Lifetime of glass nanopores in a PDMS chip for single-molecule sensing

Alawami, Mohammed F.; Bošković, Filip; Zhu, Jinbo; Chen, Kaikai; Sandler, Sarah E.; Keyser, Ulrich F.

doi:10.1016/j.isci.2022.104191

Cited by 7 publications

(7 citation statements)

References 23 publications

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“…Prior to storage or experimental use, the aptamer solution was removed and the sensors were rinsed three-fold with PBS. Nanopipettes were stored filled with Milli-Q water to reduce etching of the quartz 36 and were stored at 4 °C in high humidity environments to prevent solution evaporation, which may lead to nanoscale tip breakage upon salt crystal formation. Filling and emptying of the nanopipettes was enabled by MicroFil syringe tips (World Precision Instruments, Sarasota, FL).…”

Section: Methodsmentioning

confidence: 99%

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

Stuber

Douaki

Hengsteler

et al. 2023

Preprint

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Aptamers that undergo conformational changes upon small molecule recognition have been shown to gate the ionic flux through nanopores by rearranging charge density within the aptamer-occluded orifice. However, mechanistic insight into such systems where biomolecular interactions are confined in nanoscale spaces, is limited. To shed light on 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 novel dopamine aptamerfunctionalized nanopore sensor with femtomolar detection limits and compared the sensing behavior with a serotonin sensor fabricated with the same methodology. When sensing these two neurotransmitters with comparable mass and equal charge, 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 highly sensitive aptamer-modified nanopores correlates with the structure-switching mechanisms unique to the selected aptamers targeting specific small-molecule analytes. 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.

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Section: Methodsmentioning

confidence: 99%

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

Stuber

Douaki

Hengsteler

et al. 2023

Preprint

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“…In ex-vivo measurements, hardware limitations only permitted voltage cycling between −0.2 and +0.2 V. However, the continuous renewal of solution via flow facilitated the reset of the sensors. To increase the longevity of the aptamer-functionalized nanopipettes, the sensors were rinsed, filled, then stored with Milli-Q water to reduce etching of the quartz . Sensors were stored in high humidity environments to prevent evaporation, which could lead to a buffer crystal formation and breakage of the nanoscale tip.…”

Section: Methodsmentioning

confidence: 99%

“…To increase the longevity of the aptamer-functionalized nanopipettes, the sensors were rinsed, filled, then stored with Milli-Q water to reduce etching of the quartz. 52 Sensors were stored in high humidity environments to prevent evaporation, which could lead to a buffer crystal formation and breakage of the nanoscale tip. Nanopipettes were stored for reuse in centrifuge tubes filled with deionized water at 4 °C.…”

Section: Regeneration and Storage Of Aptamer-modified Nanopipettesmentioning

confidence: 99%

Interfacing Aptamer-Modified Nanopipettes with Neuronal Media and Ex Vivo Brain Tissue

Stuber,

Cavaccini,

Manole

et al. 2023

ACS Meas. Sci. Au

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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.

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Section: Preparation and Sensing Performance Of G-nanoporesmentioning

confidence: 99%

“…Alawami et al used laserassisted capillary traction to prepare 11−18 nm quartz Gnanopore biosensing platforms (Figure 4e), which were repeatedly used for up to 19 weeks as confirmed by several studies. 67 Due to the simple and fast preparation, adjustable pore size, and high reproducibility, the G-nanopore sensing platforms are promising for single molecule and single cell biosensing detections.…”

Section: Acsmentioning

confidence: 99%

Glass Capillary-Based Nanopores for Single Molecule/Single Cell Detection

Guan

Chen

et al. 2023

ACS Sens.

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A glass capillary-based nanopore (G-nanopore), due to its tapered tip, easy tunability in orifice size, and especially its flexible surface modifications that can be tailored to effectively capture and enhance the ionic current signal of single entities (single molecules, single cells, and single particles), offers a powerful and nanoconfined sensing platform for diverse biological measurements of single cells and single molecules. Compared with other artificial two-dimensional solid-state nanopores, its conical tip and high spatial and temporal resolution characteristics facilitate noninvasive single molecule and selected area (subcellular) single cell detections (e.g., DNA mutations, highly expressed proteins, and small molecule markers that reflect the change characteristics of the tumor), as a small G-nanopore (≤100 nm) does negligible damage to cell functions and cell membrane integrity when inserted through the cell membrane. In this brief review, we summarize the preparation of G-nanopores and discuss the advantages of them as solid-state sensing platforms for single molecule and single cell detection applications as well as for cancer diagnosis and treatment applications. We also describe the current bottlenecks that limit the widespread use of G-nanopores in clinical applications and provide an outlook on future developments. The brief review will provide the reader with a quick survey of this field and facilitate the rapid development of a Gnanopore sensing platform for future tumor diagnosis and personalized medicine based on single-molecule/single-cell bioassay.

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Lifetime of glass nanopores in a PDMS chip for single-molecule sensing

Cited by 7 publications

References 23 publications

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

Interfacing Aptamer-Modified Nanopipettes with Neuronal Media and Ex Vivo Brain Tissue

Glass Capillary-Based Nanopores for Single Molecule/Single Cell Detection

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