DNA sequence-dependent ionic currents in ultra-small solid-state nanopores

Abstract

Measurements of ionic currents through nanopores partially blocked by DNA have emerged as a powerful method for characterization of the DNA nucleotide sequence. Although the effect of the nucleotide sequence on the nanopore blockade current has been experimentally demonstrated, prediction and interpretation of such measurements remain a formidable challenge. Using atomic resolution computational approaches, here we show how the sequence, molecular conformation, and pore geometry affect the blockade ionic current in model solid-state nanopores. We demonstrate that the blockade current from a DNA molecule is determined by the chemical identities and conformations of at least three consecutive nucleotides. We find the blockade currents produced by the nucleotide triplets to vary considerably with their nucleotide sequence despite having nearly identical molecular conformations. Encouragingly, we find blockade current differences as large as 25% for single-base substitutions in ultra small (1.6 nm × 1.1 nm cross section; 2 nm length) solid-state nanopores. Despite the complex dependence of the blockade current on the sequence and conformation of the DNA triplets, we find that, under many conditions, the number of thymine bases is positively correlated with the current, whereas the number of purine bases and the presence of both purine and pyrimidines in the triplet are negatively correlated with the current. Based on these observations, we construct a simple theoretical model that relates the ion current to the base content of a solid-state nanopore. Furthermore, we show that compact conformations of DNA in narrow pores provide the greatest signal-to-noise ratio for single base detection, whereas reduction of the nanopore length increases the ionic current noise. Thus, the sequence dependence of nanopore blockade current can be theoretically rationalized, although the predictions will likely need to be customized for each nanopore type.

Conic shapes have higher sensitivity than cylindrical ones in nanopore DNA sequencing

“…Actually, previous experimental studies reported that the ratio of measured conductance of the phi29 connector to a-HL biological nanopore compares well with the ratio of cross-sectional areas, because the conductance of a channel is proportional to its cross-sectional area 7 . Moreover, by using atomic-resolution Brownian dynamics method, previous simulation studies reported that decreasing the cross section of the solid nanopore led to an decreased blocked current 51 . Therefore, nanopores with smaller diameters will result in larger signal amplitudes from dsDNA molecules.…”

Colloquium : Ionic phenomena in nanoscale pores through 2D materials

“…(2010), where the SNR for sensing microRNAs using SiN x increases with decreasing membrane thickness and decreasing pore diameter. Intuitively, SNR decreases with a because ions flowing far from the DNA/RNA in the pore adds noise but do not contribute to the signal (Comer and Aksimentiev, 2016). Similarly, both signal Δ I ~ 1 /h p and noise Irms~1/hp decrease with height but the signal decreases faster and so the SNR decreases with height.…”

“…Besides a high SNR for individual blockade events, it is desirable for distinguishing bases to have a high sensitivity (Comer and Aksimentiev, 2016; Garaj et al ., 2013) S=−∂ΔI∂aDNA=VR2∂ΔR∂aDNA≈2γ′aDNAVhpπa′4R2, where we used Δ R from Eq. 7, and assumed a′=a2−aDNA2 to be small, clearly necessary for large sensitivity.…”

“…7, and assumed a′=a2−aDNA2 to be small, clearly necessary for large sensitivity. Initially, scriptS can increase with h p (Comer and Aksimentiev, 2016). However, as h p gets larger, scriptS will decrease due to an increase in R .…”

tRNA Modification Detection Using Graphene Nanopores: A Simulation Study

“…Combinations of experiments and simulations have revealed a wealth of knowledge on DNA translocation through nanopores [ 41 ]. Molecular dynamics simulations have been used to understand the role of nucleotide orientation and neighboring nucleotide chemistry on the passage of ions through the nanopore [ 42 , 43 ]. Drnjic and coworkers have shown that hm 5 C modification in a double stranded DNA can be distinguished from its canonical counterpart using a solid-state nanopore [ 44 ].…”