Dominant Analytical Techniques in DNA Nanotechnology for Various Applications

Analytical Chemistry, Год журнала: 2024, Номер 96(9), С. 3687 - 3697

Опубликована: Фев. 14, 2024

DNA nanotechnology is rapidly gaining traction in numerous applications, each bearing varying degrees of tolerance to the quality and quantity necessary for viable nanostructure function. Despite distinct objectives application, they are united their reliance on essential analytical techniques, such as purification characterization. This tutorial aims guide reader through current state chemistry, outlining important factors consider when designing, assembling, purifying, characterizing a downstream applications.

Язык: Английский

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Proximity-Induced Bipedal DNA Walker for Accurately Visualizing microRNA in Living Cancer Cell

Analytical Chemistry, Год журнала: 2024, Номер 96(26), С. 10669 - 10676

Опубликована: Июнь 24, 2024

DNA walker, a type of dynamic device that is capable moving progressively along prescribed walking tracks, has emerged as an ideal and powerful tool for biosensing bioimaging. However, most the reported three-dimensional (3D) walker were merely designed detection single target, they not achieving universal applicability. Herein, we first time development proximity-induced 3D bipedal imaging low abundance biomolecules. As proof concept, miRNA-34a, biomarker breast cancer, chosen model system to demonstrate this approach. In our design, can be generated only by specific recognition two proximity probes miRNA-34a. Meanwhile, it stochastically autonomously traveled on tracks (gold nanoparticles) via catalytic hairpin assembly (CHA), resulting in amplified fluorescence signal. comparison with some conventional walkers utilized living cell imaging, induced ligation assay greatly improve ensure high selectivity bioanalysis. By taking advantage these unique features, successfully realizes accurate effective monitoring target miRNA-34a expression levels cells, affording universal, valuable, promising platform low-abundance cancer identification cancer.

Язык: Английский

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Pyrene-Based Light-Harvesting Antenna Molecules

The Journal of Physical Chemistry Letters, Год журнала: 2025, Номер unknown, С. 2468 - 2478

Опубликована: Фев. 28, 2025

Light-harvesting antenna systems (AS) with multiple light-absorbing chromophores play a vital role in absorbing sunlight and transferring the excitation energy to reaction centers during photosynthesis process. Learning from nature, set of simple artificial pyrene-based light-harvesting have been designed re-examined self-developing chemical intermediates, via combining electron-donating 4,4-dimethoxy-triphenylamine moieties as for donors center. These exhibit positive correlation between molar absorption coefficient (ε), enhanced photoluminescence efficiency unchanged emission peak, two-photon cross-section an increasing number TPA-OMe solution. Moreover, excited-state dynamics these AS indicated that coexistence charge transfer (CT) state separation (CS) plays significant affecting behavior. The short-lived CS was affected by increased low polar solvent, which can boost decay recombination (CR), resulting emission. On contrary, long-lived would overwhelm CT high solvent or molecules containing one two units.

Язык: Английский

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Sequestration within peptide coacervates improves the fluorescence intensity, kinetics, and limits of detection of dye-based DNA biosensors

Communications Chemistry, Год журнала: 2024, Номер 7(1)

Опубликована: Фев. 29, 2024

Peptide-based liquid-liquid phase separated domains, or coacervates, are a biomaterial gaining new interest due to their exciting potential in fields ranging from biosensing drug delivery. In this study, we demonstrate that coacervates provide simple and biocompatible medium improve nucleic acid biosensors through the sequestration of both biosensor target strands within coacervate, thereby increasing local concentration. Using well-established polyarginine (R

Язык: Английский

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Sculpting photoproducts with DNA origami

Chem, Год журнала: 2024, Номер 10(5), С. 1553 - 1575

Опубликована: Апрель 5, 2024

Язык: Английский

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Purification of DNA Nanoparticles Using Photocleavable Biotin Tethers

