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1.
Nature ; 622(7982): 292-300, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37704731

RESUMO

The past decades have witnessed the evolution of electronic and photonic integrated circuits, from application specific to programmable1,2. Although liquid-phase DNA circuitry holds the potential for massive parallelism in the encoding and execution of algorithms3,4, the development of general-purpose DNA integrated circuits (DICs) has yet to be explored. Here we demonstrate a DIC system by integration of multilayer DNA-based programmable gate arrays (DPGAs). We find that the use of generic single-stranded oligonucleotides as a uniform transmission signal can reliably integrate large-scale DICs with minimal leakage and high fidelity for general-purpose computing. Reconfiguration of a single DPGA with 24 addressable dual-rail gates can be programmed with wiring instructions to implement over 100 billion distinct circuits. Furthermore, to control the intrinsically random collision of molecules, we designed DNA origami registers to provide the directionality for asynchronous execution of cascaded DPGAs. We exemplify this by a quadratic equation-solving DIC assembled with three layers of cascade DPGAs comprising 30 logic gates with around 500 DNA strands. We further show that integration of a DPGA with an analog-to-digital converter can classify disease-related microRNAs. The ability to integrate large-scale DPGA networks without apparent signal attenuation marks a key step towards general-purpose DNA computing.


Assuntos
Computadores Moleculares , DNA , Algoritmos , DNA/química , Oligonucleotídeos/química , MicroRNAs/classificação , Doença/genética
2.
Proc Natl Acad Sci U S A ; 121(11): e2312596121, 2024 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-38437555

RESUMO

Self-assembled DNA crystals offer a precise chemical platform at the ångström-scale for DNA nanotechnology, holding enormous potential in material separation, catalysis, and DNA data storage. However, accurately controlling the crystallization kinetics of such DNA crystals remains challenging. Herein, we found that atomic-level 5-methylcytosine (5mC) modification can regulate the crystallization kinetics of DNA crystal by tuning the hybridization rates of DNA motifs. We discovered that by manipulating the axial and combination of 5mC modification on the sticky ends of DNA tensegrity triangle motifs, we can obtain a series of DNA crystals with controllable morphological features. Through DNA-PAINT and FRET-labeled DNA strand displacement experiments, we elucidate that atomic-level 5mC modification enhances the affinity constant of DNA hybridization at both the single-molecule and macroscopic scales. This enhancement can be harnessed for kinetic-driven control of the preferential growth direction of DNA crystals. The 5mC modification strategy can overcome the limitations of DNA sequence design imposed by limited nucleobase numbers in various DNA hybridization reactions. This strategy provides a new avenue for the manipulation of DNA crystal structure, valuable for the advancement of DNA and biomacromolecular crystallography.


Assuntos
5-Metilcitosina , DNA , Cristalização , Catálise , Cristalografia
3.
Nat Mater ; 23(6): 854-862, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38448659

RESUMO

Thrombosis is a leading global cause of death, in part due to the low efficacy of thrombolytic therapy. Here, we describe a method for precise delivery and accurate dosing of tissue plasminogen activator (tPA) using an intelligent DNA nanodevice. We use DNA origami to integrate DNA nanosheets with predesigned tPA binding sites and thrombin-responsive DNA fasteners. The fastener is an interlocking DNA triplex structure that acts as a thrombin recognizer, threshold controller and opening switch. When loaded with tPA and intravenously administrated in vivo, these DNA nanodevices rapidly target the site of thrombosis, track the circulating microemboli and expose the active tPA only when the concentration of thrombin exceeds a threshold. We demonstrate their improved therapeutic efficacy in ischaemic stroke and pulmonary embolism models, supporting the potential of these nanodevices to provide accurate tPA dosing for the treatment of different thromboses.


Assuntos
DNA , Terapia Trombolítica , Ativador de Plasminogênio Tecidual , Ativador de Plasminogênio Tecidual/química , Ativador de Plasminogênio Tecidual/administração & dosagem , Ativador de Plasminogênio Tecidual/uso terapêutico , DNA/química , Animais , Terapia Trombolítica/métodos , Nanoestruturas/química , Trombose/tratamento farmacológico , Camundongos , Fibrinolíticos/administração & dosagem , Fibrinolíticos/química , Fibrinolíticos/uso terapêutico , Humanos
4.
Nat Mater ; 23(7): 993-1001, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38594486

