Detection of DNA and poly-l-lysine using CVD graphene-channel FET biosensors.

A graphene channel field-effect biosensor is demonstrated for detecting the binding of double-stranded DNA and poly-l-lysine. Sensors consist of chemical vapor deposition graphene transferred using a clean, etchant-free transfer method. The presence of DNA and poly-l-lysine are detected by the conductance change of the graphene transistor. A readily measured shift in the Dirac voltage (the voltage at which the graphene's resistance peaks) is observed after the graphene channel is exposed to solutions containing DNA or poly-l-lysine. The 'Dirac voltage shift' is attributed to the binding/unbinding of charged molecules on the graphene surface. The polarity of the response changes to positive direction with poly-l-lysine and negative direction with DNA. This response results in detection limits of 8 pM for 48.5 kbp DNA and 11 pM for poly-l-lysine. The biosensors are easy to fabricate, reusable and are promising as sensors of a wide variety of charged biomolecules.

Stamp transferred suspended graphene mechanical resonators for radio frequency electrical readout.

We present a simple micromanipulation technique to transfer suspended graphene flakes onto any substrate and to assemble them with small localized gates into mechanical resonators. The mechanical motion of the graphene is detected using an electrical, radio frequency (RF) reflection readout scheme where the time-varying graphene capacitor reflects a RF carrier at f = 5-6 GHz producing modulation sidebands at f ± f(m). A mechanical resonance frequency up to f(m) = 178 MHz is demonstrated. We find both hardening/softening Duffing effects on different samples and obtain a critical amplitude of ~40 pm for the onset of nonlinearity in graphene mechanical resonators. Measurements of the quality factor of the mechanical resonance as a function of dc bias voltage V(dc) indicates that dissipation due to motion-induced displacement currents in graphene electrode is important at high frequencies and large V(dc).

High-Q nanomechanics via destructive interference of elastic waves.

Mechanical dissipation poses a ubiquitous challenge to the performance of nanomechanical devices. Here we analyze the support-induced dissipation of high-stress nanomechanical resonators. We develop a model for this loss mechanism and test it on Si(3)N(4) membranes with circular and square geometries. The measured Q values of different harmonics present a nonmonotonic behavior which is successfully explained. For azimuthal harmonics of the circular geometry we predict that destructive interference of the radiated waves leads to an exponential suppression of the clamping loss in the harmonic index. Our model can also be applied to graphene drums under high tension.

Real-time synchronous imaging of electromechanical resonator mode and equilibrium profiles.

Interferometric imaging of normal mode dynamics in electromechanical resonators, oscillating in the rf regime, is demonstrated by synchronous imaging with a pulsed nanosecond laser. Profiles of mechanical modes in suspended thin film structures and their equilibrium profiles are measured through all-optical Fabry-Perot reflectance fits to the temporal traces. As a proof of principle, the mode patterns of a microdrum silicon resonator are visualized, and the extracted vibration modes and equilibrium profile show good agreement with numerical estimations.

Nanoelectromechanical systems.

Nanoelectromechanical systems are evolving, with new scientific studies and technical applications emerging. Mechanical devices are shrinking in thickness and width to reduce mass, increase resonant frequency, and lower the force constants of these systems. Advances in the field include improvements in fabrication processes and new methods for actuating and detecting motion at the nanoscale. Lithographic approaches are capable of creating freestanding objects in silicon and other materials, with thickness and lateral dimensions down to about 20 nanometers. Similar processes can make channels or pores of comparable dimensions, approaching the molecular scale. This allows access to a new experimental regime and suggests new applications in sensing and molecular interactions.

Separation of long DNA molecules in a microfabricated entropic trap array.

A nanofluidic channel device, consisting of many entropic traps, was designed and fabricated for the separation of long DNA molecules. The channel comprises narrow constrictions and wider regions that cause size-dependent trapping of DNA at the onset of a constriction. This process creates electrophoretic mobility differences, thus enabling efficient separation without the use of a gel matrix or pulsed electric fields. Samples of long DNA molecules (5000 to approximately 160,000 base pairs) were efficiently separated into bands in 15-millimeter-long channels. Multiple-channel devices operating in parallel were demonstrated. The efficiency, compactness, and ease of fabrication of the device suggest the possibility of more practical integrated DNA analysis systems.

