Molecularly imprinted nanopores for multiplexed sensing, release, and in-edge computing

D. Garoli; A. Douaki; S. Weng; S. Dante; N. Nakatsuka et al. 

In nanopore technology, the development of multiplexed detection and release platforms with high spatial and temporal resolution remains a significant challenge due to the difficulty in distinguishing signals originating from different nanopores in a single chip. In this work, we present a solid-state nanopore system functionalized with molecularly imprinted polymers (MIPs) for the selective detection and controlled release of neurotransmitters. We designed a nanopore array where each nanopore is functionalized with a specific MIP able to recognize specific neurotransmitters (dopamine, gamma-aminobutyric acid, and histamine, respectively). The platform demonstrated high performance in terms of sensitivity, selectivity, recovery, and stability. Multiplexed detection with high spatiotemporal resolution “110 ms / 3 µm” was achieved by specifically depositing MIPs and conductive hydrogels on different nanopores prepared on a single solid-state membrane. The different functionalization of the nanopores prevented signal cross-talk, thereby enabling simultaneous detection and release of multiple neurotransmitters. Finally, we demonstrated computing with different logic gates and in-edge computing. This nanopore platform represents a novel approach towards hybrid solid-state nanopores able to perform real-time multiplex detection, controlled biomolecule release, and ionic logic computing, addressing key challenges in neurochemical sensing and bio-computation.

Spatially Controlled 3‐D Multiplexed Aptamer Patterning in Hydrogels

K. Roost; A. Stuber; K. Wei; M. de Lapeyrière; K. Yang et al. 

The integration of bioreceptors with biocompatible substrates is crucial for advancing in vitro microphysiological systems used in disease modeling, drug screening, and biological research. Expanding spatial control over 3‐D bioreceptor patterning enables localized analyte detection, targeted molecular release, and selective sequestration. This study presents strategies for high‐resolution, multiplexed aptamer patterning within hydrogels, achieving the smallest 3‐D aptamer features reported to date (≈2 µm). Aptamers, synthetically engineered single‐stranded DNA or RNA, offer small size, high target specificity, and ease of chemical modification for covalent hydrogel integration. As a proof of concept, two DNA‐based aptamers targeting serotonin and dopamine were immobilized in a norbornene‐functionalized polyvinyl alcohol hydrogel. Systematic evaluation of UV photopatterning, digital light processing, and two‐photon polymerization enabled multiplexed, 3‐D aptamer patterns with micron‐scale resolution. This work establishes a framework for spatially resolved aptamer localization within 3‐D hydrogels, which is particularly important for biosensing in complex in vitro environments, where referencing specific binding requires precise positioning of control DNA near specific aptamers. These advances in spatially controlled aptamer functionalization open new possibilities for engineering modular biointerfaces.

Interfacing with the Brain: How Nanotechnology Can Contribute

A. A. A. Ahmed; N. Alegret; B. Almeida; R. Alvarez-Puebla; A. M. Andrews et al. 

Interfacing artificial devices with the human brain is the central goal of neurotechnology. Yet, our imaginations are often limited by currently available paradigms and technologies. Suggestions for brain-machine interfaces have changed over time, along with the available technology. Mechanical levers and cable winches were used to move parts of the brain during the mechanical age. Sophisticated electronic wiring and remote control have arisen during the electronic age, ultimately leading to plug-and-play computer interfaces. Nonetheless, our brains are so complex that these visions, until recently, largely remained unreachable dreams. The general problem, thus far, is that most of our technology is mechanically and/or electrically engineered, whereas the brain is a living, dynamic entity. As a result, these worlds are difficult to interface with one another. Nanotechnology, which encompasses engineered solid-state objects and integrated circuits, excels at small length scales of single to a few hundred nanometers and, thus, matches the sizes of biomolecules, biomolecular assemblies, and parts of cells. Consequently, we envision nanomaterials and nanotools as opportunities to interface with the brain in alternative ways. Here, we review the existing literature on the use of nanotechnology in brain-machine interfaces and look forward in discussing perspectives and limitations based on the authors’ expertise across a range of complementary disciplines-from neuroscience, engineering, physics, and chemistry to biology and medicine, computer science and mathematics, and social science and jurisprudence. We focus on nanotechnology but also include information from related fields when useful and complementary.

A mussel-inspired cold-water fish gelatin adhesive for surface endothelialization

T. Hammer; A. Abukar; A. Stuber; N. Nakatsuka; W. Wang et al. 

A cold water-fish gelatin-based biopolymeric adhesive shows the potential in promoting surface endothelialization of cardiovascular device surfaces.

Aptamer-Functionalized Interface Nanopores Enable Amino Acid-Specific Peptide Detection

T. Schlotter; T. Kloter; J. Hengsteler; K. Yang; L. Zhan et al. 

Single-molecule proteomics based on nanopore technology has made significant advances in recent years. However, to achieve nanopore sensing with single amino acid resolution, several bottlenecks must be tackled: controlling nanopore sizes with nanoscale precision and slowing molecular translocation events. Herein, we address these challenges by integrating amino acid-specific DNA aptamers into interface nanopores with dynamically tunable pore sizes. A phenylalanine aptamer was used as a proof-of-concept: aptamer recognition of phenylalanine moieties led to the retention of specific peptides, slowing translocation speeds. Importantly, while phenylalanine aptamers were isolated against the free amino acid, the aptamers were determined to recognize the combination of the benzyl or phenyl and the carbonyl group in the peptide backbone, enabling binding to specific phenylalanine-containing peptides. We decoupled specific binding between aptamers and phenylalanine-containing peptides from nonspecific interactions (e.g., electrostatics and hydrophobic interactions) using optical waveguide lightmode spectroscopy. Aptamer-modified interface nanopores differentiated peptides containing phenylalanine vs. control peptides with structurally similar amino acids (i.e., tyrosine and tryptophan). When the duration of aptamer–target interactions inside the nanopore were prolonged by lowering the applied voltage, discrete ionic current levels with repetitive motifs were observed. Such reoccurring signatures in the measured signal suggest that the proposed method has the possibility to resolve amino acid-specific aptamer recognition, a step toward single-molecule proteomics.