RESUMO

DNA origami is capable of spatially organizing molecules into sophisticated geometric patterns with nanometric precision. Here we describe a reconfigurable, two-dimensional DNA origami with geometrically patterned CD95 ligands that regulates immune cell signalling to alleviate rheumatoid arthritis. In response to pH changes, the device reversibly transforms from a closed to an open configuration, displaying a hexagonal pattern of CD95 ligands with ~10 nm intermolecular spacing, precisely mirroring the spatial arrangement of CD95 receptor clusters on the surface of immune cells. In a collagen-induced arthritis mouse model, DNA origami elicits robust and selective activation of CD95 death-inducing signalling in activated immune cells located in inflamed synovial tissues. Such localized immune tolerance ameliorates joint damage with no noticeable side effects. This device allows for the precise spatial control of cellular signalling, expanding our understanding of ligand-receptor interactions and is a promising platform for the development of pharmacological interventions targeting these interactions.


Assuntos
Artrite Reumatoide , DNA , Tolerância Imunológica , Transdução de Sinais , Receptor fas , Artrite Reumatoide/imunologia , Artrite Reumatoide/metabolismo , Artrite Reumatoide/patologia , Animais , DNA/química , DNA/imunologia , Camundongos , Receptor fas/metabolismo , Receptor fas/imunologia , Proteína Ligante Fas/metabolismo , Proteína Ligante Fas/imunologia , Humanos
5.
Nat Mater ; 23(2): 271-280, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37957270

RESUMO

Interfacing molecular machines to inorganic nanoparticles can, in principle, lead to hybrid nanomachines with extended functions. Here we demonstrate a ligand engineering approach to develop atomically precise hybrid nanomachines by interfacing gold nanoclusters with tetraphenylethylene molecular rotors. When gold nanoclusters are irradiated with near-infrared light, the rotation of surface-decorated tetraphenylethylene moieties actively dissipates the absorbed energy to sustain the photothermal nanomachine with an intact structure and steady efficiency. Solid-state nuclear magnetic resonance and femtosecond transient absorption spectroscopy reveal that the photogenerated hot electrons are rapidly cooled down within picoseconds via electron-phonon coupling in the nanomachine. We find that the nanomachine remains structurally and functionally intact in mammalian cells and in vivo. A single dose of near-infrared irradiation can effectively ablate tumours without recurrence in tumour-bearing mice, which shows promise in the development of nanomachine-based theranostics.


Assuntos
Nanopartículas , Neoplasias , Estilbenos , Animais , Camundongos , Fototerapia/métodos , Nanopartículas/química , Ouro/química , Mamíferos
6.
Chem Soc Rev ; 53(4): 1892-1914, 2024 Feb 19.
Artigo em Inglês | MEDLINE | ID: mdl-38230701

RESUMO

Molecular assembly is the process of organizing individual molecules into larger structures and complex systems. The self-assembly approach is predominantly utilized in creating artificial molecular assemblies, and was believed to be the primary mode of molecular assembly in living organisms as well. However, it has been shown that the assembly of many biological complexes is "catalysed" by other molecules, rather than relying solely on self-assembly. In this review, we summarize these catalysed-assembly (catassembly) phenomena in living organisms and systematically analyse their mechanisms. We then expand on these phenomena and discuss related concepts, including catalysed-disassembly and catalysed-reassembly. Catassembly proves to be an efficient and highly selective strategy for synergistically controlling and manipulating various noncovalent interactions, especially in hierarchical molecular assemblies. Overreliance on self-assembly may, to some extent, hinder the advancement of artificial molecular assembly with powerful features. Furthermore, inspired by the biological catassembly phenomena, we propose guidelines for designing artificial catassembly systems and developing characterization and theoretical methods, and review pioneering works along this new direction. Overall, this approach may broaden and deepen our understanding of molecular assembly, enabling the construction and control of intelligent assembly systems with advanced functionality.

7.
Nano Lett ; 2024 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-39259830

RESUMO

DNA encodes genetic information and forms various structural conformations with distinct physical, chemical, and biological properties. Over the past 30 years, advancements in force manipulation technology have enabled the precise manipulation of DNA at nanometer and piconewton resolutions. This mini-review discusses these force manipulation techniques for exploring the mechanical properties of DNA at the single-molecule level. We summarize the distinct mechanical features of different DNA forms while considering the impact of the force geometry. We highlight the role of DNA mechanics in origami structures that serve as self-assembled building blocks or mechanically responsive/active nanomachines. Accordingly, we emphasize how DNA mechanics are integral to the functionality of origami structures for achieving mechanical capabilities. Finally, we provide an outlook on the intrinsic mechanical properties of DNA, from single stranded to self-assembled higher-dimensional structures. This understanding is expected to inspire new design strategies in DNA mechanics, paving the way for innovative applications and technologies.

