Tailoring the hydrophobicity of graphene for its use as nanopores for DNA translocation

Abstract

Graphene nanopores are potential successors to biological and silicon-based nanopores. For sensing applications, it is however crucial to understand and block the strong nonspecific hydrophobic interactions between DNA and graphene. Here we demonstrate a novel scheme to prevent DNA-graphene interactions, based on a tailored self-assembled monolayer. For bare graphene, we encounter a paradox: whereas contaminated graphene nanopores facilitated DNA translocation well, clean crystalline graphene pores very quickly exhibit clogging of the pore. We attribute this to strong interactions between DNA nucleotides and graphene, yielding sticking and irreversible pore closure. We develop a general strategy to noncovalently tailor the hydrophobic surface of graphene by designing a dedicated self-assembled monolayer of pyrene ethylene glycol, which renders the surface hydrophilic. We demonstrate that this prevents DNA to adsorb on graphene and show that singlestranded DNA can now be detected in graphene nanopores with excellent nanopore durability and reproducibility.

Understanding the interaction between energetic ions and freestanding graphene towards practical 2D perforation

“…By decreasing the number of He + hitting the monolayer graphene to 2.7×10 5 we were able to produce holes with 2.6-nm-wide diameter (Figure 4e), comparable to pore sizes drilled in graphene using TEM systems. 21, 49 Our results show a significant advancement in graphene patterning via FIB milling in terms of feature size and array dimension, enabled by detailed knowledge of the interaction mechanisms involved and the 2D nature of our target material. Use of freestanding graphene allowed us to create patterns while avoiding undesirable secondary effects during FIB milling (e.g., ion implanting and substrate swelling), unlike frequently reported for the supported graphene samples.…”

Graphene nanodevices for DNA sequencing

“…(b) TEM image (80 kV) of a 3 nm nanopore with clean and crystalline edge drilled in STEM mode at 600 • C (scale bar is 1 nm). From [37]. (c) dsDNA current blockades are larger for graphene nanopores (blue) than for SiN pores (red) due to their thin membranes.…”

“…In a next step towards sequencing, single-stranded DNA was detected. To do so, the attractive hydrophobic π-π stacking interactions between the nucleobases and graphene were overcome by applying a hydrophilic coating to the graphene to prevent attachment of the DNA to the graphene and the associated clogging of the pore [37]. In another experimental report, the opposite approach was taken and the adsorption and desorption of DNA bases on the graphene was in fact exploited to slow down DNA during translocation.…”

Sensing at the Surface of Graphene Field‐Effect Transistors

“…3g (right panel, highly oriented pyrolytic graphite (HOPG) was applied in this case). [128] This strong nonspecific ssDNA adsorption can be avoided by first self-assembling a monolayer of pyrene ethylene glycol, thus rendering the surface of graphene hydrophilic and preventing ssDNA adsorption via hydrophobic interactions (left panel, Fig. 3g).…”

“…Surface passivation against unwanted non-specific binding (pyrene ethylene glycol to prevent any hydrophobic interactions, [128] for example) is crucial to achieve very low detection limits in the presence of high ionic background levels and to avoid false positives when complex biological samples are assayed. [131] Importantly, the transfer of large and clean (and crack-and fold-free) graphene sheets is still a critical challenge.…”