Solid-State Nanopores for Biomolecular Analysis and Detection

Aptamer Renaissance for Neurochemical Biosensing

A. Stuber; N. Nakatsuka 

Unraveling the complexities of brain function, which is crucial for advancing human health, remains a grand challenge. This endeavor demands precise monitoring of small molecules such as neurotransmitters, the chemical messengers in the brain. In this Perspective, we explore the potential of aptamers, selective synthetic bioreceptors integrated into electronic affinity platforms to address limitations in neurochemical biosensing. We emphasize the importance of characterizing aptamer thermodynamics and target binding to realize functional biosensors in biological systems. We focus on two label-free affinity platforms spanning the micro- to nanoscale: field-effect transistors and nanopores. Integration of well-characterized structure-switching aptamers overcame nonspecific binding, a challenge that has hindered the translation of biosensors from the lab to the clinic. In a transformative era driven by neuroscience breakthroughs, technological innovations, and multidisciplinary collaborations, an aptamer renaissance holds the potential to bridge technological gaps and reshape the landscape of diagnostics and neuroscience.

Modular Plasmonic Nanopore for Opto-Thermal Gating

A. Douaki; S. Weng; G. Lanzavecchia; A. Sapunova; A. Stuber et al. 

Solid-state nanopore gating inspired by biological ion channels is gaining increasing traction due to a large range of applications in biosensing and drug delivery. Integration of stimuli-responsive molecules such as poly(N-isopropylacrylamide) (PNIPAM) inside nanopores can enable temperature-dependent gating, which so far has only been demonstrated using external heaters. In this work, plasmonic resonators are combined inside the nanopore architecture with PNIPAM to enable optical gating of individual or multiple nanopores with micrometer resolution and a switching speed of a few milliseconds by thermo-plasmonics effects. A temperature change of 40 kelvin per millisecond is achieved and demonstrates the efficacy of this method using nanopore ionic conductivity measurements that enable selective activation of individual nanopores in an array. Moreover, the selective gating of specific nanopores in an array can set distinct ionic conductance levels: low, medium, and high (i.e., “0,” “1,” and “2”), which can be exploited for logical gating with optical signal control. Such selective optical gating in nanopore arrays marks a breakthrough in nanofluidics, as it paves the way toward smart devices that offer multifunctional applications including biosensing, targeted drug delivery, and fluidic mixing.

Single-Step Functionalization Strategy of Graphene Microtransistor Array with Chemically Modified Aptamers for Biosensing Applications

S. Brosel-Oliu; G. Rius; A. Aviño; N. Nakatsuka; X. Illa et al. 

Graphene solution-gated field-effect transistors (gSGFETs) offer high potential for chemical and biochemical sensing applications. Among the current trends to improve this technology, the functionalization processes are gaining relevance for its crucial impact on biosensing performance. Previous efforts are focused on simplifying the attachment procedure from standard multi-step to single-step strategies, but they still suffer from overreaction, and impurity issues and are limited to a particular ligand. Herein, a novel strategy for single-step immobilization of chemically modified aptamers with fluorenylmethyl and acridine moieties, based on a straightforward synthetic route to overcome the aforementioned limitations is presented. This approach is benchmarked versus a standard multi-step strategy using thrombin as detection model. In order to assess the reliability of the functionalization strategies 48-gSGFETs arrays are employed to acquire large datasets with multiple replicas. Graphene surface characterization demonstrates robust and higher efficiency in the chemical coupling of the aptamers with the single-step strategy, while the electrical response evaluation validates the sensing capability, allowing to implement different alternatives for data analysis and reduce the sensing variability. In this work, a new tool capable of overcome the functionalization challenges of graphene surfaces is provided, paving the way toward the standardization of gSGFETs for biosensing purposes.

Interfacing aptamer-modified nanopipettes with neuronal media and ex vivo brain tissue

A. Stuber; A. Cavaccini; A. Manole; A. Burdina; Y. Massoud et al. 

Aptamer-functionalized biosensors exhibit high selectivity for monitoring neurotransmitters in complex environments. We translated nanoscale aptamer-modified nanopipette sensors to detect endogenous dopamine release in vitro and ex vivo. These sensors employ quartz nanopipettes with nanoscale pores (ca. 10 nm diameter) that are functionalized with aptamers that enable the selective capture of dopamine through target-specific conformational changes. The dynamic behavior of aptamer structures upon dopamine binding leads to the rearrangement of surface charge within the nanopore, resulting in measurable changes in ionic current. To assess sensor performance in real time, we designed a fluidic platform to characterize the temporal dynamics of nanopipette sensors. We then conducted differential biosensing by deploying control sensors modified with nonspecific DNA alongside dopamine-specific sensors in biological milieu. Our results confirm the functionality of aptamer-modified nanopipettes for direct measurements in undiluted complex fluids, specifically in the culture media of human-induced pluripotent stem cell-derived dopaminergic neurons. Moreover, sensor implantation and repeated measurements in acute brain slices was possible, likely owing to the protected sensing area inside nanoscale DNA-filled orifices, minimizing exposure to nonspecific interferents and preventing clogging. Further, differential recordings of endogenous dopamine released through electrical stimulation in the dorsolateral striatum demonstrate the potential of aptamer-modified nanopipettes for ex vivo recordings with unprecedented spatial resolution and reduced tissue damage.

