Third generation DNA sequencing relies on monitoring the ionic current blockage during the DNA molecule’s threading through a nanoscale pore.It is still really tough to attain the single base discrimination on a DNA strand by merely analyzing the ionic current due to speedy DNA translocation and low spatial resolution.More integrated configurations are pursued to present versatile comparative dissimilarities of the four bases by enhancing the spatial resolution within a DNA molecule translocation event,such as transverse tunneling current,local potential change,and capacitance oriented voltage resonance.In this mini review,the insight is provided into the status quo on several functionalized techniques and methodologies for DNA sequencing and furthermore concluding remark and outlook are presented.
The nanopore size effect on translocation of poly(dT)30through Si3N4 membrane is investigated.In this paper,we report that the speed of the poly(dT)30 transport through Si3N4 nanopores can be slowed down by half through increasing the nanopore diameter from 4.8 nm to 10.8 nm.The results are consistent with our simulation results.Besides,the current blockage induced by DNA passing through the nanopore is less obvious as pore diameter is larger,which is in good agreement with the theoretical prediction.The conclusion about DNA transport through nanopores is beneficial for the design of DNA sequencing devices.
DNA sequencing based on nanopore sensors is a promising tool for third-generation sequencing technology because of its special properties,such as revolutionized speed and low cost.With about two decades of nanopore technology development,the pioneering work has demonstrated the ability of nanopores to perform single-molecule detection and DNA sequencing.However,the microscopic mechanisms of DNA transport dynamics through nanopores remain largely unknown.Currently,DNA microscopic transport in a nanopore is difficult to characterize and several unexpected experimental observations are equivocal.This limitation can be resolved using theoretical calculations and simulations.These computational methods can monitor the entire dynamic process that DNA undergoes in solution at a single-atom resolution that can accurately unveil the mystery of DNA transport dynamics and predict certain unexpected phenomena.This paper mainly reports the recent applications of computational and simulation methods applied to the study of DNA transport through both biological and synthetic nanopores.We hope the theoretical calculations and simulations of DNA transport through nanopores can benefit the design of DNA sequencing devices.
Porous graphene has a high mechanical strength and an atomic-layer thickness that makes it a promising material for material separation and biomolecule sensing. Electrostatic interactions between charges in aqueous solutions are a type of strong long-range interaction that may greatly influence fluid transport through nanopores. In this study, molecular dynamic simulations were conducted to investigate ion and water transport through 1.05-nm diameter monolayer graphene nanopores, with their edges charge-modified. Our results indicated that these nanopores are selective to counterions when they are charged. As the charge amount increases, the total ionic currents show an increase–decrease profile while the coion currents monotonically decrease. The co-ion rejection can reach 76.5% and 90.2% when the nanopores are negatively and positively charged, respectively. The Cl-ion current increases and reaches a plateau, and the Na+current decreases as the charge amount increases in systems in which Na+ions act as counterions. In addition, charge modification can enhance water transport through nanopores. This is mainly due to the ion selectivity of the nanopores. Notably, positive charges on the pore edges facilitate water transport much more strongly than negative charges.