8.
Nano Lett ; 24(11): 3421-3431, 2024 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-38377170

RESUMO

Natural killer (NK) cell-based adoptive immunotherapy has demonstrated encouraging therapeutic effects in clinical trials for hematological cancers. However, the effectiveness of treatment for solid tumors remains a challenge due to insufficient recruitment and infiltration of NK cells into tumor tissues. Herein, a programmed nanoremodeler (DAS@P/H/pp) is designed to remodel dense physical stromal barriers and for dysregulation of the chemokine of the tumor environment to enhance the recruitment and infiltration of NK cells in tumors. The DAS@P/H/pp is triggered by the acidic tumor environment, resulting in charge reversal and subsequent hyaluronidase (HAase) release. HAase effectively degrades the extracellular matrix, promoting the delivery of immunoregulatory molecules and chemotherapy drugs into deep tumor tissues. In mouse models of pancreatic cancer, this nanomediated strategy for the programmed remodeling of the tumor microenvironment significantly boosts the recruitment of NK92 cells and their tumor cell-killing capabilities under the supervision of multiplexed near-infrared-II fluorescence.


Assuntos
Neoplasias , Neoplasias Pancreáticas , Animais , Camundongos , Linhagem Celular Tumoral , Neoplasias/patologia , Imunoterapia/métodos , Imunoterapia Adotiva/métodos , Neoplasias Pancreáticas/patologia , Células Matadoras Naturais , Microambiente Tumoral
9.
Nano Lett ; 2024 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-39298669

RESUMO

Super-resolution (SR) microscopy provides a revolutionary optical imaging approach by breaking the diffraction limit of light, while the commonly required special instrumentation with complex optical setup hampers its popularity. Here, we present a scanning switch-off microscopy (SSM) concept that exploits the omnipresent switch-off response of fluorophores to enable super-resolution imaging using a commercial confocal microscope. We validated the SSM model with theoretical calculations and experiments. An imaging resolution of ∼100 nm was obtained for DNA origami nanostructures and cellular cytoskeletons using fluorescent labels of Alexa 405, Alexa 488, Cy3, and Atto 488. Notably, super-resolution imaging of live cells was realized with SSM, by employing a dronpa fluorescent protein as the fluorescent label. In principle, this SSM method can be applied to any excitation laser scanning-based microscope.

10.
Nano Lett ; 24(29): 8956-8963, 2024 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-38984788

RESUMO

Nanoparticle assemblies with interparticle ohmic contacts are crucial for nanodevice fabrication. Despite tremendous progress in DNA-programmable nanoparticle assemblies, seamlessly welding discrete components into welded continuous three-dimensional (3D) configurations remains challenging. Here, we introduce a single-stranded DNA-encoded strategy to customize welded metal nanostructures with tunable morphologies and plasmonic properties. We demonstrate the precise welding of gold nanoparticle assemblies into continuous metal nanostructures with interparticle ohmic contacts through chemical welding in solution. We find that the welded gold nanoparticle assemblies show a consistent morphology with welded efficiency over 90%, such as the rod-like, triangular, and tetrahedral metal nanostructures. Next, we show the versatility of this strategy by welding gold nanoparticle assemblies of varied sizes and shapes. Furthermore, the experiment and simulation show that the welded gold nanoparticle assemblies exhibit defined plasmonic coupling. This single-stranded DNA encoded welding system may provide a new route for accurately building functional plasmonic nanomaterials and devices.

11.
Nano Lett ; 24(15): 4682-4690, 2024 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-38563501

RESUMO

Multienzyme assemblies mediated by multivalent interaction play a crucial role in cellular processes. However, the three-dimensional (3D) programming of an enzyme complex with defined enzyme activity in vitro remains unexplored, primarily owing to limitations in precisely controlling the spatial topological configuration. Herein, we introduce a nanoscale 3D enzyme assembly using a tetrahedral DNA framework (TDF), enabling the replication of spatial topological configuration and maintenance of an identical edge-to-edge distance akin to natural enzymes. Our results demonstrate that 3D nanoscale enzyme assemblies in both two-enzyme systems (glucose oxidase (GOx)/horseradish peroxidase (HRP)) and three-enzyme systems (amylglucosidase (AGO)/GOx/HRP) lead to enhanced cascade catalytic activity compared to the low-dimensional structure, resulting in ∼5.9- and ∼7.7-fold enhancements over homogeneous diffusional mixtures of free enzymes, respectively. Furthermore, we demonstrate the enzyme assemblies for the detection of the metabolism biomarkers creatinine and creatine, achieving a low limit of detection, high sensitivity, and broad detection range.