Theoretical analysis of divalent cation effects on aptamer recognition of neurotransmitter targets

A. Douaki; A. Stuber; J. Hengsteler; D. Momotenko; D. Rogers et al. 

Aptamer-based sensing of small molecules such as dopamine and serotonin in the brain, requires characterization of the specific aptamer sequences in solutions mimicking the in vivo environment with physiological ionic concentrations. In particular, divalent cations (Mg2+ and Ca2+) present in brain fluid, have been shown to affect the conformational dynamics of aptamers upon target recognition. Thus, for biosensors that transduce aptamer structure switching as the signal response, it is critical to interrogate the influence of divalent cations on each unique aptamer sequence. Herein, we demonstrate the potential of molecular dynamics (MD) simulations to predict the behaviour of dopamine and serotonin aptamers on sensor surfaces. The simulations enable molecular-level visualization of aptamer conformational changes that, in some cases, are significantly influenced by divalent cations. The correlations of theoretical simulations with experimental findings validate the potential for MD simulations to predict aptamer-specific behaviors on biosensors.

Driving electrochemical reactions at the microscale using CMOS microelectrode arrays

J. Duru; A. Rüfenacht; J. Löhle; M. Pozzi; C. Forró et al. 

Precise control of pH values at electrode interfaces enables the systematic investigation of pH-dependent processes by electrochemical means. In this work, we employed high-density complementary metal-oxide-semiconductor (CMOS) microelectrode arrays (MEAs) as miniaturized systems to induce and confine electrochemical reactions in areas corresponding to the pitch of single electrodes (17.5 μm). First, we present a strategy for generating localized pH patterns on the surface of the CMOS MEA with unprecedented spatial resolution. Leveraging the versatile routing capabilities of the switch matrix beneath the CMOS MEA, we created arbitrary combinations of anodic and cathodic electrodes and hence pH patterns. Moreover, we utilized the system to produce polymeric surface patterns by additive and subtractive methods. For additive patterning, we controlled the in situ formation of polydopamine at the microelectrode surface through oxidation of free dopamine above a threshold pH > 8.5. For subtractive patterning, we removed cell-adhesive poly-L-lysine from the electrode surface and backfilled the voids with antifouling polymers. Such polymers were chosen to provide a proof-of-concept application of controlling neuronal growth via electrochemically-induced patterns on the CMOS MEA surface. Importantly, our platform is compatible with commercially available high-density MEAs and requires no custom equipment, rendering the findings generalizable and accessible.

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

A. Stuber; A. Douaki; J. Hengsteler; D. Buckingham; D. Momotenko et al. 

Aptamers that undergo conformational changes upon small-molecule recognition have been shown to gate the ionic flux through nanopores by rearranging the charge density within the aptamer-occluded orifice. However, mechanistic insight into such systems where biomolecular interactions are confined in nanoscale spaces is limited. To understand the fundamental mechanisms that facilitate the detection of small-molecule analytes inside structure-switching aptamer-modified nanopores, we correlated experimental observations to theoretical models. We developed a dopamine aptamer-functionalized nanopore sensor with femtomolar detection limits and compared the sensing behavior with that of a serotonin sensor fabricated with the same methodology. When these two neurotransmitters with comparable mass and equal charge were detected, the sensors showed an opposite electronic behavior. This distinctive phenomenon was extensively studied using complementary experimental techniques such as quartz crystal microbalance with dissipation monitoring, in combination with theoretical assessment by the finite element method and molecular dynamic simulations. Taken together, our studies demonstrate that the sensing behavior of aptamer-modified nanopores in detecting specific small-molecule analytes correlates with the structure-switching mechanisms of individual aptamers. We believe that such investigations not only improve our understanding of the complex interactions occurring in confined nanoscale environments but will also drive further innovations in biomimetic nanopore technologies.

Polymeric integration of structure-switching aptamers on transistors for histamine sensing

B. Shkodra; M. Petrelli; K-A. Yang; A. Tagliaferri; P. Lugli et al. 

Aptamers that undergo large conformational rearrangements at the surface of electrolyte-gated field-effect transistor (EG-FETs)-based biosensors can overcome the Debye length limitation in physiological high ionic strength environments. For the sensitive detection of small molecules, carbon nanotubes (CNTs) that approach the dimensions of analytes of interest are promising channel materials for EG-FETs. However, functionalization of CNTs with bioreceptors using frequently reported surface modification strategies (e.g., π–π stacking), requires highly pristine CNTs deposited through methods that are incompatible with low-cost fabrication methods and flexible substrates. In this work, we explore alternative non-covalent surface chemistry to functionalize CNTs with aptamers. We harnessed the adhesive properties of poly-D-lysine (PDL), to coat the surface of CNTs and then grafted histamine-specific DNA aptamers electrostatically in close proximity to the CNT semiconducting channel. The layer-by-layer assembly was monitored by complementary techniques such as X-ray photoelectron spectroscopy, optical waveguide lightmode spectroscopy, and fluorescence microscopy. Surface characterization confirmed histamine aptamer integration into PDL-coated CNTs and revealed ∼5-fold higher aptamer surface coverage when using CNT networks with high surface areas. Specific aptamers assembled on EG-CNTFETs enabled histamine detection in undiluted high ionic strength solutions in the concentration range of 10 nM to 100 μM. Sequence specificity was demonstrated via parallel measurements with control EG-CNTFETs functionalized with scrambled DNA. Histamine aptamer-modified EG-CNTFETs showed high selectivity vs. histidine, the closest structural analog and precursor to histamine. Taken together, these results implied that target-specific aptamer conformational changes on CNTs facilitate signal transduction, which was corroborated by circular dichroism spectroscopy. Our work suggests that layer-by-layer polymer chemistry enables integration of structure-switching aptamers into flexible EG-CNTFETs for small-molecule biosensing.

