Marija Drndic

DNA Translocation through Graphene Nanopores

We report on DNA translocations through nanopores created in graphene membranes. Devices consist of 1-5 nm thick graphene membranes with electron-beam sculpted nanopores from 5 to 10 nm in diameter. Due to the thin nature of the graphene membranes, we observe larger blocked currents than for traditional solid-state nanopores. However, ionic current noise levels are several orders of magnitude larger than those for silicon nitride nanopores. These fluctuations are reduced with the atomic-layer deposition of 5 nm of titanium dioxide over the device. Unlike traditional solid-state nanopore materials that are insulating, graphene is an excellent electrical conductor. Use of graphene as a membrane material opens the door to a new class of nanopore devices in which electronic sensing and control are performed directly at the pore.

Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors

Small RNA molecules have an important role in gene regulation and RNA silencing therapy, but it is challenging to detect these molecules without the use of time-consuming radioactive labelling assays or error-prone amplification methods. Here, we present a platform for the rapid electronic detection of probe-hybridized microRNAs from cellular RNA. In this platform, a target microRNA is first hybridized to a probe. This probe:microRNA duplex is then enriched through binding to the viral protein p19. Finally, the abundance of the duplex is quantified using a nanopore. Reducing the thickness of the membrane containing the nanopore to 6 nm leads to increased signal amplitudes from biomolecules, and reducing the diameter of the nanopore to 3 nm allows the detection and discrimination of small nucleic acids based on differences in their physical dimensions. We demonstrate the potential of this approach by detecting picogram levels of a liver-specific miRNA from rat liver RNA.

Electron beam nanosculpting of suspended graphene sheets

We demonstrate high-resolution modification of suspended multilayer graphene sheets by controlled exposure to the focused electron beam of a transmission electron microscope. We show that this technique can be used to realize, on time scales of a few seconds, a variety of features, including nanometer-scale pores, slits, and gaps that are stable and do not evolve over time. Despite the extreme thinness of the suspended graphene sheets, extensive removal of material to produce the desired feature geometries is found not to introduce long-range distortion of the suspended sheet structure.

Integrated nanopore sensing platform with sub-microsecond temporal resolution.

Nanopore sensors have attracted considerable interest for high-throughput sensing of individual nucleic acids and proteins without the need for chemical labels or complex optics. A prevailing problem in nanopore applications is that the transport kinetics of single biomolecules are often faster than the measurement time resolution. Methods to slow down biomolecular transport can be troublesome and are at odds with the natural goal of high-throughput sensing. Here we introduce a low-noise measurement platform that integrates a complementary metal-oxide semiconductor (CMOS) preamplifier with solid-state nanopores in thin silicon nitride membranes. With this platform we achieved a signal-to-noise ratio exceeding five at a bandwidth of 1 MHz, which to our knowledge is the highest bandwidth nanopore recording to date. We demonstrate transient signals as brief as 1 μs from short DNA molecules as well as current signatures during molecular passage events that shed light on submolecular DNA configurations in small nanopores.

Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules

Modified DNA bases are widespread in biology. 5-Methylcytosine (mC) is a predominant epigenetic marker in higher eukaryotes involved in gene regulation, development, aging, cancer, and disease. Recently, 5-hydroxymethylcytosine (hmC) was identified in mammalian brain tissue and stem cells. However, most of the currently available assays cannot distinguish mC from hmC in DNA fragments. We investigate here the physical properties of DNA with modified cytosines, in efforts to develop a physical tool that distinguishes mC from hmC in DNA fragments. Molecular dynamics simulations reveal that polar cytosine modifications affect internal base pair dynamics, while experimental evidence suggest a correlation between the modified cytosines polarity, DNA flexibility, and duplex stability. On the basis of these physical differences, solid-state nanopores can rapidly discriminate among DNA fragments with mC or hmC modification by sampling a few hundred molecules in the solution. Further, the relative proportion of hmC in the sample can be determined from the electronic signature of the intact DNA fragment.

