Thermofluidics and Nanotechnology for Sustainable Energy Systems Laboratory, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India.
Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India.
Langmuir. 2024 Apr 9;40(14):7300-7309. doi: 10.1021/acs.langmuir.3c02816. Epub 2024 Mar 27.
DNA sequencing and sensing using nanopore technology delves critically into the alterations in the measurable electrical signal as single-stranded DNA is drawn through a tiny passage. To make such precise measurements, however, slowing down the DNA in the tightly confined passage is a key requirement, which may be achieved by grafting the nanopore walls with a polyelectrolyte layer (PEL). This soft functional layer at the wall, under an off-design condition, however, may block the DNA passage completely, leading to the complete loss of output signal from the nanobio sensor. Whereas theoretical postulates have previously been put forward to explain the essential physics of DNA translocation in nanopores, these have turned out to be somewhat inadequate when confronted with the experimental findings on functionalized nanopores, including the prediction of the events of complete signal losses. Circumventing these constraints, herein we bring out a possible decisive role of the interplay between the inevitable variabilities in the ionic distribution along the nanopore axis due to its finite length as opposed to its idealized "infinite" limit as well as the differential permittivity of PEL and bulk solution that cannot be captured by the commonly used one-dimensional variant of the electrical double layer theory. Our analysis, for the first time, captures variations in the ionic concentration distribution across multidimensional physical space and delineates its impact on the DNA translocation characteristics that have hitherto remained unaddressed. Our results reveal possible complete blockages of DNA translocation as influenced by less-than-threshold permittivity values or greater-than-threshold grafting densities of the PEL. In addition, electrohydrodynamic blocking is witnessed due to the ion-selective nature of the nanopore at low ionic concentrations. Hence, our study establishes a functionally active regime over which the PEL layer in a finite-length nanopore facilitates controllable DNA translocation, enabling successful sequencing and sensing through the explicit modulation of translocation speed.
利用纳米孔技术进行 DNA 测序和传感，深入研究了单链 DNA 通过微小通道时可测量电信号的变化。然而，为了进行如此精确的测量，将 DNA 在紧密限制的通道中减速是一个关键要求，这可以通过在纳米孔壁上接枝聚电解质层 (PEL) 来实现。然而，在非设计条件下，这种在壁上的软官能层可能会完全阻止 DNA 通过，导致纳米生物传感器的输出信号完全丢失。虽然以前已经提出了理论假设来解释纳米孔中 DNA 迁移的基本物理原理，但当面对功能化纳米孔的实验结果时，这些假设被证明有些不足，包括对完全信号丢失事件的预测。为了克服这些限制，本文提出了一种可能的决定性作用，即由于纳米孔轴上的离子分布不可避免的变化与其理想化的“无限”极限之间的相互作用，以及 PEL 和本体溶液的差分介电常数之间的相互作用，而这些在常用的一维电双层理论变体中无法捕捉到。我们的分析首次捕捉到了离子浓度分布在多维物理空间中的变化，并描述了其对 DNA 迁移特性的影响，这些特性迄今尚未得到解决。我们的结果揭示了 DNA 迁移可能由于介电常数值低于阈值或 PEL 的接枝密度大于阈值而完全受阻。此外，由于纳米孔的离子选择性，在低离子浓度下会出现电动力学阻塞。因此，我们的研究建立了一个功能活跃的区域，在该区域内，有限长度纳米孔中的 PEL 层可以促进可控的 DNA 迁移，通过明确调节迁移速度，实现成功的测序和传感。
