Electrically Controllable Single-Point Covalent Functionalization of Spin-Cast Carbon-Nanotube Field-Effect Transistor Arrays

RNA adapts its flexibility to efficiently fold and resist unfolding

Recent studies have demonstrated that the mechanisms through which biopolymers like RNA interconvert between multiple folded structures are critical for their cellular functions. A major obstacle to elucidating these mechanisms is the lack of experimental approaches that can resolve these interconversions between functionally relevant biomolecular structures. Here, using a nano-electronic device with microsecond time resolution, we dissect the complete set of structural rearrangements executed by an ultra-stable RNA, the UUCG stem-loop, at the single-molecule level. We show that the stem-loop samples at least four conformations along two folding pathways leading to two distinct folded structures, only one of which has been previously observed. By modulating its flexibility, the stem-loop can adaptively select between these pathways, enabling it to both fold rapidly and resist unfolding. This paradigm of stabilization through compensatory changes in flexibility broadens our understanding of stable RNA structures and is expected to serve as a general strategy employed by all biopolymers.

Carbon-nanotube field-effect transistors for resolving single-molecule aptamer-ligand binding kinetics

Small molecules such as neurotransmitters are critical for biochemical functions in living systems. While conventional ultraviolet-visible spectroscopy and mass spectrometry lack portability and are unsuitable for time-resolved measurements in situ, techniques such as amperometry and traditional field-effect detection require a large ensemble of molecules to reach detectable signal levels. Here we demonstrate the potential of carbon-nanotube-based single-molecule field-effect transistors (smFETs), which can detect the charge on a single molecule, as a new platform for recognizing and assaying small molecules. smFETs are formed by the covalent attachment of a probe molecule, in our case a DNA aptamer, to a carbon nanotube. Conformation changes on binding are manifest as discrete changes in the nanotube electrical conductance. By monitoring the kinetics of conformational changes in a binding aptamer, we show that smFETs can detect and quantify serotonin at the single-molecule level, providing unique insights into the dynamics of the aptamer-ligand system. In particular, we show the involvement of G-quadruplex formation and the disruption of the native hairpin structure in the conformational changes of the serotonin-aptamer complex. The smFET is a label-free approach to analysing molecular interactions at the single-molecule level with high temporal resolution, providing additional insights into complex biological processes.

Characterizing the Conformational Free-Energy Landscape of RNA Stem-Loops Using Single-Molecule Field-Effect Transistors

We have developed and used single-molecule field-effect transistors (smFETs) to characterize the conformational free-energy landscape of RNA stem-loops. Stem-loops are one of the most common RNA structural motifs and serve as building blocks for the formation of complex RNA structures. Given their prevalence and integral role in RNA folding, the kinetics of stem-loop (un)folding has been extensively characterized using both experimental and computational approaches. Interestingly, these studies have reported vastly disparate timescales of (un)folding, which has been interpreted as evidence that (un)folding of even simple stem-loops occurs on a highly rugged conformational energy landscape. Because smFETs do not rely on fluorophore reporters of conformation or mechanical (un)folding forces, they provide a unique approach that has allowed us to directly monitor tens of thousands of (un)folding events of individual stem-loops at a 200 μs time resolution. Our results show that under our experimental conditions, stem-loops (un)fold over a 1-200 ms timescale during which they transition between ensembles of unfolded and folded conformations, the latter of which is composed of at least two sub-populations. The 1-200 ms timescale of (un)folding we observe here indicates that smFETs report on complete (un)folding trajectories in which unfolded conformations of the RNA spend long periods of time wandering the free-energy landscape before sampling one of several misfolded conformations or the natively folded conformation. Our findings highlight the extremely rugged landscape on which even the simplest RNA structural elements fold and demonstrate that smFETs are a unique and powerful approach for characterizing the conformational free-energy of RNA.

Nucleotide detection mechanism and comparison based on low-dimensional materials: A review

