Understanding DNA interactions in crowded environments with a coarse-grained model
| العنوان: | Understanding DNA interactions in crowded environments with a coarse-grained model |
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| المؤلفون: | John S. Schreck, Fan Hong, Petr Šulc |
| المصدر: | Nucleic Acids Research |
| بيانات النشر: | Oxford University Press (OUP), 2020. |
| سنة النشر: | 2020 |
| مصطلحات موضوعية: | 0303 health sciences, AcademicSubjects/SCI00010, Base pair, Inverted Repeat Sequences, Kinetics, Computational Biology, DNA, Molecular Dynamics Simulation, Biology, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, Reaction rate, 03 medical and health sciences, chemistry.chemical_compound, Molecular dynamics, chemistry, Excluded volume, Genetics, Nucleic acid, Biophysics, A-DNA, Base Pairing, 030304 developmental biology |
| الوصف: | Nucleic acid interactions under crowded environments are of great importance for biological processes and nanotechnology. However, the kinetics and thermodynamics of nucleic acid interactions in a crowded environment remain poorly understood. We use a coarse-grained model of DNA to study the kinetics and thermodynamics of DNA duplex and hairpin formation in crowded environments. We find that crowders can increase the melting temperature of both an 8-mer DNA duplex and a hairpin with a stem of 6-nt depending on the excluded volume fraction of crowders in solution and the crowder size. The crowding induced stability originates from the entropic effect caused by the crowding particles in the system. Additionally, we study the hybridization kinetics of DNA duplex formation and the formation of hairpin stems, finding that the reaction rate kon is increased by the crowding effect, while koff is changed only moderately. The increase in kon mostly comes from increasing the probability of reaching a transition state with one base pair formed. A DNA strand displacement reaction in a crowded environment is also studied with the model and we find that rate of toehold association is increased, with possible applications to speeding up strand displacement cascades in nucleic acid nanotechnology. |
| تدمد: | 1362-4962 0305-1048 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3b9fe5ebd7ff2685f05eb7f119f16e5c https://doi.org/10.1093/nar/gkaa854 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....3b9fe5ebd7ff2685f05eb7f119f16e5c |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 13624962 03051048 |
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