Effect of surface functionalization on DNA sequencing using MXene-based nanopores.

As one of the most promising types of label-free nanopores has great potential for DNA sequencing via fast detection of different DNA bases. As one of the most promising types of label-free nanopores, two-dimensional nanopore materials have been developed over the past two decades. However, how to detect different DNA bases efficiently and accurately is still a challenging problem. In the present work, the translocation of four homogeneous DNA strands (i.e., poly(A)20, poly(C)20, poly(G)20, and poly(T)20) through two-dimensional transition-metal carbide (MXene) membrane nanopores with different surface terminal groups is investigated via all-atom molecular dynamics simulations. Interestingly, it is found that the four types of bases can be distinguished by different ion currents and dwell times when they are transported through the Ti3C2(OH)2 nanopore. This is mainly attributed to the different orientation and position distributions of the bases, the hydrogen bonding inside the MXene nanopore, and the interaction of the ssDNA with the nanopore. The present study enhances the understanding of the interaction between DNA strands and MXene nanopores with different functional groups, which may provide useful guidelines for the design of MXene-based devices for DNA sequencing in the future.

Exploring the non-monotonic DNA capture behavior in a charged graphene nanopore.

Nanopore-based biomolecule detection has emerged as a promising and sought-after innovation, offering high throughput, rapidity, label-free analysis, and cost-effectiveness, with potential applications in personalized medicine. However, achieving efficient and tunable biomolecule capture into the nanopore remains a significant challenge. In this study, we employ all-atom molecular dynamics simulations to investigate the capture of double-stranded DNA (dsDNA) molecules into graphene nanopores with varying positive charges. We discover a non-monotonic relationship between the DNA capture rate and the charge of the graphene nanopore. Specifically, the capture rate initially decreases and then increases with an increase in nanopore charge. This behavior is primarily attributed to differences in the electrophoretic force, rather than the influence of electroosmosis or counterions. Furthermore, we also observe this non-monotonic trend in various ionic solutions, but not in ionless solutions. Our findings shed light on the design of novel DNA sequencing devices, offering valuable insights into enhancing biomolecule capture rates in nanopore-based sensing platforms.

Controlling ion transport in a C2N-based nanochannel with tunable interlayer spacing.

Selective ion transport through a nanochannel formed by stacked two-dimensional materials plays a key role in water desalination, nanofiltration, and ion separation. Although there have been many functional nanomaterials used in these applications, how to well control ion transport in a laminar structure so as to obtain the desired selectivity still remains a challenging problem. In the present work, the transport of ions through a C2N-based nanochannel is investigated by using all-atom molecular dynamics simulation. It is found that C2N-based nanochannels with different interlayer spacing posses diverse ion selectivity, which is mainly attributed to the distinct loading capability among ions and the different velocity of ions inside the nanochannel. Moreover, we also find that the ion selectivity is dependent on the electric field, but nearly independent of the salt concentration. The present study may provide some physical insights into the experimental design of C2N-based nanodevices in nanofiltration.