Aptamer-functionalized capacitive biosensors

S. Weaver; M. Mohammadi; N. Nakatsuka 

The growing use of aptamers as target recognition elements in label-free biosensing necessitates corresponding transducers that can be used in relevant environments. While popular in many fields, capacitive sensors have seen relatively little, but growing use in conjunction with aptamers for sensing diverse targets. Few reports have shown physiologically relevant sensitivity in laboratory conditions and a cohesive picture on how target capture modifies the measured capacitance has been lacking. In this review, we assess the current state of the field in three areas: small molecule, protein, and cell sensing. We critically analyze the proposed hypotheses on how aptamer-target capture modifies the capacitance, as many mechanistic postulations appear to conflict between published works. As the field matures, we encourage future works to investigate individual aptamer-target interactions and to interrogate the physical mechanisms leading to measured changes in capacitance. To this point, we provide recommendations on best practices for developing aptasensors with a particular focus on considerations for biosensing in clinical settings.

Aptamer-modified biosensors to visualize neurotransmitter flux

C. Moraldo; E. Vuille-Dit-Bille; B. Shkodra; T. Kloter; N. Nakatsuka 

Chemical biosensors with the capacity to continuously monitor various neurotransmitter dynamics can be powerful tools to understand complex signaling pathways in the brain. However, in vivo detection of neurochemicals is challenging for many reasons such as the rapid release and clearance of neurotransmitters in the extracellular space, or the low target analyte concentrations in a sea of interfering biomolecules. Biosensing platforms with adequate spatiotemporal resolution coupled to specific and selective receptors termed aptamers, demonstrate high potential to tackle such challenges. Herein, we review existing literature in this field. We first discuss nanoparticle-based systems, which have a simple in vitro implementation and easily interpretable results. We then examine methods employing near-infrared detection for deeper tissue imaging, hence easier translation to in vivo implementation. We conclude by reviewing live cell imaging of neurotransmitter release via aptamer-modified platforms. For each of these sensors, we discuss the associated challenges for translation to real-time in vivo neurochemical imaging. Realization of in vivo biosensors for neurotransmitters will drive future development of early prevention strategies, treatments, and therapeutics for psychiatric and neurodegenerative diseases.

Aptamer-field-effect transistors for small-molecule sensing in complex environments

Electrolyte-gated carbon nanotube field-effect transistorbased biosensors: Principles and applications

B. Shkodra; M. Petrelli; M. Angeli; D. Garoli; N. Nakatsuka et al. 

Nowadays, there is a high demand for sensitive and selective real-time analytical methods suitable for a wide range of applications, from personalized telemedicine, drug discovery, food safety, and quality control, to defense, security, as well as environmental monitoring. Biosensors are analytical devices able to detect bio-chemical analytes (e.g., neurotransmitters, cancer biomarkers, bio-molecules, and ions), through the combination of a bio-recognition element and a bio-transduction device. The use of customized bio-recognition elements such as enzymes, antibodies, aptamers, and ion-selective membranes facilitates achieving high selectivity. Among the different bio-transduction devices currently available, electrolyte-gated field-effect transistors, in which the dielectric is represented by an ionic liquid buffer solution containing the targeted analyte, are gaining increasing attention. Indeed, these biotransduction devices are characterized by superior electronic properties and intrinsic signal amplification that allow the detection of a wide range of biomolecules with high sensitivity (down to pM concentration). A promising semiconducting material for bio-transduction devices is represented by carbon nanotubes, due to their unique electrical properties, nanosize, bio-compatibility, and their simple low-cost processability. This work provides a comprehensive and critical review of electrolyte-gated carbon nanotube field-effect transistor-based biosensors. First, an introduction to these bio-sensing devices is given. Next, the device configurations and operating principles are presented, and the most used materials and processes are reviewed with a particular focus on carbon nanotubes as the active material. Subsequently, different functionalization strategies reported in the literature, based on enzymes, antibodies, aptamers, and ion-selective membranes, are analyzed critically. Finally, present issues and challenges faced in the area are investigated, the conclusions are drawn, and a perspective outlook over the field of bio-sensing technologies, in general, is provided.

Implantable aptamer–field-effect transistor neuroprobes for in vivo neurotransmitter monitoring

C. Zhao; K. Cheung; -w. Huang; H. Yang; N. Nakatsuka et al. 

While tools for monitoring in vivo electrophysiology have been extensively developed, neurochemical recording technologies remain limited. Nevertheless, chemical communication via neurotransmitters plays central roles in brain information processing. We developed implantable aptamer–field-effect transistor (FET) neuroprobes for monitoring neurotransmitters. Neuroprobes were fabricated using high-throughput microelectromechanical system (MEMS) technologies, where 150 probes with shanks of either 150- or 50-μm widths and thicknesses were fabricated on 4-inch Si wafers. Nanoscale FETs with ultrathin (~3 to 4 nm) In2O3 semiconductor films were prepared using sol-gel processing. The In2O3 surfaces were coupled with synthetic oligonucleotide receptors (aptamers) to recognize and to detect the neurotransmitter serotonin. Aptamer-FET neuroprobes enabled femtomolar serotonin detection limits in brain tissue with minimal biofouling. Stimulated serotonin release was detected in vivo. This study opens opportunities for integrated neural activity recordings at high spatiotemporal resolution by combining these aptamer-FET sensors with other types of Si-based implantable probes to advance our understanding of brain function.

