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Effective length factors and critical buckling lengths for DNAs suspended in solution or with fix-bead constraint.
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Persistence length is a significant criterion to characterize the semi-flexibility of DNA molecules. The mechanical constraints applied on DNA chains in new single-molecule experiments play a complex role in measuring DNA persistence length; however, there is a difficulty in quantitatively characterizing the mechanical constraint effects due to the...
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Context 1
... to the low goodness of fit for DNA adsorbed on the substrate, this section only focuses on DNAs suspended in solution and with fix-bead constraint. The average effective length factors and critical buckling lengths and their standard deviations for the two constrained DNA states are obtained from corresponding data in Table 1, and listed in Table 2. By substituting the averaged values of critical buckling lengths l cb , effective length factors µ, and standard deviation of µ under different constrained states in Table 2 into Equation (7) with temperature T = 298 K, we can predict DNA persistence length versus monovalent ionic concentration as shown in Figure 2, and the error bars in Figure 2 is caused by the standard deviation of averaged effective length factors µ. ...Context 2
... average effective length factors and critical buckling lengths and their standard deviations for the two constrained DNA states are obtained from corresponding data in Table 1, and listed in Table 2. By substituting the averaged values of critical buckling lengths l cb , effective length factors µ, and standard deviation of µ under different constrained states in Table 2 into Equation (7) with temperature T = 298 K, we can predict DNA persistence length versus monovalent ionic concentration as shown in Figure 2, and the error bars in Figure 2 is caused by the standard deviation of averaged effective length factors µ. Regardless of mechanical constraints, the DNA persistence length decreases with ionic concentration overall, which is consistent with reported experimental results [9,10,[15][16][17]49] and theoretical predictions [28,31,34]. ...Context 3
... average critical buckling lengths 5.95 nm and 8.43 nm at 298 K listed in T 2 and the obtained gradient are used to obtain the linear expression of DNA critical b ling lengths varying with temperature for DNA suspended in solution or with fixconstraint, respectively, i.e., (12) and (13), the critical buckling lengths ying with temperature for DNAs with two end-constraint conditions are shown in Fi 5, obviously the increasing temperature results in a decrease in critical buckling leng Second, it is assumed that the gradient of buckling length varying with temperature in Equation (11), i.e., −0.0359 nm/K, is also applicable for other mechanical end-constraints. The average critical buckling lengths 5.95 nm and 8.43 nm at 298 K listed in Table 2 and the obtained gradient are used to obtain the linear expression of DNA critical buckling lengths varying with temperature for DNA suspended in solution or with fix-bead constraint, respectively, i.e., ...Citations
The temperature-dependent bend and twist elasticities of dsDNA, as well as their couplings, were explored through all-atom molecular dynamics simulations. Three rotational parameters, tilt, roll, and twist, were employed to...
Periodic boundary conditions are commonly applied in molecular dynamics simulations in the microcanonical (NVE), canonical (NVT), and isothermal–isobaric (NpT) ensembles. In their simplest application, a biological system of interest is placed in the middle of a solvation box, which is chosen ‘sufficiently large’ to minimize any numerical artifacts associated with the periodic boundary conditions. This practical approach brings limitations to the size of biological systems that can be simulated. Here, we study simulations of effectively infinitely long nucleic acids, which are solvated in the directions perpendicular to the polymer chain, while periodic boundary conditions are also applied along the polymer chain. We study the effects of these asymmetric periodic boundary conditions (APBC) on the simulated results, including the mechanical properties of biopolymers and the properties of the surrounding solvent. To get some further insights into the advantages of using the APBC, a coarse-grained worm-like chain model is first studied, illustrating how the persistence length can be extracted from the local properties of the polymer chain, which are less affected by the APBC than some global averages. This is followed by all-atom molecular dynamics simulations of DNA in ionic solutions, where we use the APBC to investigate sequence-dependent properties of DNA molecules and properties of the surrounding solvent.
