Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

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.

Real-Time Monitoring of Neurotransmitters in the Brain of Living Animals

Neurotransmitters, as important chemical small molecules, perform the function of neural signal transmission from cell to cell. Excess concentrations of neurotransmitters are often closely associated with brain diseases, such as Alzheimer's disease, depression, schizophrenia, and Parkinson's disease. On the other hand, the release of neurotransmitters under the induced stimulation indicates the occurrence of reward-related behaviors, including food and drug addiction. Therefore, to understand the physiological and pathological functions of neurotransmitters, especially in complex environments of the living brain, it is urgent to develop effective tools to monitor their dynamics with high sensitivity and specificity. Over the past 30 years, significant advances in electrochemical sensors and optical probes have brought new possibilities for studying neurons and neural circuits by monitoring the changes in neurotransmitters. This Review focuses on the progress in the construction of sensors for in vivo analysis of neurotransmitters in the brain and summarizes current attempts to address key issues in the development of sensors with high selectivity, sensitivity, and stability. Combined with the latest advances in technologies and methods, several strategies for sensor construction are provided for recording chemical signal changes in the complex environment of the brain.

Effects of Nucleic Acid Structural Heterogeneity on the Electrochemistry of Tethered Redox Molecules

The cation condensation-induced collapse of electrode-bound nucleic acids and the resulting change in the electrochemical signal is a useful tool to predict the structure and redox probe location of heterogeneous structures of surface-tethered DNA probes─a common architecture employed in the development of electrochemical sensors. In this paper, we measure the faradaic current of an appended redox molecule at the 3' position of the nucleic acid using cyclic voltammetry before and after nucleic acid collapse for various nucleic acid architectures and heterogeneous mixtures on the same electrode surface. The voltammetric peak current change with collapse correlates with the proximity of the redox molecules from the surface. For stem-loop probes, the terminal methylene blue is initially held closer to the surface, such that inducing collapse, by reducing the dielectric permittivity of the interrogation solution, results in a ∼30% increase in current. However, when incorporating pseudoknot probes that hold methylene blue further away from the electrode surface, the current change is much larger (∼120%), indicating a larger conformation change. Upon a 50:50 ratio of the two, we observe a change in current that relates to the ratiometric distribution of the probe used to make the surfaces. Additionally, using cyclic voltammetry, we find that the change between diffusion-limited and diffusion-independent peak currents is dependent upon the distinct structural characteristics of DNA probes on the surface (stem-loop or pseudoknot), as well as the ratios of different DNA probes on the surface. Thus, we demonstrate that the heterogeneous nature of DNA probes governs the corresponding electrochemical signals, which can lead to a better understanding on how to predict the structures of functional nucleic acids on electrode surfaces and how this affects surface-to-surface variability and electrochemical response.

RE-SELEX: restriction enzyme-based evolution of structure-switching aptamer biosensors

Aptamers are widely employed as recognition elements in small molecule biosensors due to their ability to recognize small molecule targets with high affinity and selectivity. Structure-switching aptamers are particularly promising for biosensing applications because target-induced conformational change can be directly linked to a functional output. However, traditional evolution methods do not select for the significant conformational change needed to create structure-switching biosensors. Modified selection methods have been described to select for structure-switching architectures, but these remain limited by the need for immobilization. Herein we describe the first homogenous, structure-switching aptamer selection that directly reports on biosensor capacity for the target. We exploit the activity of restriction enzymes to isolate aptamer candidates that undergo target-induced displacement of a short complementary strand. As an initial demonstration of the utility of this approach, we performed selection against kanamycin A. Four enriched candidate sequences were successfully characterized as structure-switching biosensors for detection of kanamycin A. Optimization of biosensor conditions afforded facile detection of kanamycin A (90 μM to 10 mM) with high selectivity over three other aminoglycosides. This research demonstrates a general method to directly select for structure-switching biosensors and can be applied to a broad range of small-molecule targets.