Powering an inorganic nanodevice with a biomolecular motor.

Biomolecular motors such as F1-adenosine triphosphate synthase (F1-ATPase) and myosin are similar in size, and they generate forces compatible with currently producible nanoengineered structures. We have engineered individual biomolecular motors and nanoscale inorganic systems, and we describe their integration in a hybrid nanomechanical device powered by a biomolecular motor. The device consisted of three components: an engineered substrate, an F1-ATPase biomolecular motor, and fabricated nanopropellers. Rotation of the nanopropeller was initiated with 2 mM adenosine triphosphate and inhibited by sodium azide.

Microfabrication as a scientific tool.

Research in microfabrication not only serves the microelectronics industry but also can provide research tools for studying the behavior of matter at submicrometer dimensions. A variety of techniques including optical, x-ray, and electron beam lithography and reactive ion etching can be used to make structures, devices, and arrays only hundreds of atoms across. Microfabrication techniques have been applied to experiments on surface-enhanced Raman scattering, transport in one-dimensional conductors, and macroscopic quantum tunneling. Recent progress is extending these techniques to scales of less than 100 angstroms.

Conformation, length, and speed measurements of electrodynamically stretched DNA in nanochannels.

A method is presented to rapidly and precisely measure the conformation, length, speed, and fluorescence intensity of single DNA molecules constrained by a nanochannel. DNA molecules were driven electrophoretically from a nanoslit into a nanochannel to confine and dynamically elongate them beyond their equilibrium length for repeated detection via laser-induced fluorescence spectroscopy. A single-molecule analysis algorithm was developed to analytically model bursts of fluorescence and determine the folding conformation of each stretched molecule. This technique achieved a molecular length resolution of 114 nm and an analysis time of around 20 ms per molecule, which enabled the sensitive investigation of several aspects of the physical behavior of DNA in a nanochannel. lambda-bacteriophage DNA was used to study the dependence of stretching on the applied device bias, the effect of conformation on speed, and the amount of DNA fragmentation in the device. A mixture of lambda-bacteriophage with the fragments of its own HindIII digest, a standard DNA ladder, was sized by length as well as by fluorescence intensity, which also allowed the characterization of DNA speed in a nanochannel as a function of length over two and a half orders of magnitude.

Tunable phonon-cavity coupling in graphene membranes.

A major achievement of the past decade has been the realization of macroscopic quantum systems by exploiting the interactions between optical cavities and mechanical resonators. In these systems, phonons are coherently annihilated or created in exchange for photons. Similar phenomena have recently been observed through phonon-cavity coupling-energy exchange between the modes of a single system mediated by intrinsic material nonlinearity. This has so far been demonstrated primarily for bulk crystalline, high-quality-factor (Q > 10(5)) mechanical systems operated at cryogenic temperatures. Here, we propose graphene as an ideal candidate for the study of such nonlinear mechanics. The large elastic modulus of this material and capability for spatial symmetry breaking via electrostatic forces is expected to generate a wealth of nonlinear phenomena, including tunable intermodal coupling. We have fabricated circular graphene membranes and report strong phonon-cavity effects at room temperature, despite the modest Q factor (∼100) of this system. We observe both amplification into parametric instability (mechanical lasing) and the cooling of Brownian motion in the fundamental mode through excitation of cavity sidebands. Furthermore, we characterize the quenching of these parametric effects at large vibrational amplitudes, offering a window on the all-mechanical analogue of cavity optomechanics, where the observation of such effects has proven elusive.

A polymeric microchip with integrated tips and in situ polymerized monolith for electrospray mass spectrometry.