The recent pandemic has led to the fabrication of new nucleic acid sensors that can detect infinitesimal limits immediately and effectively. Therefore, various techniques have been demonstrated using low-dimensional materials that exhibit ultrahigh detection and accuracy. Numerous detection approaches have been reported, and new methods for impulse sensing are being explored. All ongoing research converges at one unique point, that is, an impetus: the enhanced limit of detection of sensors. There are several reviews on the detection of viruses and other proteins related to disease control point of care; however, to the best of our knowledge, none summarizes the various nucleotide sensors and describes their limits of detection and mechanisms. To understand the far-reaching impact of this discipline, we briefly discussed conventional and nanomaterial-based sensors, and then proposed the feature prospects of these devices. Two types of sensing mechanisms were further divided into their sub-branches: polymerase chain reaction and photospectrometric-based sensors. The nanomaterial-based sensor was further subdivided into optical and electrical sensors. The optical sensors included fluorescence (FL), surface plasmon resonance (SPR), colorimetric, and surface-enhanced Raman scattering (SERS), while electrical sensors included electrochemical luminescence (ECL), microfluidic chip, and field-effect transistor (FET). A synopsis of sensing materials, mechanisms, detection limits, and ranges has been provided. The sensing mechanism and materials used were discussed for each category in terms of length, collectively forming a fusing platform to highlight the ultrahigh detection technique of nucleotide sensors. We discussed potential trends in improving the fabrication of nucleotide nanosensors based on low-dimensional materials. In this area, particular aspects, including sensitivity, detection mechanism, stability, and challenges, were addressed. The optimization of the sensing performance and selection of the best sensor were concluded. Recent trends in the atomic-scale simulation of the development of Deoxyribonucleic acid (DNA) sensors using 2D materials were highlighted. A critical overview of the challenges and opportunities of deoxyribonucleic acid sensors was explored, and progress made in deoxyribonucleic acid detection over the past decade with a family of deoxyribonucleic acid sensors was described. Areas in which further research is needed were included in the future scope.

Dynamic Gate Control of Aryldiazonium Chemistry on Graphene Field-Effect Transistors

As graphene field-effect transistors (GFETs) are becoming increasingly valued for sensor applications, efficiency and control of their surface functionalization become critical. Here, we introduce an innovative method using a gate electrode to precisely modulate aryldiazonium functionalization directly on graphene devices. Although this covalent chemistry is well-known, we show that its spontaneous reaction on GFETs is highly heterogeneous with a low overall yield. By dynamically tuning the gate voltage in the presence of the reactant, we can quickly enable or suppress the reaction, resulting in a high degree of homogeneity between devices. We are also able to monitor and control functionalization kinetics in real time. The mechanism for our approach is based on electron transfer availability, analogous to chemical, substrate-based, or electrochemical doping, but has the practical advantage of being fully implementable on devices or chips. This work illustrates how powerful the FET platforms are to study surface reactions on nanomaterials in real time.

The molecular origin of the electrostatic gating of single-molecule field-effect biosensors investigated by molecular dynamics simulations

Field-effect biosensors (bioFETs) offer a novel way to measure the kinetics of biomolecular events such as protein function and DNA hybridization at the single-molecule level on a wide range of time scales. These devices generate an electrical current whose fluctuations are correlated to the kinetics of the biomolecule under study. BioFETs are indeed highly sensitive to changes in the electrostatic potential (ESP) generated by the biomolecule. Here, using all-atom solvent explicit molecular dynamics simulations, we further investigate the molecular origin of the variation of this ESP for two prototypical cases of proteins or nucleic acids attached to a carbon nanotube bioFET: the function of the lysozyme protein and the hybridization of a 10-nt DNA sequence, as previously done experimentally. Our results show that the ESP changes significantly on the surface of the carbon nanotube as the state of these two biomolecules changes. More precisely, the ESP distributions calculated for these molecular states explain well the magnitude of the conductance fluctuations measured experimentally. The dependence of the ESP with salt concentration is found to agree with the reduced conductance fluctuations observed experimentally for the lysozyme, but to differ for the case of DNA, suggesting that other mechanisms might be at play in this case. Furthermore, we show that the carbon nanotube does not impact significantly the structural stability of the lysozyme, corroborating that the kinetic rates measured using bioFETs are similar to those measured by other techniques. For DNA, we find that the structural ensemble of the single-stranded DNA is significantly impacted by the presence of the nanotube, which, combined with the ESP analysis, suggests a stronger DNA-device interplay. Overall, our simulations strengthen the comprehension of the inner working of field-effect biosensors used for single-molecule kinetics measurements on proteins and nucleic acids.

Charge Transport in and Electroluminescence from sp3-Functionalized Carbon Nanotube Networks

The controlled covalent functionalization of semiconducting single-walled carbon nanotubes (SWCNTs) with luminescent sp³ defects leads to additional narrow and tunable photoluminescence features in the near-infrared and even enables single-photon emission at room temperature, thus strongly expanding their application potential. However, the successful integration of sp³-functionalized SWCNTs in optoelectronic devices with efficient defect state electroluminescence not only requires control over their emission properties but also a detailed understanding of the impact of functionalization on their electrical performance, especially in dense networks. Here, we demonstrate ambipolar, light-emitting field-effect transistors based on networks of pristine and functionalized polymer-sorted (6,5) SWCNTs. We investigate the influence of sp³ defects on charge transport by employing electroluminescence and (charge-modulated) photoluminescence spectroscopy combined with temperature-dependent current-voltage measurements. We find that sp³-functionalized SWCNTs actively participate in charge transport within the network as mobile carriers efficiently sample the sp³ defects, which act as shallow trap states. While both hole and electron mobilities decrease with increasing degree of functionalization, the transistors remain fully operational, showing electroluminescence from the defect states that can be tuned by the defect density.