Assuntos
Enzimas Imobilizadas , Glucose Oxidase , Enzimas Imobilizadas/química , Peroxidase do Rábano Silvestre/química , Glucose Oxidase/química , DNA/química
12.
J Am Chem Soc ; 146(9): 6317-6325, 2024 03 06.
Artigo em Inglês | MEDLINE | ID: mdl-38391280

RESUMO

Repetitive sequences, which make up over 50% of human DNA, have diverse applications in disease diagnosis, forensic identification, paternity testing, and population genetic analysis due to their crucial functions for gene regulation. However, representative detection technologies such as sequencing and fluorescence imaging suffer from time-consuming protocols, high cost, and inaccuracy of the position and order of repetitive sequences. Here, we develop a precise and cost-effective strategy that combines the high resolution of atomic force microscopy with the shape customizability of DNA origami for repetitive sequence-specific gene localization. "Tri-block" DNA structures were specifically designed to connect repetitive sequences to DNA origami tags, thereby revealing precise genetic information in terms of position and sequence for high-resolution and high-precision visualization of repetitive sequences. More importantly, we achieved the results of simultaneous detection of different DNA repetitive sequences on the gene template with a resolution of ∼6.5 nm (19 nt). This strategy is characterized by high efficiency, high precision, low operational complexity, and low labor/time costs, providing a powerful complement to sequencing technologies for gene localization of repetitive sequences.


Assuntos
DNA , Sequências Repetitivas de Ácido Nucleico , Humanos , DNA/genética , DNA/química , Mapeamento Cromossômico , Microscopia de Força Atômica/métodos , Conformação de Ácido Nucleico , Nanotecnologia/métodos
13.
J Am Chem Soc ; 146(8): 5461-5469, 2024 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-38355136

RESUMO

Two-dimensional (2D) DNA origami assembly represents a powerful approach to the programmable design and construction of advanced 2D materials. Within the context of hybridization-mediated 2D DNA origami assembly, DNA spacers play a pivotal role as essential connectors between sticky-end regions and DNA origami units. Here, we demonstrated that programming the spacer length, which determines the binding radius of DNA origami units, could effectively tune sticky-end hybridization reactions to produce distinct 2D DNA origami arrays. Using DNA-PAINT super-resolution imaging, we unveiled the significant impact of spacer length on the hybridization efficiency of sticky ends for assembling square DNA origami (SDO) units. We also found that the assembly efficiency and pattern diversity of 2D DNA origami assemblies were critically dependent on the spacer length. Remarkably, we realized a near-unity yield of ∼98% for the assembly of SDO trimers and tetramers via this spacer-programmed strategy. At last, we revealed that spacer lengths and thermodynamic fluctuations of SDO are positively correlated, using molecular dynamics simulations. Our study thus paves the way for the precision assembly of DNA nanostructures toward higher complexity.


Assuntos
DNA , Nanoestruturas , DNA Intergênico , Conformação de Ácido Nucleico , DNA/química , Nanoestruturas/química , Hibridização de Ácido Nucleico , Nanotecnologia
14.
J Am Chem Soc ; 146(25): 17094-17102, 2024 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-38867462

RESUMO

The photoluminescent properties of atomically precise metal nanoclusters (MCs) have garnered significant attention in the fields of chemical sensing and biological imaging. However, the limited brightness of single-component nanoclusters hinders their practical applications, and the conventional ligand engineering approaches have proven insufficient in enhancing the emission efficiency of MCs. Here, we present a DNA framework-guided strategy to prepare highly luminescent metal cluster nanoaggregates. Our approach involves an amphiphilic DNA framework comprising a hydrophobic alkyl core and a rigid DNA framework shell, serving as a nucleation site and providing well-defined nanoconfinements for the self-limiting aggregation of MCs. Through this method, we successfully produced homogeneous MC nanoaggregates (10.1 ± 1.2 nm) with remarkable nanoscale precision. Notably, this strategy proves adaptable to various MCs, leading to a substantial enhancement in emission and quantum yield, up to 3011- and 87-fold, respectively. Furthermore, our investigation using total internal reflection fluorescence microscopy at the single-particle level uncovered a more uniform photon number distribution and higher photostability for MC nanoaggregates compared to template-free counterparts. This DNA-templating strategy introduces a conceptually innovative approach for studying the photoluminescent properties of aggregates with nanoscale precision and holds promise for constructing highly luminescent MC nanoparticles for diverse applications.