Computational Design of Virus-like Protein Assemblies on Carbon Nanotube Surfaces

Proteins are designed to bind to specific surfaces while also presenting a programmed surface superstructure. There is a general need for the engineering of protein-like molecules that organize into geometrically specific superstructures on molecular surfaces, directing further functionalization to create richly textured, multilayered assemblies. Here we describe a computational approach whereby the surface properties and symmetry of a targeted surface define the sequence and superstructure of surface-organizing peptides. Computational design proceeds in a series of steps that encode both surface recognition and favorable intersubunit packing interactions. This procedure is exemplified in the design of peptides that assemble into a tubular structure surrounding single-walled carbon nanotubes (SWNTs). The geometrically defined, virus-like coating created by these peptides converts the smooth surfaces of SWNTs into highly textured assemblies with long-scale order, capable of directing the assembly of gold nanoparticles into helical arrays along the SWNT axis.

Efficient polymer-nanocrystal quantum-dot photodetectors

We have realized highly efficient photodetectors based on composites of the semiconducting polymer poly[2-methoxy-5-(2′-ethylhexyloxy)-1,4-phenylenevinylene] and PbSe nanocrystal quantum dots. The external quantum efficiency in these devices is greater than 1 for electric fields E∼7×105V∕cm. The observed photocurrent gain could be attributed to the carrier multiplication in PbSe nanocrystal quantum dots via multiple exciton generation, and the efficient charge conduction through the host polymer material. This photocurrent gain is observed only when the PbSe nanocrystal band gap is at least three times smaller than the optical energy gap of the active polymer material.

Transport properties of annealed CdSe colloidal nanocrystal solids

Transport properties of artificial solids composed of colloidal CdSe nanocrystals (NCs) are studied from 6 to 250 K, before and after annealing. After the solids are annealed, three changes are observed. First, transmission electron micrographs show that the separation between NCs decreases with annealing. Second, the optical absorption spectrum changes: the excitonic peaks of the NC solids shift to lower energies and broaden with annealing. These redshifts can result from the change of the dielectric environment around the NCs. Last, annealing results in greatly enhanced dark current and photocurrent. This increased current can be attributed to the enhancement of interdot tunneling caused by the decreased separation between NCs and by chemical changes in their organic cap. In addition, the dark current is an exponential function of the applied electric field and it is only weakly temperature dependent. Our measurements also suggest that Coulomb interactions between charges on neighboring NCs play an impo...

DNA Base-Specific Modulation of Microampere Transverse Edge Currents through a Metallic Graphene Nanoribbon with a Nanopore

We study two-terminal devices for DNA sequencing that consist of a metallic graphene nanoribbon with zigzag edges (ZGNR) and a nanopore in its interior through which the DNA molecule is translocated. Using the nonequilibrium Green functions combined with density functional theory, we demonstrate that each of the four DNA nucleobases inserted into the nanopore, whose edge carbon atoms are passivated by either hydrogen or nitrogen, will lead to a unique change in the device conductance. Unlike other recent biosensors based on transverse electronic transport through translocated DNA, which utilize small (of the order of pA) tunneling current across a nanogap or a nanopore yielding a poor signal-to-noise ratio, our device concept relies on the fact that in ZGNRs local current density is peaked around the edges so that drilling a nanopore away from the edges will not diminish the conductance. Inserting a nucleobase into the nanopore affects the charge density in the surrounding area, thereby modulating edge conduction currents whose magnitude is of the order of microampere at bias voltage 0.1 V. The proposed biosensors are not limited to ZGNRs and they could be realized with other nanowires supporting transverse edge currents, such as chiral GNRs or wires made of two-dimensional topological insulators.

Guiding Neutral Atoms on a Chip

We demonstrate the guiding of neutral atoms by the magnetic fields due to microfabricated current-carrying wires on a chip. Atoms are guided along a magnetic field minimum parallel to and above the current-carrying wires. Two guide configurations are demonstrated: one using two wires with an external magnetic field, and a second using four wires without an external field. These guide geometries can be extended to integrated atom optics circuits, including beam splitters.