ACS Applied Materials & Interfaces, Год журнала: 2024, Номер 16(17), С. 22334 - 22343

Опубликована: Апрель 18, 2024

The number of applications self-assembled deoxyribonucleic acid (DNA) origami nanoparticles (DNA NPs) has increased drastically, following the development a variety single-stranded template DNA (ssDNA) that can serve as scaffold strand. In addition to viral genomes, such M13 bacteriophage and lambda DNAs, enzymatically produced ssDNA from various sources is rapidly gaining traction being applied for NP preparation. However, separating fully formed NPs have custom scaffolds crude assembly mixes often multistep process first its enzymatic amplification then isolating assembled excess precursor strands. Only sample ready downstream characterization application. this work, we highlight single-step purification sequence- or M13-derived scaffold-based using photocleavable biotin tethers. only requires an inexpensive ultraviolet (UV) lamp, with up 90% yield high purity are obtained. We show versatility in two multihelix bundle structures wireframe polyhedral architecture.

Язык: Английский

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Single‐Molecule Assessment of DNA Hybridization Kinetics on Dye‐Loaded DNA Nanostructures

Small, Год журнала: 2024, Номер unknown

Опубликована: Июнь 6, 2024

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

Язык: Английский

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DNA-Based Fluorescent Nanoprobe for Cancer Cell Membrane Imaging

Molecules, Год журнала: 2024, Номер 29(1), С. 267 - 267

Опубликована: Янв. 4, 2024

As an important barrier between the cytoplasm and microenvironment of cell, cell membrane is essential for maintenance normal cellular physiological activities. An abnormal a crucial symbol body dysfunction occurrence variant diseases; therefore, visualization monitoring biomolecules associated with membranes disease markers are utmost importance in revealing biological functions membranes. Due to their biocompatibility, programmability, modifiability, DNA nanomaterials have become increasingly popular fluorescence imaging recent years. In addition, can be combined specific manner enable real-time signal molecules on membrane, allowing progression. This article examines application First, we present conditions microenvironment, such as ATP, pH, etc. Second, summarize applications receptors other molecules. Finally, some difficulties challenges presented.

Язык: Английский

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Minimizing Structural Heterogeneity in DNA Self-Assembled Dye Templating via DNA Origami-Tuned Conformations

Langmuir, Год журнала: 2024, Номер 40(19), С. 10195 - 10207

Опубликована: Май 1, 2024

With recent advances in DNA-templated dye aggregation for leveraging and engineering molecular excitons, a need exists minimizing structural heterogeneity. Holliday Junction complexes (HJ) are commonly used to covalently template aggregates on their core; however, the global conformation of HJ is detrimentally dynamic. Here, selectively tuned by restricting its position orientation using sheet-like DNA origami construct (DOC) physisorbed glass. The arms fixed with four different designed interduplex angles (IDAs). Atomic force microscopy confirmed that HJs bound surface DOC IDAs. Dye distributions were determined combining dipole imaging super-resolution microscopy. All IDAs led orientations having dispersed along planes perpendicular plane, suggesting stacking occurred between neighboring bases. dye-base interpretation was supported increasing size core cavity. narrowest IDA minimizes heterogeneity suggests intercalation. A strong correlation found plane. These results show imposes restrictions dye-DNA interactions always present regardless conformation. implications our discussed scalability self-assembly. Our methodology provides an avenue solid-supported single-molecule characterization assemblies templated biomolecules─such as protein templates involved light-harvesting catalysis─with conformations restricted orientation.

Язык: Английский

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Site-specific photo-crosslinking in a double crossover DNA tile facilitated by squaraine dye aggregates: advancing thermally stable and uniform DNA nanostructures

Biomaterials Science, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

We investigated the role of dichloro-squaraine (SQ) dye aggregates in facilitating thymine–thymine interstrand photo-crosslinking double crossover (DX) tiles to improve thermal and structural stability two-dimension DNA-based nanostructures.

Язык: Английский

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