Assuntos
DNA , DNA/química , Nanopartículas Metálicas/química , Luminescência
15.
J Am Chem Soc ; 146(28): 18948-18957, 2024 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-38959409

RESUMO

Single-molecule localization methods have been popularly exploited to obtain super-resolved images of biological structures. However, the low blinking frequency of randomly switching emission states of individual fluorophores greatly limits the imaging speed of single-molecule localization microscopy (SMLM). Here we present an ultrafast SMLM technique exploiting spontaneous fluorescence blinking of cyanine dye aggregates confined to DNA framework nanostructures. The DNA template guides the formation of static excimer aggregates as a "light-harvesting nanoantenna", whereas intermolecular excitation energy transfer (EET) between static excimers causes collective ultrafast fluorescence blinking of fluorophore aggregates. This DNA framework-based strategy enables the imaging of DNA nanostructures with 12.5-fold improvement in speed compared to conventional SMLM. Further, we demonstrate the use of this strategy to track the movement of super-resolved DNA nanostructures for over 20 min in a microfluidic system. Thus, this ultrafast SMLM holds great potential for revealing the dynamic processes of biomacromolecules in living cells.


Assuntos
DNA , Corantes Fluorescentes , Nanoestruturas , DNA/química , Corantes Fluorescentes/química , Nanoestruturas/química , Imagem Individual de Molécula/métodos , Carbocianinas/química , Microscopia de Fluorescência/métodos
16.
J Am Chem Soc ; 146(36): 25253-25262, 2024 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-39196310

RESUMO

Nanoparticle (NP) delivery systems have been actively exploited for cancer therapy and vaccine development. Nevertheless, the major obstacle to targeted delivery lies in the substantial liver sequestration of NPs. Here we report a DNA-engineered approach to circumvent liver phagocytosis for enhanced tumor-targeted delivery of nanoagents in vivo. We find that a monolayer of DNA molecules on the NP can preferentially adsorb a dysopsonin protein in the serum to induce functionally invisibility to livers; whereas the tumor-specific uptake is triggered by the subsequent degradation of the DNA shell in vivo. The degradation rate of DNA shells is readily tunable by the length of coated DNA molecules. This DNA-engineered invisibility cloaking (DEIC) is potentially generic as manifested in both Ag2S quantum dot- and nanoliposome-based tumor-targeted delivery in mice. Near-infrared-II imaging reveals a high tumor-to-liver ratio of up to ∼5.1, approximately 18-fold higher than those with conventional nanomaterials. This approach may provide a universal strategy for high-efficiency targeted delivery of theranostic agents in vivo.


Assuntos
DNA , Nanopartículas , DNA/química , Animais , Camundongos , Nanopartículas/química , Humanos , Neoplasias/tratamento farmacológico , Linhagem Celular Tumoral , Fígado/metabolismo
17.
J Am Chem Soc ; 146(9): 5883-5893, 2024 03 06.
Artigo em Inglês | MEDLINE | ID: mdl-38408317

RESUMO

DNA monolayers with inherent chirality play a pivotal role across various domains including biosensors, DNA chips, and bioelectronics. Nonetheless, conventional DNA chiral monolayers, typically constructed from single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA), often lack structural orderliness and design flexibility at the interface. Structural DNA nanotechnology has emerged as a promising solution to tackle these challenges. In this study, we present a strategy for crafting highly adaptable twisted DNA origami-based chiral monolayers. These structures exhibit distinct interfacial assembly characteristics and effectively mitigate the structural disorder of dsDNA monolayers, which is constrained by a limited persistence length of ∼50 nm of dsDNA. We highlight the spin-filtering capabilities of seven representative DNA origami-based chiral monolayers, demonstrating a maximal one-order-of-magnitude increase in spin-filtering efficiency per unit area compared with conventional dsDNA chiral monolayers. Intriguingly, our findings reveal that the higher-order tertiary chiral structure of twisted DNA origami further enhances the spin-filtering efficiency. This work paves the way for the rational design of DNA chiral monolayers.