KAT Ligation for Rapid and Facile Covalent Attachment of Biomolecules to Surfaces

A. Fracassi; A. Ray; N. Nakatsuka; C. Passiu; M. Tanriver et al. 

The efficient and bioorthogonal chemical ligation reaction between potassium acyltrifluoroborates (KATs) and hydroxylamines (HAs) was used for the surface functionalization of a self-assembled monolayer (SAM) with biomolecules. An alkane thioether molecule with one terminal KAT group (S-KAT) was synthesized and adsorbed onto a gold surface, placing a KAT group on the top of the monolayer (KAT-SAM). As an initial test case, an aqueous solution of a hydroxylamine (HA) derivative of poly(ethylene glycol) (PEG) (HA-PEG) was added to this KAT-SAM at room temperature to perform the surface KAT ligation. Quartz crystal microbalance with dissipation (QCM-D) monitoring confirmed the rapid attachment of the PEG moiety onto the SAM. By surface characterization methods such as contact angle and ellipsometry, the attachment of PEG layer was confirmed, and covalent amide-bond formation was established by X-ray photoelectron spectroscopy (XPS). In a proof-of-concept study, the applicability of this surface KAT ligation for the attachment of biomolecules to surfaces was tested using a model protein, green fluorescent protein (GFP). A GFP was chemically modified with an HA linker to synthesize HA-GFP and added to the KAT-SAM under aqueous dilute conditions. A rapid attachment of the GFP on the surface was observed in real time by QCM-D. Despite the fact that such biomolecules have a variety of unprotected functional groups within their structures, the surface KAT ligation proceeded rapidly in a chemoselective manner. Our results demonstrate the versatility of the KAT ligation for the covalent attachment of a variety of water-soluble molecules onto SAM surfaces under dilute and biocompatible conditions to form stable, natural amide bonds.

Nonspecific Binding—Fundamental Concepts and Consequences for Biosensing Applications

A. Frutiger; A. Tanno; S. Hwu; R. Tiefenauer; J. Vörös et al. 

Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.

Sensing serotonin secreted from human serotonergic neurons using aptamer-modified nanopipettes

N. Nakatsuka; K. Heard; A. Faillétaz; D. Momotenko; J. Vörös et al. 

The serotonergic system in the human brain modulates several physiological processes, and altered serotonergic neurotransmission has been implicated in the neuropathology of several psychiatric disorders. The study of serotonergic neurotransmission in psychiatry has long been restricted to animal models, but advances in cell reprogramming technology have enabled the generation of serotonergic neurons from patient-induced pluripotent stem cells (iPSCs). While iPSC-derived human serotonergic neurons offer the possibility to study serotonin (5-HT) release and uptake, particularly by 5-HT-modulating drugs such as selective serotonin reuptake inhibitors (SSRIs), a major limitation is the inability to reliably quantify 5-HT secreted from neurons in vitro. Herein, we address this technical gap via a novel sensing technology that couples 5-HT-specific DNA aptamers into nanopores (glass nanopipettes) with orifices of ~10 nm to detect 5-HT in complex neuronal culture medium with higher selectivity, sensitivity, and stability than existing methods. The 5-HT aptamers undergo conformational rearrangement upon target capture and serve as gatekeepers of ionic flux through the nanopipette opening. We generated human serotonergic neurons in vitro and detected secreted 5-HT using aptamer-coated nanopipettes in a low nanomolar range, with the possibility of detecting significantly lower (picomolar) concentrations. Furthermore, as a proof of concept, we treated human serotonergic neurons in vitro with the SSRI citalopram and detected a significant increase in extracellular 5-HT using the aptamer-modified nanopipettes. We demonstrate the utility of such methods for 5-HT detection, raising the possibility of fast quantification of neurotransmitters secreted from patient-derived live neuronal cells.

Aptamer Conformational Change Enables Serotonin Biosensing with Nanopipettes

N. Nakatsuka; A. Faillétaz; D. Eggemann; C. Forró; J. Vörös et al. 

We report artificial nanopores in the form of quartz nanopipettes with ca. 10 nm orifices functionalized with molecular recognition elements termed aptamers that reversibly recognize serotonin with high specificity and selectivity. Nanoscale confinement of ion fluxes, analyte-specific aptamer conformational changes, and related surface charge variations enable serotonin sensing. We demonstrate detection of physiologically relevant serotonin amounts in complex environments such as neurobasal media, in which neurons are cultured in vitro. In addition to sensing in physiologically relevant matrices with high sensitivity (picomolar detection limits), we interrogate the detection mechanism via complementary techniques such as quartz crystal microbalance with dissipation monitoring and electrochemical impedance spectroscopy. Moreover, we provide a novel theoretical model for structure-switching aptamer-modified nanopipette systems that supports experimental findings. Validation of specific and selective small-molecule detection, in parallel with mechanistic investigations, demonstrates the potential of conformationally changing aptamer-modified nanopipettes as rapid, label-free, and translatable nanotools for diverse biological systems.

