Understanding how supercoiled DNA releases intramolecular stress is essential for its functional realization.However,the molecular mechanism underlying the relaxation process remains insufficiently explored.Here we em...Understanding how supercoiled DNA releases intramolecular stress is essential for its functional realization.However,the molecular mechanism underlying the relaxation process remains insufficiently explored.Here we employed MD simulations based on the oxDNA2 model to investigate the relaxation process of a 336-base pair supercoiled minicircular DNA under double-strand breaks with two fixed endpoints.Our simulations show that the conformational changes in the DNA occur continuously,with intramolecular stress release happening abruptly only when the DNA chain traverses the breakage site.The relaxation process is influenced not only by the separation distance between the fixed ends but also their angle.Importantly,we observe an inhibitory effect on the relaxation characterized by small angles,where short terminal loops impede DNA conformational adjustments,preserving the supercoiled structure.These findings elucidate the intricate interplay between DNA conformational change,DNA motion and intramolecular stress release,shedding light on the mechanisms governing the relaxation of supercoiled DNA at the molecular level.展开更多
Combining self-consistent-field theory and density-functional theory, we systematically study the deformation of copolymer micelles induced by the presence of amphiphilic dimer particles. Due to the amphiphilic nature...Combining self-consistent-field theory and density-functional theory, we systematically study the deformation of copolymer micelles induced by the presence of amphiphilic dimer particles. Due to the amphiphilic nature, dimer particles tend to accumulate onto the interface of the copolymer micelle. With increasing concentration of the symmetric dimer particles, which are made of two identical spherical particles, the micelle deforms from the initial sphere to ellipse, dumbbell, and finally separates into two micelles. Furthermore, asymmetric dimer particles, composed by two particles with different sizes, are considered to investigate the influence of geometry of dimer particles on the deformation of the micelle. It is found that the micelle inclines to deform into dumbbell due to the additional curvature originating in the gathering of asymmetric dimer particles onto the interface of the micelle. The present study on the deformation of micelles is useful to understand the possible shape variation in the course of cell division/fusion.展开更多
基金supported by the National Natural Science Foundation of China(Nos.12274212,12347102 and 12174184).
文摘Understanding how supercoiled DNA releases intramolecular stress is essential for its functional realization.However,the molecular mechanism underlying the relaxation process remains insufficiently explored.Here we employed MD simulations based on the oxDNA2 model to investigate the relaxation process of a 336-base pair supercoiled minicircular DNA under double-strand breaks with two fixed endpoints.Our simulations show that the conformational changes in the DNA occur continuously,with intramolecular stress release happening abruptly only when the DNA chain traverses the breakage site.The relaxation process is influenced not only by the separation distance between the fixed ends but also their angle.Importantly,we observe an inhibitory effect on the relaxation characterized by small angles,where short terminal loops impede DNA conformational adjustments,preserving the supercoiled structure.These findings elucidate the intricate interplay between DNA conformational change,DNA motion and intramolecular stress release,shedding light on the mechanisms governing the relaxation of supercoiled DNA at the molecular level.
基金financially supported by the National Natural Science Foundation of China(No.10804045)
文摘Combining self-consistent-field theory and density-functional theory, we systematically study the deformation of copolymer micelles induced by the presence of amphiphilic dimer particles. Due to the amphiphilic nature, dimer particles tend to accumulate onto the interface of the copolymer micelle. With increasing concentration of the symmetric dimer particles, which are made of two identical spherical particles, the micelle deforms from the initial sphere to ellipse, dumbbell, and finally separates into two micelles. Furthermore, asymmetric dimer particles, composed by two particles with different sizes, are considered to investigate the influence of geometry of dimer particles on the deformation of the micelle. It is found that the micelle inclines to deform into dumbbell due to the additional curvature originating in the gathering of asymmetric dimer particles onto the interface of the micelle. The present study on the deformation of micelles is useful to understand the possible shape variation in the course of cell division/fusion.
