Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA.
Bionano Genomics, Inc., 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA.
J Chem Phys. 2019 Sep 21;151(11):114903. doi: 10.1063/1.5121305.
DNA confinement in a nanochannel typically is understood via mapping to the confinement of an equivalent neutral polymer by hard walls. This model has proven to be effective for confinement in relatively large channels where hairpin formation is frequent. An analysis of existing experimental data for Escherichia coli DNA extension in channels smaller than the persistence length, combined with an additional dataset for λ-DNA confined in a 34 nm wide channel, reveals a breakdown in this approach as the channel size approaches the Odijk regime of strong confinement. In particular, the predicted extension distribution obtained from the asymptotic solution to the weakly correlated telegraph model for a confined wormlike chain deviates significantly from the experimental distribution obtained for DNA confinement in the 34 nm channel, and the discrepancy cannot be resolved by treating the alignment fluctuations or the effective channel size as fitting parameters. We posit that the DNA-wall electrostatic interactions, which are sensible throughout a significant fraction of the channel cross section in the Odijk regime, are the source of the disagreement between theory and experiment. Dimensional analysis of the wormlike chain propagator in channel confinement reveals the importance of a dimensionless parameter, reflecting the magnitude of the DNA-wall electrostatic interactions relative to thermal energy, which has not been considered explicitly in the prevailing theories for DNA confinement in a nanochannel.
DNA 在纳米通道中的限制通常通过映射到等效中性聚合物的限制来理解，该限制由硬壁施加。该模型已被证明在相对较大的通道中限制是有效的，在这些通道中发夹形成很常见。对大肠杆菌 DNA 在小于弛豫长度的通道中延伸的现有实验数据进行分析，结合在 34nm 宽通道中限制的 λ-DNA 的附加数据集，表明当通道尺寸接近强限制的 Odijk 区时，该方法会失效。特别是，从受限蠕虫链的弱相关电报模型的渐近解获得的预测延伸分布与在 34nm 通道中限制的 DNA 获得的实验分布有很大差异，并且不能通过将对齐波动或有效通道尺寸作为拟合参数来解决这种差异。我们假设 DNA-壁静电相互作用，在 Odijk 区的通道横截面的很大一部分中都有意义，是理论与实验之间存在分歧的原因。通道限制中蠕虫链传播子的维度分析揭示了一个无量纲参数的重要性，该参数反映了 DNA-壁静电相互作用相对于热能的大小，这在纳米通道中限制 DNA 的现有理论中并未明确考虑。