Divalent Cation Dependence Enhances Dopamine Aptamer Biosensing

N. Nakatsuka; J. Abendroth; K-A. Yang; A. M. Andrews 

Oligonucleotide receptors (aptamers), which change conformation upon target recognition, enable electronic biosensing under high ionic-strength conditions when coupled to field-effect transistors (FETs). Because highly negatively charged aptamer backbones are influenced by ion content and concentration, biosensor performance and target sensitivities were evaluated under application conditions. For a recently identified dopamine aptamer, physiological concentrations of Mg2+ and Ca2+ in artificial cerebrospinal fluid produced marked potentiation of dopamine FET-sensor responses. By comparison, divalent cation-associated signal amplification was not observed for FET sensors functionalized with a recently identified serotonin aptamer or a previously reported dopamine aptamer. Circular dichroism spectroscopy revealed Mg2+- and Ca2+-induced changes in target-associated secondary structure for the new dopamine aptamer, but not the serotonin aptamer nor the old dopamine aptamer. Thioflavin T displacement corroborated the Mg2+ dependence of the new dopamine aptamer for target detection. These findings imply allosteric binding interactions between divalent cations and dopamine for the new dopamine aptamer. Developing and testing sensors in ionic environments that reflect intended applications are best practices for identifying aptamer candidates with favorable attributes and elucidating sensing mechanisms.

Detecting DNA and RNA and Differentiating Single-Nucleotide Variations via Field-Effect Transistors

K. Cheung; J. Abendroth; N. Nakatsuka; B. Zhu; Y. Yang et al. 

We detect short oligonucleotides and distinguish between sequences that differ by a single base, using label-free, electronic field-effect transistors (FETs). Our sensing platform utilizes ultrathin-film indium oxide FETs chemically functionalized with single-stranded DNA (ssDNA). The ssDNA-functionalized semiconducting channels in FETs detect fully complementary DNA sequences and differentiate these sequences from those having different types and locations of single base-pair mismatches. Changes in charge associated with surface-bound ssDNA vs double-stranded DNA (dsDNA) alter FET channel conductance to enable detection due to differences in DNA duplex stability. We illustrate the capability of ssDNA-FETs to detect complementary RNA sequences and to distinguish from RNA sequences with single nucleotide variations. The development and implementation of electronic biosensors that rapidly and sensitively detect and differentiate oligonucleotides present new opportunities in the fields of disease diagnostics and precision medicine.

Phenylalanine Monitoring via Aptamer-Field-Effect Transistor Sensors

K. Cheung; K-A. Yang; N. Nakatsuka; C. Zhao; M. Ye et al. 

Determination of the amino acid phenylalanine is important for lifelong disease management in patients with phenylketonuria, a genetic disorder in which phenylalanine accumulates and persists at levels that alter brain development and cause permanent neurological damage and cognitive dysfunction. Recent approaches for treating phenylketonuria focus on injectable medications that efficiently break down phenylalanine but sometimes result in detrimentally low phenylalanine levels. We have identified new DNA aptamers for phenylalanine in two formats, initially as fluorescent sensors and then, incorporated with field-effect transistors (FETs). Aptamer-FET sensors detected phenylalanine over a wide range of concentrations (fM to mM). para-Chlorophenylalanine, which inhibits the enzyme that converts phenylalanine to tyrosine, was used to induce hyperphenylalaninemia during brain development in mice. Aptamer-FET sensors were specific for phenylalanine versus para-chlorophenylalanine and differentiated changes in mouse serum phenylalanine at levels expected in patients. Aptamer-FETs can be used to investigate models of hyperphenylalanemia in the presence of structurally related enzyme inhibitors, as well as naturally occurring amino acids. Nucleic acid-based receptors that discriminate phenylalanine analogs, some that differ by a single substituent, indicate a refined ability to identify aptamers with binding pockets tailored for high affinity and specificity. Aptamers of this type integrated into FETs enable rapid, electronic, label-free phenylalanine sensing.

Hierarchically Patterned Polydopamine-Containing Membranes for Periodontal Tissue Engineering

M. Hasani-Sadrabadi; P. Sarrion; N. Nakatsuka; T. Young; N. Taghdiri et al. 

Periodontitis is a common chronic inflammatory disease that affects tooth-supporting tissues. We engineer a multifunctional periodontal membrane for the guided tissue regeneration of lost periodontal tissues. The major drawback of current periodontal membranes is the lack of tissue regeneration properties. Here, a series of nanofibrous membranes based on poly(ε-caprolactone) with tunable biochemical and biophysical properties were developed for periodontal tissue regeneration. The engineered membranes were surface coated using biomimetic polydopamine to promote the adhesion of therapeutic proteins and cells. We demonstrate successful cellular localization on the surface of the engineered membrane by morphological patterning. Polydopamine accelerates osteogenic differentiation of dental-derived stem cells by promoting hydroxyapatite mineralization. Such multiscale designs can mimic the complex extracellular environment of periodontal tissue and serve as functional tissue constructs for periodontal regeneration. In a periodontal defect model in rats, our engineered periodontal membrane successfully promoted the regeneration of periodontal tissue and bone repair. Altogether, our data demonstrate that our biomimetic membranes have potential as protein/cell delivery platforms for periodontal tissue engineering.

