DNA translocation through an array of kinked nanopores

Abstract

Synthetic solid-state nanopores are being intensively investigated as single-molecule sensors for detection and characterization of DNA, RNA and proteins. This field has been inspired by the exquisite selectivity and flux demonstrated by natural biological channels and the dream of emulating these behaviours in more robust synthetic materials that are more readily integrated into practical devices. So far, the guided etching of polymer films, focused ion-beam sculpting, and electron-beam lithography and tuning of silicon nitride membranes have emerged as three promising approaches to define synthetic solid-state pores with sub-nanometre resolution. These procedures have in common the formation of nominally cylindrical or conical pores aligned normal to the membrane surface. Here we report the formation of 'kinked' silica nanopores, using evaporation-induced self-assembly, and their further tuning and chemical derivatization using atomic-layer deposition. Compared with 'straight through' proteinaceous nanopores of comparable dimensions, kinked nanopores exhibit up to fivefold reduction in translocation velocity, which has been identified as one of the critical issues in DNA sequencing. Additionally, we demonstrate an efficient two-step approach to create a nanopore array exhibiting nearly perfect selectivity for ssDNA over dsDNA. We show that a coarse-grained drift-diffusion theory with a sawtooth-like potential can reasonably describe the velocity and translocation time of DNA through the pore. By control of pore size, length and shape, we capture the main functional behaviours of protein pores in our solid-state nanopore system.

Mesoporous Silica Nanoparticles Loaded with Surfactant: Low Temperature Magic Angle Spinning 13C and 29Si NMR Enhanced by Dynamic Nuclear Polarization

“…2 SiROX with R = PUP, X = H or Me), and T 3 ((SiO) 3 SiR with R = PUP). No line broadening was observed in the DNP-enhanced spectra of Ex-MSN and S-MSN because in both samples the CP process is only effective for 13 C and 29 Si nuclei that are not directly affected by the unpaired electrons of TOTAPOL.…”

Translocation of biomolecules through solid‐state nanopores: Theory meets experiments

“…Reducing the translocation speed in a fivefold manner compared to bio-pores was also achieved using arrays of kinked silica nanopores. 39 These arrays showed nearly perfect selectivity of ss-DNA over ds-DNA.…”

Trinucleotide duplex formation inside a confined nanospace under supercooled conditions

“…Mesoporous silica synthesized by supramolecular templating approach has uniform cylindrical pores of approximately the diameter of oligonucleotide duplexes (B2 nm; refs [9][10][11][12]. Functional groups attached to the inner surfaces of these pores can be used to fine-tune surface character, effective pore diameter and the microenvironment inside the pore 13 .…”