We describe the integration of a cyclo-olefin polymer based microchip with a sheathless capillary tip for electrospray ionization-mass spectrometry (ESI-MS). The microchip was fabricated by hot embossing and thermal bonding. Its design includes a side channel for adjusting the composition of the electrospray solution so that analytes in 100% water can be analyzed. The fused silica capillaries, used for sample introduction, and the electrospray tips for MS coupling were directly inserted into the microchannel before thermal bonding of the device. A microfabricated on-chip gold microelectrode was used to apply the electrospray voltage. Annealing the device after thermal bonding increased the pressure resistance of the microchip. The cross section of the microchannel was imaged by scanning electron microscopy to estimate the effects of the annealing step. The relationship between the applied electrospray voltages and MS signal was measured at different flow rates by coupling the device to an ion trap mass spectrometer. The performance of the microchip was evaluated by MS analysis of imipramine in ammonium acetate buffer solution by direct infusion. An alkylacrylate based monolith polymer bed for on-chip sample pretreatment and separation was polymerized in the microchannel and tested for ESI-MS applications.

An Lrp-type transcriptional regulator from Agrobacterium tumefaciens condenses more than 100 nucleotides of DNA into globular nucleoprotein complexes.

The PutR protein of Agrobacterium tumefaciens positively regulates expression of the putA gene in response to exogenous proline, resulting in the utilization of proline as a source of carbon and nitrogen. PutR activity required a region of DNA extending more than 106 nt upstream of the putA transcription start site. Purified PutR bound to this region with high degree of affinity and repressed expression of the putR promoter in vitro. PutR also activated the putA promoter in vitro in the presence of proline, though less strongly than in whole cells. PutR protected a DNA interval extending from nucleotides -30 to -140, but protected only one helical face over most of this interval, suggesting that it may bind only to this face of the DNA. The addition of proline caused a slight decrease in binding affinity and altered DNase I protection patterns along the entire length of the binding site. PutR-DNA complexes were found by atomic force microscopy to be globular rather than elongated. Although the DNA fragment in these complexes was 190 nm in length, the length of the visible DNA was only 150 nm, indicating that 40 nm of DNA (115 nt) must be condensed with protein. PutR caused a net bend of this binding site, and under some conditions, proline shifted the center of this bend by one helical turn.

Transfer printing of CVD graphene FETs on patterned substrates.

We describe a simple and scalable method for the transfer of CVD graphene for the fabrication of field effect transistors. This is a dry process that uses a modified RCA-cleaning step to improve the surface quality. In contrast to conventional fabrication routes where lithographic steps are performed after the transfer, here graphene is transferred to a pre-patterned substrate. The resulting FET devices display nearly zero Dirac voltage, and the contact resistance between the graphene and metal contacts is on the order of 910 ± 340 Ω µm. This approach enables formation of conducting graphene channel lengths up to one millimeter. The resist-free transfer process provides a clean graphene surface that is promising for use in high sensitivity graphene FET biosensors.

Preferential glial cell attachment to microcontact printed surfaces.

Microcontact printing is introduced as a method for fabricating test surfaces for attachment of cells to chemically patterned silicon surfaces. Tests with astroglial cells indicate that cells attach to microcontact printed surfaces similarly to surfaces produced by traditional photolithographic methods. Astroglial cells attach selectively to 50 microns wide bars of N1[3-(Trimethoxysilyl)propyl]diethylenetriamine (DETA) self-assembled monolayers (SAMs) on surfaces prepared using variable width spaces generated from microcontact printing with octadecyltrichlorosilane (OTS) as the ink. Our results demonstrate that microcontact printing provides an effective and rapid method for routine production of patterned self-assembled monolayers that can be used for directing cell attachment and studying cell morphology.

Brain responses to micro-machined silicon devices.