Interaction of Luminescent Defects in Carbon Nanotubes with Covalently Attached Stable Organic Radicals

The functionalization of single-walled carbon nanotubes (SWCNTs) with luminescent sp³ defects has greatly improved their performance in applications such as quantum light sources and bioimaging. Here, we report the covalent functionalization of purified semiconducting SWCNTs with stable organic radicals (perchlorotriphenylmethyl, PTM) carrying a net spin. This model system allows us to use the near-infrared photoluminescence arising from the defect-localized exciton as a highly sensitive probe for the short-range interaction between the PTM radical and the SWCNT. Our results point toward an increased triplet exciton population due to radical-enhanced intersystem crossing, which could provide access to the elusive triplet manifold in SWCNTs. Furthermore, this simple synthetic route to spin-labeled defects could enable magnetic resonance studies complementary to in vivo fluorescence imaging with functionalized SWCNTs and facilitate the scalable fabrication of spintronic devices with magnetically switchable charge transport.

Building Tailored Interfaces through Covalent Coupling Reactions at Layers Grafted from Aryldiazonium Salts

Aryldiazonium ions are widely used reagents for surface modification. Attractive aspects of their use include wide substrate compatibility (ranging from plastics to carbons to metals and metal oxides), formation of stable covalent bonding to the substrate, simplicity of modification methods that are compatible with organic and aqueous solvents, and the commercial availability of many aniline precursors with a straightforward conversion to the active reagent. Importantly, the strong bonding of the modifying layer to the surface makes the method ideally suited to further on-surface (postfunctionalization) chemistry. After an initial grafting from a suitable aryldiazonium ion to give an anchor layer, a target species can be coupled to the layer, hugely expanding the range of species that can be immobilized. This strategy has been widely employed to prepare materials for numerous applications including chemical sensors, biosensors, catalysis, optoelectronics, composite materials, and energy conversion and storage. In this Review our goal is first to summarize how a target species with a particular functional group may be covalently coupled to an appropriate anchor layer. We then review applications of the resulting materials.

Chemical-free and scalable process for the fabrication of a uniform array of liquid-gated CNTFET, evaluated by KCl electrolyte

Biosensors based on liquid-gated carbon nanotubes field-effect transistors (LG-CNTFETs) have attracted considerable attention, as they offer high sensitivity and selectivity; quick response and label-free detection. However, their practical applications are limited due to the numerous fabrication challenges including resist-based lithography, in which after the lithography process, the resist leaves trace level contaminations over the CNTs that affect the performance of the fabricated biosensors. Here, we report the realization of LG-CNTFET devices using silicon shadow mask-based chemical-free lithography process on a 3-in. silicon wafer, yielding 21 sensor chips. Each sensor chip consists of 3 × 3 array of LG-CNTFET devices. Field emission scanning electron microscope (FESEM) and Raman mapping confirm the isolation of devices within the array chip having 9 individual devices. A reference electrode (Ag/AgCl) is used to demonstrate the uniformity of sensing performances among the fabricated LG-CNTFET devices in an array using different KCl molar solutions. The average threshold voltage (V_th) for all 9 devices varies from 0.46 to 0.19 V for 0.1 mM to 1 M KCl concentration range. This developed chemical-free process of LG-CNTFET array fabrication is simple, inexpensive, rapid having a commercial scope and thus opens a new realm of scalable realization of various biosensors.

A One-Step Chemical Strategy for the Formation of Carbon Nanotube Junctions in Aqueous Solution: Reaction of DNA-Wrapped Carbon Nanotubes with Diazonium Salts

A single-step chemical strategy allows the formation of single-walled carbon nanotube (SWCNT) molecular junctions in aqueous solution. SWCNTs were first wrapped with DNA to be water soluble and solution processable. Diazonium salts, which have been shown to react spontaneously with carbon nanotubes in water at room temperature, were then employed to covalently link SWCNT segments. The DNA wrapping of the nanotubes acted as a protective layer that limits the functionalization predominantly to the nanotube terminal ends, therefore allowing the assembly of linear SWCNT junctions. Upon increasing the concentration of the linker, we observed first the formation of side-to-end junctions, and eventually the assembly, through side-to-side interactions, of SWCNTs into bundles. This approach demonstrates the possibility of tuning the formation of linear and branched carbon nanotube junctions that in turn is of importance for the sustainable fabrication of solution-processable CNT-based nanoscale systems and devices.