The interactions between DNA nanostructures and cells: A critical overview from a cell biology perspective

Frtús, Adam; Smolková, Barbora; Uzhytchak, Mariia; Lunová, Mariia; Jirsa, M; Henry, Skylar J.W.; Dejneka, Alexandr; Stephanopoulos, Nicholas; Lunov, Oleg

doi:10.1016/j.actbio.2022.04.046

Cited by 16 publications

(18 citation statements)

References 197 publications

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“…Self-assembled synthetic membrane channels are particularly attractive due to their ease of fabrication 25 . To this end, Watson-Crick pairing based hybridization of single-stranded DNA (ssDNA) can rationally and in a bottom-up manner design self-assembled DNA origami structures 26 that mimic membrane proteins with sophisticated architectures [27][28][29][30] and varied functionalities [31][32][33] . Here, we merge synthetic self-assembled DNA nanopores based ion-channels with H + selective Pd-based bioprotonic contacts to create a biotic-abiotic device that records and modulates H + currents traversing across the bilayer membrane (Fig.…”

Section: Mainmentioning

confidence: 99%

DNA nanopores as artificial membrane channels for origami-based bioelectronics

Luo

Manda

Park

et al. 2023

Preprint

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SummaryBiological membrane channels mediate information exchange between cells and facilitate molecular recognition1-4. While tuning the shape and function of membrane channels for precision molecular sensing via de-novo routes is complex, an even more significant challenge is interfacing membrane channels with electronic devices for signal readout5-8. This challenge at the biotic-abiotic interface results in low efficiency of information transfer - one of the major barriers to the continued development of high-performance bioelectronic devices9. To this end, we integrate membrane spanning DNA nanopores with bioprotonic contacts to create programmable, modular, and efficient artificial ion-channel interfaces that resolve the ‘iono-electronic’ disparity between the biotic environment and electronics. Through simulations and experiments, we show that cholesterol modified DNA nanopores spontaneously and with remarkable affinity span the lipid bilayer formed over the planar bio-protonic electrode surface and mediate proton transport across the bilayer. Using the ability to easily modify DNA nanostructures, we illustrate that this bioelectronic device can be programmed for electronic recognition of biomolecular signals such as presence of Streptavidin, without disrupting the native environment of the biomolecule. We anticipate this robust biotic-abiotic interface will allow facile electronic measurement of inter-cellular ionic communication and also open the door for active control of cell behavior through externally controlled selective gating of the channels.

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Section: Mainmentioning

confidence: 99%

DNA nanopores as artificial membrane channels for origami-based bioelectronics

Luo

Manda

Park

et al. 2023

Preprint

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“…[11d] As main components of cell membrane system, the transmembrane molecules and lipid bilayers enable resistance to non-specific protein absorption in biofluid. [52] Meanwhile, the densely lipid bilayers also can avoid intercellular adhesion at the special interface. This phenomenon provides a better idea to improve the selectivity of biosensors.…”

Section: Engineering Of Cell Surface With Tdns For Biosensingmentioning

confidence: 99%

“…The cell surface is the interface for cells communicating with outside environment [11d] . As main components of cell membrane system, the transmembrane molecules and lipid bilayers enable resistance to non‐specific protein absorption in biofluid [52] . Meanwhile, the densely lipid bilayers also can avoid intercellular adhesion at the special interface.…”

Section: Engineering Of Interfaces With Tdns For Biosensing Applicationsmentioning

confidence: 99%

Engineering of Interfaces with Tetrahedra DNA Nanostructures for Biosensing Applications

et al. 2022

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The probe‐target interactions in the interfaces are significantly critical to biosensing. However, the disordered arrangement of probes and nonspecific adsorption of proteins in the biosensing interfaces for conventional biosensors often restricted the accessibility and recognition efficiency of probes towards targets, leading to poor detection performances (e. g., sensitivity and selectivity). Engineering of biosensing interfaces with functional molecules or nanomaterials has provided a promising molecular toolkit for enhanced accessibility and efficient recognition of biosensing probes. Among them, DNA has been an appealing material for interface engineering, because of its unique merits of biocompatible, predictable hybridization, and unparallel self‐assembly ability. In particular, employing tetrahedra DNA nanostructures (TDNs) to engineer interfaces has been a powerful means to improve biosensor performance. Here, this review introduces the recent progress in TDN‐based interface engineering. Then, we summarize the roles of TDNs in tailoring the properties of different interfaces, including electrode surface, channel surface, cell surface, etc., and highlight their biosensing applications. Finally, scientific challenges and future perspectives of TDN‐engineered biosensing interface are also discussed.

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“…Tetrahedral DNA nanostructures (TDNs), as a robust small-scale three-dimensional (3D) framework, , will improve its enzyme resistance and natural biocompatibility with negligible toxicity. , Besides, the design of its unique spatial structure provides an excellent carrier for the precise arrangement of probes in multiple directions. , Signal amplification approaches based on TDNs were considered as effective tools for the sensitive detection of targets owing to their high reliability . However, traditional hairpin-based amplification strategies using TDN monomers as carriers, like catalytic hairpin assembly (CHA) and hybridization chain reaction (HCR), are constricted by relatively high background and false-positive results, implying some hindrances for the application in living cells .…”

Section: Introductionmentioning

confidence: 99%

Entropy-Driven Three-Dimensional DNA Nanofireworks for Simultaneous Real-Time Imaging of Telomerase and MicroRNA in Living Cells

et al. 2023

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Real-time monitoring of different types of intracellular tumor-related biomarkers is of key importance for the identification of tumor cells. However, it is hampered by the low abundance of biomarkers, inefficient free diffusion of reactants, and complex cytoplasmic milieu. Herein, we present a stable and general method for in situ imaging of microRNA-21 and telomerase utilizing simple highly integrated dual tetrahedral DNA nanostructures (TDNs) that can naturally enter cells, which could initiate to form the three-dimensional (3D) higher-order DNA superstructures (DNA nanofireworks, DNFs) through a reliable target-triggered entropy-driven strand displacement reaction in living cells for remarkable signal amplification. Importantly, the excellent biostability, biocompatibility, and sensitivity of this approach benefited from (i) the precise multidirectional arrangement of probes with a pure DNA structure and (ii) the local target concentration enhanced by the spatially confined microdomain inside the DNFs. This strategy provides a pivotal molecular toolbox for broad applications such as biomedical imaging and early precise cancer diagnosis.

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The interactions between DNA nanostructures and cells: A critical overview from a cell biology perspective

Cited by 16 publications

References 197 publications

DNA nanopores as artificial membrane channels for origami-based bioelectronics

DNA nanopores as artificial membrane channels for origami-based bioelectronics

Engineering of Interfaces with Tetrahedra DNA Nanostructures for Biosensing Applications

Entropy-Driven Three-Dimensional DNA Nanofireworks for Simultaneous Real-Time Imaging of Telomerase and MicroRNA in Living Cells

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