Micro-machined neural prosthetic devices can be designed and fabricated to permit recording and stimulation of specific sites in the nervous system. Unfortunately, the long-term use of these devices is compromised by cellular encapsulation. The goals of this study were to determine if device size, surface characteristics, or insertion method affected this response. Devices with two general designs were used. One group had chisel-shaped tips, sharp angular corners, and surface irregularities on the micrometer size scale. The second group had rounded corners, and smooth surfaces. Devices of the first group were inserted using a microprocessor-controlled inserter. Devices of the second group were inserted by hand. Comparisons were made of responses to the larger devices in the first group with devices from the second group. Responses were assessed 1 day and 1, 2, 4, 6, and 12 weeks after insertions. Tissues were immunochemically labeled for glial fibrillary acidic protein (GFAP) or vimentin to identify astrocytes, or for ED1 to identify microglia. For the second comparison devices from the first group with different cross-sectional areas were analyzed. Similar reactive responses were observed following insertion of all devices; however, the volume of tissue involved at early times, <1 week, was proportional to the cross-sectional area of the devices. Responses observed after 4 weeks were similar for all devices. Thus, the continued presence of devices promotes formation of a sheath composed partly of reactive astrocytes and microglia. Both GFAP-positive and -negative cells were adherent to all devices. These data indicate that device insertion promotes two responses-an early response that is proportional to device size and a sustained response that is independent of device size, geometry, and surface roughness. The early response may be associated with the amount of damage generated during insertion. The sustained response is more likely due to tissue-device interactions.

Topographically modified surfaces affect orientation and growth of hippocampal neurons.

Extracellular matrix molecules provide biochemical and topographical cues that influence cell growth in vivo and in vitro. Effects of topographical cues on hippocampal neuron growth were examined after 14 days in vitro. Neurons from hippocampi of rat embryos were grown on poly-L-lysine-coated silicon surfaces containing fields of pillars with varying geometries. Photolithography was used to fabricate 1 microm high pillar arrays with different widths and spacings. Beta(III)-tubulin and MAP-2 immunocytochemistry and scanning electron microscopy were used to describe neuronal processes. Automated two-dimensional tracing software quantified process orientation and length. Process growth on smooth surfaces was random, while growth on pillared surfaces exhibited the most faithful alignment to pillar geometries with smallest gap sizes. Neurite lengths were significantly longer on pillars with the smallest inter-pillar spacings (gaps) and 2 microm pillar widths. These data indicate that physical cues affect neuron growth, suggesting that extracellular matrix topography may contribute to cell growth and differentiation. These results demonstrate new strategies for directing and promoting neuronal growth that will facilitate studies of synapse formation and function and provide methods to establish defined neural networks.

Characterizing electroosmotic flow in microfluidic devices.

The current-monitoring method was used to measure the electroosmotic flow (EOF) in borosilicate glass capillaries and zeonor plastic microfluidic devices. The surface of the zeonor devices must be oxidized to support EOF and this treatment shows signs of aging within 6 days. Oxidized zeonor devices showed the same response to changes in applied field, pH, and ionic concentration as the capillaries. The effects of several common dynamic surfactant coatings on the walls were also studied (0.1%, v/v solutions of POP-6, POP4, Pluronics L81, and NP-40). These generally significantly suppressed the EOF but required several days to stabilize.

Microfabricated cantilevers for measurement of subcellular and molecular forces.

We present two new microfabricated cantilever-beam force transducers. The transducers were fabricated from thin silicon-nitride films, and were used respectively to measure forces generated by two small-muscle preparations: the single myofibril, and the single actin filament in contact with a myosin-coated surface. A simple resonance method was developed to characterize the transducers. Because of the high reproducibility of lever dimensions and the consistency of the modulus of elasticity, few calibration measurements sufficed to characterize the stiffness of all the levers on a single wafer.

Stress and silicon nitride: a crack in the universal dissipation of glasses.

High-stress silicon nitride microresonators exhibit a remarkable room temperature Q factor that even exceeds that of single crystal silicon. A study of the temperature dependent variation of the Q of a 255 micromx255 micromx30 nm thick high-stress Si3N4 membrane reveals that the dissipation Q-1 decreases with lower temperatures and is approximately 3 orders of magnitude smaller than the universal behavior. Stress-relieved cantilevers fabricated from the same material show a Q that is more consistent with typical disordered materials. e-beam and x-ray studies of the nitride film's structure reveal characteristics consistent with a disordered state. Thus, it is shown that stress alters the Q-1, violating the universality of dissipation in disordered materials in a self-supporting structure.