Assuntos
DNA de Cadeia Simples , DNA , DNA/química , Nanotecnologia , Conformação de Ácido Nucleico
18.
Anal Chem ; 96(25): 10332-10340, 2024 06 25.
Artigo em Inglês | MEDLINE | ID: mdl-38865206

RESUMO

The neurofilament protein light chain (NEFL) is a potential biomarker of neurodegenerative diseases, and interleukin-6 (IL-6) is also closely related to neuroinflammation. Especially, NEFL and IL-6 are the two most low-abundance known protein markers of neurological diseases, making their detection very important for the early diagnosis and prognosis prediction of such kinds of diseases. Nevertheless, quantitative detection of low concentrations of NEFL and IL-6 in serum remains quite difficult, especially in the point-of-care test (POCT). Herein, we developed a portable, sensitive electrochemical biosensor combined with smartphones that can be applied to multiple scenarios for the quantitative detection of NEFL and IL-6, meeting the need of the POCT. We used a double-antibody sandwich configuration combined with polyenzyme-catalyzed signal amplification to improve the sensitivity of the biosensor for the detection of NEFL and IL-6 in sera. We could detect NEFL as low as 5.22 pg/mL and IL-6 as low as 3.69 pg/mL of 6 µL of serum within 2 h, demonstrating that this electrochemical biosensor worked well with serum systems. Results also showed its superior detection capabilities over those of high-sensitivity ELISA for serum samples. Importantly, by detecting NEFL and IL-6 in sera, the biosensor showed its potential for the POCT model detection of all known biomarkers of neurological diseases, making it possible for the mass screening of patients with neurodegenerative diseases.


Assuntos
Biomarcadores , Técnicas Biossensoriais , Técnicas Eletroquímicas , Interleucina-6 , Técnicas Biossensoriais/métodos , Humanos , Biomarcadores/sangue , Biomarcadores/análise , Interleucina-6/sangue , Interleucina-6/análise , Testes Imediatos , Proteínas de Neurofilamentos/sangue , Doenças do Sistema Nervoso/diagnóstico , Doenças do Sistema Nervoso/sangue , Limite de Detecção , Smartphone
19.
Small ; : e2402870, 2024 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-38844986

RESUMO

DNA nanostructures offer a versatile platform for precise dye assembly, making them promising templates for creating photonic complexes with applications in photonics and bioimaging. However, despite these advancements, the effect of dye loading on the hybridization kinetics of single-stranded DNA protruding from DNA nanostructures remains unexplored. In this study, the DNA points accumulation for imaging in the nanoscale topography (DNA-PAINT) technique is employed to investigate the accessibility of functional binding sites on DNA-templated excitonic wires. The results indicate that positively charged dyes on DNA frameworks can accelerate the hybridization kinetics of protruded ssDNA through long-range electrostatic interactions. Furthermore, the impacts of various charged dyes and binding sites are explored on diverse DNA frameworks with varying cross-sizes. The research underscores the crucial role of electrostatic interactions in DNA hybridization kinetics within DNA-dye complexes, offering valuable insights for the functionalization and assembly of biomimetic photonic systems.

20.
Opt Express ; 32(11): 20218-20229, 2024 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-38859137

RESUMO

Traditional camera-based single-molecule localization microscopy (SMLM), with its high imaging resolution and localization throughput, has made significant advancements in biological and chemical researches. However, due to the limitation of the fluorescence signal-to-noise ratio (SNR) of a single molecule, its resolution is difficult to reach to 5 nm. Optical lattice produces a nondiffracting beam pattern that holds the potential to enhance microscope performance through its high contrast and penetration depth. Here, we propose a new method named LatticeFLUX which utilizes the wide-field optical lattice pattern illumination for individual molecule excitation and localization. We calculated the Cramér-Rao lower bound of LatticeFLUX resolution and proved that our method can improve the single molecule localization precision by 2.4 times compared with the traditional SMLM. We propose a scheme using 9-frame localization, which solves the problem of uneven lattice light illumination. Based on the experimental single-molecule fluorescence SNR, we coded the image reconstruction software to further verify the resolution enhancement capability of LatticeFLUX on simulated punctate DNA origami, line pairs, and cytoskeleton. LatticeFLUX confirms the feasibility of using 2D structured light illumination to obtain high single-molecule localization precision under high localization throughput. It paves the way for further implementation of ultra-high resolution full 3D structured-light-illuminated SMLM.

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