Aptamer–field-effect transistors overcome Debye length limitations for small-molecule sensing

N. Nakatsuka; K-A. Yang; J. Abendroth; K. Cheung; X. Xu et al. 

Detection of analytes by means of field-effect transistors bearing ligand-specific receptors is fundamentally limited by the shielding created by the electrical double layer (the “Debye length” limitation). We detected small molecules under physiological high–ionic strength conditions by modifying printed ultrathin metal-oxide field-effect transistor arrays with deoxyribonucleotide aptamers selected to bind their targets adaptively. Target-induced conformational changes of negatively charged aptamer phosphodiester backbones in close proximity to semiconductor channels gated conductance in physiological buffers, resulting in highly sensitive detection. Sensing of charged and electroneutral targets (serotonin, dopamine, glucose, and sphingosine-1-phosphate) was enabled by specifically isolated aptameric stem-loop receptors.

Aptamer Recognition of Multiplexed Small-Molecule-Functionalized Substrates

N. Nakatsuka; H. Cao; S. Deshayes; A. Melkonian; A. Kasko et al. 

Aptamers are chemically synthesized oligonucleotides or peptides with molecular recognition capabilities. We investigated recognition of substrate-tethered small-molecule targets, using neurotransmitters as examples, and fluorescently labeled DNA aptamers. Substrate regions patterned via microfluidic channels with dopamine or   l-tryptophan were selectively recognized by previously identified dopamine or l-tryptophan aptamers, respectively. The on-substrate dissociation constant determined for the dopamine aptamer was comparable to, though, slightly greater than the previously determined solution dissociation constant. Using prefunctionalized neurotransmitter-conjugated oligo(ethylene glycol) alkanethiols and microfluidics patterning, we produced multiplexed substrates to capture and to sort aptamers. Substrates patterned with l-3,4-dihydroxyphenylalanine, l-threo-dihydroxyphenylserine, and l-5-hydroxytryptophan enabled comparison of the selectivity of the dopamine aptamer for different targets via simultaneous determination of in situ binding constants. Thus, beyond our previous demonstrations of recognition by protein binding partners (i.e., antibodies and G-protein-coupled receptors), strategically optimized small-molecule-functionalized substrates show selective recognition of nucleic acid binding partners. These substrates are useful for side-by-side target comparisons and future identification and characterization of novel aptamers targeting neurotransmitters or other important small molecules.

Small-Molecule Patterning via Prefunctionalized Alkanethiols

H. Cao; N. Nakatsuka; S. Deshayes; J. Abendroth; H. Yang et al. 

Interactions between small molecules and biomolecules are important physiologically and for biosensing, diagnostic, and therapeutic applications. To investigate these interactions, small molecules can be tethered to substrates through standard coupling chemistries. While convenient, these approaches co-opt one or more of the few small-molecule functional groups needed for biorecognition. Moreover, for multiplexing, individual probes require different surface functionalization chemistries, conditions, and/or protection/deprotection strategies. Thus, when placing multiple small molecules on surfaces, orthogonal chemistries are needed that preserve all functional groups and are sequentially compatible. Alternately, we approach high-fidelity small-molecule patterning by coupling small-molecule neurotransmitter precursors, as examples, to monodisperse asymmetric oligo(ethylene glycol)alkanethiols during synthesis and prior to self-assembly on Au substrates. We use chemical lift-off lithography to singly and doubly pattern substrates. Selective antibody recognition of prefunctionalized thiols was comparable to or better than recognition of small molecules functionalized to alkanethiols after surface assembly. These findings demonstrate that synthesis and patterning approaches that circumvent sequential surface conjugation chemistries enable biomolecule recognition and afford gateways to multiplexed small-molecule functionalized substrates.

Polyserotonin Nanoparticles as Multifunctional Materials for Biomedical Applications

N. Nakatsuka; M. Hasani-Sadrabadi; K. Cheung; T. Young; G. Bahlakeh et al. 

Serotonin-based nanoparticles represent a class of previously unexplored multifunctional nanoplatforms with potential biomedical applications. Serotonin, under basic conditions, self-assembles into monodisperse nanoparticles via autoxidation of serotonin monomers. To demonstrate potential applications of polyserotonin nanoparticles for cancer therapeutics, we show that these particles are biocompatible, exhibit photothermal effects when exposed to near-infrared radiation, and load the chemotherapeutic drug doxorubicin, releasing it contextually and responsively in specific microenvironments. Quantum mechanical and molecular dynamics simulations were performed to interrogate the interactions between surface-adsorbed drug molecules and polyserotonin nanoparticles. To investigate the potential of polyserotonin nanoparticles for in vivo targeting, we explored their nano–bio interfaces by conducting protein corona experiments. Polyserotonin nanoparticles had reduced surface–protein interactions under biological conditions compared to polydopamine nanoparticles, a similar polymer material widely investigated for related applications. These findings suggest that serotonin-based nanoparticles have advantages as drug-delivery platforms for synergistic chemo- and photothermal therapy associated with limited nonspecific interactions.

High-Affinity Nucleic-Acid-Based Receptors for Steroids

K-A. Yang; H. Chun; Y. Zhang; S. Pecic; N. Nakatsuka et al. 

Artificial receptors for hydrophobic molecules usually have moderate affinities and limited selectivities. We describe three new classes of high affinity hydrophobic receptors for nonaromatic steroids based on deoxyribonucleotides, obtained through five high stringency selections coupled with tailored counter-selections. The isolation of multiple classes of high affinity steroid receptors demonstrates the surprising breadth of moderately sized hydrophobic binding motifs (<40 nucleotides) available to natural nucleic acids. Studies of interactions with analogs indicate that two classes, four-way junctions and 4XGN motifs, comprise receptors with shapes that prevent binding of specific steroid conjugates used in counter-selections. Furthermore, they strongly prefer nonhydroxylated steroid cores, which is typical for hydrophobic receptors. The third new class accommodates hydroxyl groups in high-affinity, high-selectivity binding pockets, thus reversing the preferences of the first two classes. The high-affinity binding of aptamers to targets efficiently inhibits double-helix formation in the presence of the complementary oligonucleotides. The high affinity of some of these receptors and tailored elimination of binding through counter-selections ensures that these new aptamers will enable clinical chemistry applications.

