Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA.
Phys Rev E. 2020 Jan;101(1-1):012501. doi: 10.1103/PhysRevE.101.012501.
The prevailing theories describing DNA confinement in a nanochannel are predicated on the assumption that wall-DNA electrostatic interactions are sufficiently short-ranged such that the problem can be mapped to an equivalent neutral polymer confined by hard walls with an appropriately reduced effective channel size. To determine when this hypothesis is valid, we leveraged a recently reported experimental data set for the fractional extension of DNA molecules in a 250-nm-wide poly(dimethyl siloxane) (PDMS) nanochannel with buffer ionic strengths between 0.075 and 48 mM. Evaluating these data in the context of the weakly correlated telegraph model of DNA confinement reveals that, at ionic strengths greater than 0.3 mM, the average fractional extension of the DNA molecules agree with theoretical predictions with a mean absolute error of 0.04. In contrast, experiments at ionic strengths below 0.3 mM produce average fractional extensions that are systematically smaller than the theoretical predictions with a larger mean absolute error of 0.15. The deviations between experiment and theory display a correlation coefficient of 0.82 with the decay length for the DNA-wall electrostatics, linking the deviations with a breakdown in approximating the DNA with an equivalent neutral polymer.
描述 DNA 在纳米通道中受限的主流理论基于这样的假设，即壁-DNA 静电相互作用的范围足够短，以至于可以将问题映射到等效的中性聚合物受限情况，该聚合物由具有适当减小的有效通道尺寸的硬壁限制。为了确定该假设何时有效，我们利用最近报道的实验数据集，该数据集涉及在缓冲离子强度为 0.075 至 48mM 之间的 250nm 宽聚二甲基硅氧烷 (PDMS) 纳米通道中 DNA 分子的分数延伸。在 DNA 限制的弱相关电报模型的背景下评估这些数据表明，在离子强度大于 0.3mM 时，DNA 分子的平均分数延伸与理论预测一致，平均绝对误差为 0.04。相比之下，在离子强度低于 0.3mM 的实验产生的平均分数延伸比理论预测值系统小，平均绝对误差为 0.15。实验与理论之间的偏差与 DNA-壁静电的衰减长度相关，相关系数为 0.82，将偏差与用等效中性聚合物近似 DNA 的失效联系起来。
