cd1563 500 Erp, Titus S. van affb15a4-36a5-483f-8659-13cac5092f42 500 Cuesta López, Santiago 133 500 0000-0002-7401-3889 2021-04-20T11:55:00Z 2021-04-20T11:55:00Z 2018-11 1478-3975 http://hdl.handle.net/10259/5719 10.1088/1478-3975/aac61c Although previously developed mesoscopic DNA models have successfully reproduced thermodynamic denaturation data, recent studies show that these overestimate the rate of denaturation by orders of magnitude. Using adapted Peyrard–Bishop–Dauxois (PBD) models, we have calculated the denaturation rates of several DNA hairpins and made comparison with experimental data. We show that the addition of a barrier at the onsite potential of the PBD model gives a more accurate description of the unzipping dynamics of short DNA sequences. The new models provide a refined theoretical insight on the dynamical mechanisms of unzipping which can have implications for the understanding of transcription and replication processes. Still, this class of adapted PBD models seems to have a fundamental limitation which implies that it is not possible to get agreement with available experimental results on the dynamics of long DNA sequences and at the same time maintain the good agreement regarding its thermodynamics. The reason for this is that the denaturation rate of long DNA chains is not dramatically lowered by the additional barrier—as the base-pairs that open are more likely to remain open, facilitating the opening of the full DNA molecule. Some care has to be taken, since experimental techniques suitable to the study of denaturation rates of long sequences seem not to agree with other experimental data on short DNA sequences. Further research, both theoretical and experimental, is therefore needed to resolve these inconsistencies—which will be a starting point for new minimalistic models that are able to describe both thermodynamics and dynamics at a predictive level. Spanish Ministry of Economy, Industry and Competitiveness (BES-2013-065453, FIS2012-38827) and the University of Burgos and the Anders Jahre fund (Project 40105000) application/pdf eng IOP Publishing Physical Biology. 2018, V. 15, n. 6, 066001 https://doi.org/10.1088/1478-3975/aac61c Biomolecular dynamics DNA hairpins modelling PBD model rate constants Improving the mesoscopic modeling of DNA denaturation dynamics info:eu-repo/semantics/article info:eu-repo/semantics/acceptedVersion info:eu-repo/semantics/openAccess Physical Biology 15 6 066001 THUMBNAIL Marty-bp_2018.pdf.jpg Marty-bp_2018.pdf.jpg IM Thumbnail image/jpeg 4096 https://riubu.ubu.es/bitstream/10259/5719/3/Marty-bp_2018.pdf.jpg 7db1546ce4dd45a29dc748c1176b1d0e MD5 3 LICENSE license.txt license.txt text/plain; charset=utf-8 998 https://riubu.ubu.es/bitstream/10259/5719/2/license.txt aa90105e1c90a1b4fe810649aa967b7d MD5 2 ORIGINAL Marty-bp_2018.pdf Marty-bp_2018.pdf application/pdf 523450 https://riubu.ubu.es/bitstream/10259/5719/1/Marty-bp_2018.pdf d3cb76b552352c32acbb8a6e74b04c2e MD5 1 10259/5719 oai:riubu.ubu.es:10259/5719 2024-07-25 09:24:10.015 Repositorio Institucional de la Universidad de Burgos bubrep@ubu.es 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