Free-Energy Profiles for A-/B-DNA Conformational Transitions in Isolated and Aggregated States from All-Atom Molecular Dynamics Simulation
| العنوان: | Free-Energy Profiles for A-/B-DNA Conformational Transitions in Isolated and Aggregated States from All-Atom Molecular Dynamics Simulation |
|---|---|
| المؤلفون: | George C. Schatz, Cheng Tsung Lai |
| المصدر: | The Journal of Physical Chemistry B. 122:7990-7996 |
| بيانات النشر: | American Chemical Society (ACS), 2018. |
| سنة النشر: | 2018 |
| مصطلحات موضوعية: | 0301 basic medicine, Conformational change, DNA, A-Form, Molecular Dynamics Simulation, 01 natural sciences, Phase Transition, 03 medical and health sciences, Molecular dynamics, chemistry.chemical_compound, 0103 physical sciences, Atom, Mole, Materials Chemistry, Physical and Theoretical Chemistry, Aqueous solution, Ethanol, 010304 chemical physics, Condensation, Water, Surfaces, Coatings and Films, Crystallography, 030104 developmental biology, chemistry, Nucleic Acid Conformation, Thermodynamics, DNA, B-Form, DNA |
| الوصف: | In ordinary aqueous solution, B-DNA is the major structural form of DNA. After the addition of ethanol, DNA is thought to be aggregated/condensed in the A-form structure. However, there is uncertainty as to whether the B-to-A conformational change is connected to the aggregation/condensation steps. In this study, we performed all-atom molecular dynamics simulations and calculated the free-energy surface involved in the A/B conformational transition for isolated and aggregated Dickerson-Drew dodecamers (DDDs) in water and 85% ethanol environments. We found in the case of an isolated DDD, the overall free-energy profile is entirely downhill to give the B-DNA conformation in both water and 85% ethanol. However, in the aggregated state and 85% ethanol environment, there is a free-energy minimum associated with the A-DNA region in addition to the global B-DNA minimum, and there is a ∼3 kcal/mol free-energy barrier to the A-to-B conformational change. The molecular dynamics results suggest that aggregation of DNA is essential for forming A-DNA. |
| تدمد: | 1520-5207 1520-6106 |
| DOI: | 10.1021/acs.jpcb.8b04573 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1a85e70bd726b40a329e209da7a8f846 https://doi.org/10.1021/acs.jpcb.8b04573 |
| رقم الانضمام: | edsair.doi.dedup.....1a85e70bd726b40a329e209da7a8f846 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15205207 15206106 |
|---|---|
| DOI: | 10.1021/acs.jpcb.8b04573 |