Advancing Biocapture Substrates via Chemical Lift-Off Lithography

H. Cao; N. Nakatsuka; W-S. Liao; A. Serino; S. Cheunkar et al. 

Creating small-molecule-functionalized platforms for high-throughput screening or biosensing applications requires precise placement of probes on solid substrates and the ability to capture and to sort targets from multicomponent samples. Here, chemical lift-off lithography was used to fabricate large-area, high-fidelity patterns of small-molecule probes. Lift-off lithography enables biotin–streptavidin patterned recognition with feature sizes ranging from micrometers to below 30 nm. Subtractive patterning via lift-off facilitated insertion of a different type of molecule and, thus, multiplexed side-by-side placement of small-molecule probes such that binding partners were directed to cognate probes from solution. Small molecules mimicking endogenous neurotransmitters were patterned using lift-off lithography to capture native membrane-associated receptors. We characterized patterning of alkanethiols that self-assemble on Au having different terminal functional groups to expand the library of molecules amenable to lift-off lithography enabling a wide range of functionalization chemistries for use with this simple and versatile patterning method.

Analyzing Spin Selectivity in DNA-Mediated Charge Transfer via Fluorescence Microscopy

J. Abendroth; N. Nakatsuka; M. Ye; D. Kim; E. Fullerton et al. 

Understanding spin-selective interactions between electrons and chiral molecules is critical to elucidating the significance of electron spin in biological processes and to assessing the potential of chiral assemblies for organic spintronics applications. Here, we use fluorescence microscopy to visualize the effects of spin-dependent charge transport in self-assembled monolayers of double-stranded DNA on ferromagnetic substrates. Patterned DNA arrays provide background regions for every measurement to enable quantification of substrate magnetization-dependent fluorescence due to the chiral-induced spin selectivity effect. Fluorescence quenching of photoexcited dye molecules bound within DNA duplexes is dependent upon the rate of charge separation/recombination upon photoexcitation and the efficiency of DNA-mediated charge transfer to the surface. The latter process is modulated using an external magnetic field to switch the magnetization orientation of the underlying ferromagnetic substrates. We discuss our results in the context of the current literature on the chiral-induced spin selectivity effect across various systems.

Differentiating Siblings: The Case of Dopamine and Norepinephrine

N. Nakatsuka; A. M. Andrews 

Monitoring dopamine and norepinephrine (or other structurally similar neurotransmitters) in the same brain region necessitates selective sensing. In this Viewpoint, we highlight electrochemical and optical strategies for advancing simultaneous real-time measurements of dopamine and norepinephrine transmission. The potential for DNA aptamers as recognition elements in the context of field-effect transistor sensing for selective and simultaneous neurotransmitter monitoring in vivo is also discussed.

Neurochips Enable Nanoscale Devices for High-Resolution In Vivo Neurotransmitter Sensing

N. Nakatsuka; A. M. Andrews 

Controlled DNA Patterning by Chemical Lift-Off Lithography: Matrix Matters

H. Cao; N. Nakatsuka; A. Serino; W-S. Liao; S. Cheunkar et al. 

Nucleotide arrays require controlled surface densities and minimal nucleotide–substrate interactions to enable highly specific and efficient recognition by corresponding targets. We investigated chemical lift-off lithography with hydroxyl- and oligo(ethylene glycol)-terminated alkanethiol self-assembled monolayers as a means to produce substrates optimized for tethered DNA insertion into post-lift-off regions. Residual alkanethiols in the patterned regions after lift-off lithography enabled the formation of patterned DNA monolayers that favored hybridization with target DNA. Nucleotide densities were tunable by altering surface chemistries and alkanethiol ratios prior to lift-off. Lithography-induced conformational changes in oligo(ethylene glycol)-terminated monolayers hindered nucleotide insertion but could be used to advantage via mixed monolayers or double-lift-off lithography. Compared to thiolated DNA self-assembly alone or with alkanethiol backfilling, preparation of functional nucleotide arrays by chemical lift-off lithography enables superior hybridization efficiency and tunability.

Fabrication of High-Performance Ultrathin In2O3 Film Field-Effect Transistors and Biosensors Using Chemical Lift-Off Lithography

J. Kim; Y. S. Rim; H. Chen; H. Cao; N. Nakatsuka et al. 

We demonstrate straightforward fabrication of highly sensitive biosensor arrays based on field-effect transistors, using an efficient high-throughput, large-area patterning process. Chemical lift-off lithography is used to construct field-effect transistor arrays with high spatial precision suitable for the fabrication of both micrometer- and nanometer-scale devices. Sol–gel processing is used to deposit ultrathin (∼4 nm) In2O3 films as semiconducting channel layers. The aqueous sol–gel process produces uniform In2O3 coatings with thicknesses of a few nanometers over large areas through simple spin-coating, and only low-temperature thermal annealing of the coatings is required. The ultrathin In2O3 enables construction of highly sensitive and selective biosensors through immobilization of specific aptamers to the channel surface; the ability to detect subnanomolar concentrations of dopamine is demonstrated.