Sharp bending as one of the mechanical properties of double-stranded DNA(dsDNA) on the nanoscale is essential for biological functions and processes. Force sensors with optical readout have been designed to measure th...Sharp bending as one of the mechanical properties of double-stranded DNA(dsDNA) on the nanoscale is essential for biological functions and processes. Force sensors with optical readout have been designed to measure the forces inside short, strained loops composed of both dsDNA and single-stranded DNA(ssDNA). Recent FRET singlemolecule experiments were carried out based on the same force sensor design, but provided totally contrary results. In the current work, Monte Carlo simulations were performed under three conditions to clarify the discrepancy between the two experiments. The criterion that the work done by the force exerted on dsDNA by ssDNA should be larger than the nearest-neighbor(NN) stacking interaction energy is used to identify the generation of the fork at the junction of dsDNA and ssDNA. When the contour length of dsDNA in the sensor is larger than its critical length, the fork begins to generate at the junction of dsDNA and ssDNA, even with a kink in dsDNA. The forces inferred from simulations under three conditions are consistent with the ones inferred from experiments, including extra large force and can be grouped into two different states, namely, fork states and kink states. The phase diagrams constructed in the phase space of the NN stacking interaction energy and excited energy indicate that the transition between the fork state and kink state is difficult to identify in the phase space with an ultra small or large number of forks, but it can be detected in the phase space with a medium number of forks and kinks.展开更多
With a view of detecting the effects of macromolecular crowding on the phase transition of DNA compaction confined in spherical space,Monte Carlo simulations of DNA compaction in free space,in confined spherical space...With a view of detecting the effects of macromolecular crowding on the phase transition of DNA compaction confined in spherical space,Monte Carlo simulations of DNA compaction in free space,in confined spherical space without crowders and in confined spherical space with crowders were performed separately.The simulation results indicate that macromolecular crowding effects on DNA compaction are dominant over the roles of multivalent counterions.In addition,effects of temperature on the phase transition of DNA compaction have been identified in confined spherical space with different radii.In confined spherical space without crowders,the temperature corresponding to phase transition depends on the radius of the confined spherical space linearly.In contrast,with the addition of crowders to the confined spherical space,effects of temperature on the phase transition of DNA compaction become insignificant,whereas the phase transition at different temperatures strongly depends on the size of crowder,and the critical volume fraction of crowders pertains to the diameter of crowder linearly.展开更多
基金Supported by the National Natural Science Foundation of China under Grant Nos.11204045,11464004,and 11864006the State Scholarship Fund(20173015)Guizhou Scientific and Technological Program(20185781)
文摘Sharp bending as one of the mechanical properties of double-stranded DNA(dsDNA) on the nanoscale is essential for biological functions and processes. Force sensors with optical readout have been designed to measure the forces inside short, strained loops composed of both dsDNA and single-stranded DNA(ssDNA). Recent FRET singlemolecule experiments were carried out based on the same force sensor design, but provided totally contrary results. In the current work, Monte Carlo simulations were performed under three conditions to clarify the discrepancy between the two experiments. The criterion that the work done by the force exerted on dsDNA by ssDNA should be larger than the nearest-neighbor(NN) stacking interaction energy is used to identify the generation of the fork at the junction of dsDNA and ssDNA. When the contour length of dsDNA in the sensor is larger than its critical length, the fork begins to generate at the junction of dsDNA and ssDNA, even with a kink in dsDNA. The forces inferred from simulations under three conditions are consistent with the ones inferred from experiments, including extra large force and can be grouped into two different states, namely, fork states and kink states. The phase diagrams constructed in the phase space of the NN stacking interaction energy and excited energy indicate that the transition between the fork state and kink state is difficult to identify in the phase space with an ultra small or large number of forks, but it can be detected in the phase space with a medium number of forks and kinks.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11464004 and 11864006)the State Scholarship Fund,China(Grant No.20173015)Guizhou Scientific and Technological Program,China(Grant No.20185781)
文摘With a view of detecting the effects of macromolecular crowding on the phase transition of DNA compaction confined in spherical space,Monte Carlo simulations of DNA compaction in free space,in confined spherical space without crowders and in confined spherical space with crowders were performed separately.The simulation results indicate that macromolecular crowding effects on DNA compaction are dominant over the roles of multivalent counterions.In addition,effects of temperature on the phase transition of DNA compaction have been identified in confined spherical space with different radii.In confined spherical space without crowders,the temperature corresponding to phase transition depends on the radius of the confined spherical space linearly.In contrast,with the addition of crowders to the confined spherical space,effects of temperature on the phase transition of DNA compaction become insignificant,whereas the phase transition at different temperatures strongly depends on the size of crowder,and the critical volume fraction of crowders pertains to the diameter of crowder linearly.
