Molecular Transport across the Ionic Liquid-Aqueous Electrolyte Interface in a MoS2 Nanopore.

Nanopore sequencing of DNA has been enabled by the use of a biological enzyme to thread DNA through an engineered biological nanopore while recording the ionic current flowing through the nanopore. Efforts to realize a similar concept using a solid-state nanopore have been met with several technical challenges, one of which is the high speed of DNA translocation and the other the low ionic current contrast among individual nucleotides. A promising avenue to addressing both problems is using an ionic liquid to slow DNA translocation and a tiny nanopore in the MoS2 membrane to distinguish individual nucleotides. The physical mechanisms enabling these technical advances have remained elusive. Here, we characterize the ion and DNA transport through the ionic liquid/aqueous electrolyte interface, with and without a MoS2 nanopore, using the all-atom molecular dynamics method. We find that the partial miscibility of the ionic liquid and the aqueous electrolyte considerably alters the physics of the nanopore translocation process. Thus, the interface of the two phases generates a contact potential of 600 mV, the ionic current is dominated by the motion of ionic liquid molecules through the aqueous solution phase, and the DNA nucleotides exhibit preferential partitioning into the aqueous electrolyte, which leads to spontaneous transport of DNA polymers from the ionic liquid to the aqueous solution compartment in the absence of external voltage bias. The complex physics of the two-phase nanopore system offers a multitude of opportunities for extending the functionality of nanopore-sensing platforms.

Step-defect guided delivery of DNA to a graphene nanopore.

Precision placement and transport of biomolecules are critical to many single-molecule manipulation and detection methods. One such method is nanopore sequencing, in which the delivery of biomolecules towards a nanopore controls the method's throughput. Using all-atom molecular dynamics, here we show that the precision transport of biomolecules can be realized by utilizing ubiquitous features of graphene surface-step defects that separate multilayer domains. Subject to an external force, we found that adsorbed DNA moved much faster down a step defect than up, and even faster along the defect edge, regardless of whether the motion was produced by a mechanical force or a solvent flow. We utilized this direction dependency to demonstrate a mechanical analogue of an electric diode and a system for delivering DNA molecules to a nanopore. The defect-guided delivery principle can be used for the separation, concentration and storage of scarce biomolecular species, on-demand chemical reactions and nanopore sensing.

Characterization of the Lipid Structure and Fluidity of Lipid Membranes on Epitaxial Graphene and Their Correlation to Graphene Features.

Graphene has been recognized as an enhanced platform for biosensors because of its high electron mobility. To integrate active membrane proteins into graphene-based materials for such applications, graphene's surface must be functionalized with lipids to mimic the biological environment of these proteins. Several studies have examined supported lipids on various types of graphene and obtained conflicting results for the lipid structure. Here, we present a correlative characterization technique based on fluorescence measurements in a Raman spectroscopy setup to study the lipid structure and dynamics on epitaxial graphene. Compared to other graphene variations, epitaxial graphene is grown on a substrate more conducive to production of electronics and offers unique topographic features. On the basis of experimental and computational results, we propose that a lipid sesquilayer (1.5 bilayer) forms on epitaxial graphene and demonstrate that the distinct surface features of epitaxial graphene affect the structure and diffusion of supported lipids.

PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore.

Monodispersed angstrom-size pores embedded in a suitable matrix are promising for highly selective membrane-based separations. They can provide substantial energy savings in water treatment and small molecule bioseparations. Such pores present as membrane proteins (chiefly aquaporin-based) are commonplace in biological membranes but difficult to implement in synthetic industrial membranes and have modest selectivity without tunable selectivity. Here we present PoreDesigner, a design workflow to redesign the robust beta-barrel Outer Membrane Protein F as a scaffold to access three specific pore designs that exclude solutes larger than sucrose (>360 Da), glucose (>180 Da), and salt (>58 Da) respectively. PoreDesigner also enables us to design any specified pore size (spanning 3-10 Å), engineer its pore profile, and chemistry. These redesigned pores may be ideal for conducting sub-nm aqueous separations with permeabilities exceeding those of classical biological water channels, aquaporins, by more than an order of magnitude at over 10 billion water molecules per channel per second.

Modulation of Molecular Flux Using a Graphene Nanopore Capacitor.

Modulation of ionic current flowing through nanoscale pores is one of the fundamental biological processes. Inspired by nature, nanopores in synthetic solid-state membranes are being developed to enable rapid analysis of biological macromolecules and to serve as elements of nanofludic circuits. Here, we theoretically investigate ion and water transport through a graphene-insulator-graphene membrane containing a single, electrolyte-filled nanopore. By means of all-atom molecular dynamics simulations, we show that the charge state of such a graphene nanopore capacitor can regulate both the selectivity and the magnitude of the nanopore ionic current. At a fixed transmembrane bias, the ionic current can be switched from being carried by an equal mixture of cations and anions to being carried almost exclusively by either cationic or anionic species, depending on the sign of the charge assigned to both plates of the capacitor. Assigning the plates of the capacitor opposite sign charges can either increase the nanopore current or reduce it substantially, depending on the polarity of the bias driving the transmembrane current. Facilitated by the changes of the nanopore surface charge, such ionic current modulations are found to occur despite the physical dimensions of the nanopore being an order of magnitude larger than the screening length of the electrolyte. The ionic current rectification is accompanied by a pronounced electro-osmotic effect that can transport neutral molecules such as proteins and drugs across the solid-state membrane and thereby serve as an interface between electronic and chemical signals.

Slowing DNA Transport Using Graphene-DNA Interactions.

Slowing down DNA translocation speed in a nanopore is essential to ensuring reliable resolution of individual bases. Thin membrane materials enhance spatial resolution but simultaneously reduce the temporal resolution as the molecules translocate far too quickly. In this study, the effect of exposed graphene layers on the transport dynamics of both single (ssDNA) and double-stranded DNA (dsDNA) through nanopores is examined. Nanopore devices with various combinations of graphene and Al2O3 dielectric layers in stacked membrane structures are fabricated. Slow translocations of ssDNA in nanopores drilled in membranes with layers of graphene are reported. The increased hydrophobic interactions between the ssDNA and the graphene layers could explain this phenomenon. Further confirmation of the hydrophobic origins of these interactions is obtained through reporting significantly faster translocations of dsDNA through these graphene layered membranes. Molecular dynamics simulations confirm the preferential interactions of DNA with the graphene layers as compared to the dielectric layer verifying the experimental findings. Based on our findings, we propose that the integration of multiple stacked graphene layers could slow down DNA enough to enable the identification of nucleobases.

Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene.

Control over interactions with biomolecules holds the key to applications of graphene in biotechnology. One such application is nanopore sequencing, where a DNA molecule is electrophoretically driven through a graphene nanopore. Here we investigate how interactions of single-stranded DNA and a graphene membrane can be controlled by electrically biasing the membrane. The results of our molecular dynamics simulations suggest that electric charge on graphene can force a DNA homopolymer to adopt a range of strikingly different conformations. The conformational response is sensitive to even very subtle nucleotide modifications, such as DNA methylation. The speed of DNA motion through a graphene nanopore is strongly affected by the graphene charge: a positive charge accelerates the motion, whereas a negative charge arrests it. As a possible application of the effect, we demonstrate stop-and-go transport of DNA controlled by the charge of graphene. Such on-demand transport of DNA is essential for realizing nanopore sequencing.