DNA translocation through pH-dependent soft nanopores

Ion–Solvent Interactions under Confinement Hold the Key to Tuning the DNA Translocation Speeds in Polyelectrolyte-Functionalized Nanopores

“…Contrary to the previously reported theories based on an infinitely long nanopore grafted with a polyelectrolyte layer − that delve into the transverse variation of the concentration distributions only, we investigated here the nontrivial alterations in DNA translocation due to the combined effect of the electrical permittivity mismatch between the polyelectrolyte layer (PEL) and the bulk electrolyte and the axial variations in the electrical stresses due to locally selective ion enrichment and concentration on account of a finite-sized nanopore by capturing physically realistic multidimensional interactions over space and time. For the first time, we evidenced DNA blockage at the entrance of the nanopore due to opposing electroosmotic flow (EOF) favored by a higher charge of the PEL or its lower permittivity.…”

“…Continuity, modified Stokes, and Brinkman equations: , ∇ · boldu = 0 true{ .25ex2ex − ∇ p + μ ∇ 2 u + ρ e E o = 0 j = 0 − ∇ p + μ ∇ 2 u + ρ e E o − γ u = 0 j = 1 p , μ, and γ are the pressure, fluid viscosity, and hydrodynamic friction coefficient due to the PEL, respectively. The latter is related to the degree of softness of the PEL, λ s –1 , where λ s –1 = (μ/γ) 1/2 . − …”

“…Several theoretical insights on DNA translocation through PEL-grafted nanopores were recently put forward, − with a vision of unraveling the dependence of the PEL charge, ionic concentration, and external electric field on the DNA translocation speed. However, these theories were built on an idealized paradigm that ignores the end effect due to the finite axial span of the nanopore.…”

Substantial Slowing of Electrophoretic Translocation of DNA through a Nanopore Using Coherent Multiple Entropic Traps

“…Over the past decade, various methods have been formulated to slow down the translocation rate of DNA in nanopores, such as increasing the viscosity of buffer solution, 25,26 introducing salt concentration gradient between the two sides of the nanopore, 27 adding reverse pressure as resistance, 28 modifying the inner surface of the nanopore, 29−31 manipulating the DNA, 32 depositing a new layer on the surface of the nanopore, 22,24,33−37 and pH variations. 29,38,39 Our method presented here to slow down the translocation of DNA in solid-state nanopores is distinctly different from these previous approaches. In our study, the source of the observed significant reduction of DNA translocation speed is created in the donor compartment by enabling multiple entropic traps that act on each DNA molecule.…”

“…The second obstacle is the temporal resolution because the passage speed of DNA in solid-state nanopores is very fast. , The speed of single-stranded DNA is greater than 1 nt/μs, and that of the double-stranded DNA is greater than 10 bp/μs. , Coupled with the bandwidth limitation of 250–500 kHz in various DNA translocation experiments, it is thus difficult to identify and distinguish adjacent bases. Over the past decade, various methods have been formulated to slow down the translocation rate of DNA in nanopores, such as increasing the viscosity of buffer solution, , introducing salt concentration gradient between the two sides of the nanopore, adding reverse pressure as resistance, modifying the inner surface of the nanopore, − manipulating the DNA, depositing a new layer on the surface of the nanopore, ,,− and pH variations. ,, Our method presented here to slow down the translocation of DNA in solid-state nanopores is distinctly different from these previous approaches. In our study, the source of the observed significant reduction of DNA translocation speed is created in the donor compartment by enabling multiple entropic traps that act on each DNA molecule.…”