DNA-AgNC Loaded Liposomes for Measuring Cerebral Blood Flow Using Two-Photon Fluorescence Correlation Spectroscopy

Rabies virus-mimicking liposomes for targeted gene therapy in Alzheimer's disease

RNA interference (RNAi) harbors significant potential for treating neurological disorders; nevertheless, limited efficacy has been discerned. The presence of barriers within the central nervous system, coupled with the inherent instability of nucleic acids within biological conditions, poses formidable challenges in advancing effective gene delivery strategies. In this study, we designed and prepared a virus-mimic non-viral gene vector, rabies virus glycoprotein (RVG29)-decorated liposome (f(Lipo)-RVG29), to deliver small interfering RNAs to the brain. Alzheimer's disease (AD) was chosen as a model of neurodegenerative disease in this context, and b-site APP cleaving enzyme silencing siRNA (siBACE1) was used. The developed liposomal delivery system has a particle size of under 80 nm with a spherical shape, positive zeta potential, and the ability to protect siRNA against nucleases. In vitro studies demonstrate that functionalizing the cationic liposome by the RVG29 targeting ligand significantly enhances the effectiveness of gene delivery and silencing. Examination through ex vivo imaging illustrates an increased deposition of fluorescent-labeled f(Lipo)-RVG29 within brain tissue after 12 h post application. Additionally, the in vivo delivery of f(Lipo)-RVG29 carrying siRNA has substantially suppressed BACE1 expression at both mRNA and protein levels within the brain tissue. Our results suggest that the developed non-viral vector could be a promising gene carrier system combining the synergistic effect of virus-mimic RVG29 ligand with bioinspired liposome that imitates the natural lipid bilayers of cell membranes for brain-targeted RNAi therapeutics.

Recent Advances of Strategies and Applications in Aptamer-Combined Metal Nanocluster Biosensing Systems

Metal nanoclusters (NCs) are promising alternatives to organic dyes and quantum dots. These NCs exhibit unique physical and chemical properties, such as fluorescence, chirality, magnetism and catalysis, which contribute to significant advancements in biosensing, biomedical diagnostics and therapy. Through adjustments in composition, size, chemical environments and surface ligands, it is possible to create NCs with tunable optoelectronic and catalytic activity. This review focuses on the integration of aptamers with metal NCs, detailing molecular detection strategies that utilise the effect of aptamers on optical signal emission of metal NC-based biosensing systems. This review also highlights recent advancements in biosensing and biomedical applications, as well as illustrative case studies. To conclude, the strengths, limitations, current challenges and prospects for metal NC-based systems were examined.

Two-photon brightness of NIR-emitting, atomically precise DNA-stabilized silver nanoclusters

Near-infrared (NIR) emitters with high two-photon absorption (2PA) cross-sections are of interest to enable in vivo imaging in the tissue transparency windows. This study explores the potential of DNA-stabilized silver nanoclusters (Ag N -DNAs) as water-soluble two-photon absorbers. We investigate 2PA of four different atomically precise Ag N -DNA species with far-red to NIR emission and varying nanocluster and ligand compositions. 2PA cross-sections, σ 2, were determined by two-photon excited luminescence (2PEL) technique for a wide wavelength range from 810 to 1400 nm. The Ag N -DNAs exhibited reversed strength of corresponding transitions in the two-photon regime, as compared to one-photon, which further demonstrates the complex photophysics of these emitters. Maximal 2PA cross-section value (∼582 GM) was observed for (DNA)3[Ag21]15+, which is stabilized by 3 DNA oligomers. (DNA)2[Ag16Cl2]8+ presented distinct 2PA behavior from the Ag N -DNAs without chlorido ligands, with a high 2PA of 176 GM at 1050 nm. Our findings support the potential of Ag N -DNAs as NIR-to-NIR two-photon probes that are both excited and emit in the NIR. Their high σ 2 and fluorescence quantum yield values result in superior two-photon brightness on the order of ∼102 GM, significantly higher than water-soluble organic fluorophores.

Fragmentation patterns of DNA-stabilized silver nanoclusters under mass spectrometry

DNA-stabilized silver nanoclusters (AgN-DNAs) are emitters with tuneable structures and photophysical properties. While understanding of the sequence-structure-property relationships of AgN-DNAs has advanced significantly, their chemical transformations and degradation pathways are far less understood. To advance understanding of these pathways, we analysed the fragmentation products of 21 different red and NIR AgN-DNAs using negative ion mode electrospray ionization mass spectrometry (ESI-MS). AgN-DNAs were found to lose Ag+ under ESI-MS conditions, and sufficient loss of silver atoms can lead to a transition to a lesser number of effective valence electrons, N0. Of more than 400 mass spectral peaks analysed, only even values of N0 were identified, suggesting that solution-phase AgN-DNAs with odd values of N0 are unlikely to be stable. AgN-DNAs stabilized by three DNA strands were found to fragment significantly more than AgN-DNAs stabilized by two DNA strands. Moreover, the fragmentation behaviour depends strongly on the DNA template sequence, with diverse fragmentation patterns even for AgN-DNAs with similar molecular formulae. Molecular dynamics simulations, with forces calculated from density functional theory, of the fragmentation of (DNA)2(Ag16Cl2)8+ with a known crystal structure show that the 6-electron Ag16Cl2 core fragments into a 4-electron Ag10 and a 2-electron Ag6, preserving electron-pairing rules even at early stages of the fragmentation process, in agreement with experimental observation. These findings provide new insights into the mechanisms by which AgN-DNAs degrade and transform, with relevance for their applications in sensing and biomedical applications.

Multi-Objective Design of DNA-Stabilized Nanoclusters Using Variational Autoencoders With Automatic Feature Extraction

DNA-stabilized silver nanoclusters (AgN-DNAs) have sequence-tuned compositions and fluorescence colors. High-throughput experiments together with supervised machine learning models have recently enabled design of DNA templates that select for AgN-DNA properties, including near-infrared (NIR) emission that holds promise for deep tissue bioimaging. However, these existing models do not enable simultaneous selection of multiple AgN-DNA properties, and require significant expert input for feature engineering and class definitions. This work presents a model for multiobjective, continuous-property design of AgN-DNAs with automatic feature extraction, based on variational autoencoders (VAEs). This model is generative, i.e., it learns both the forward mapping from DNA sequence to AgN-DNA properties and the inverse mapping from properties to sequence, and is trained on an experimental data set of DNA sequences paired with AgN-DNA fluorescence properties. Experimental testing shows that the model enables effective design of AgN-DNA emission, including bright NIR AgN-DNAs with 4-fold greater abundance compared to training data. In addition, Shapley analysis is employed to discern learned nucleobase patterns that correspond to fluorescence color and brightness. This generative model can be adapted for a range of biomolecular systems with sequence-dependent properties, enabling precise design of emerging biomolecular nanomaterials.

Fluorescent Pdots Facilitate High-Resolution Mapping of the Intact Meningeal Vascular Network and Eye-Brain Connections

Meningeal vascular network is significant in neurology and neurosurgery. However, high-resolution imaging of intact meningeal vascular network is lacking. In this work, we develop a practical experimental method to ensure that the intact meninges are morphologically unfolded and fixed in an agarose gel. With the help of high-brightness polymer dots (Pdots) as probe, macroscopic and detailed imaging of the vascular network on the intact dorsal meninges can be performed. Meningeal vessels are symmetrically distributed along the superior sagittal sinus, and the distribution of meningeal vessels had a certain degree of hierarchy. The meninges are thicker blood vessels and capillary networks from the outside to the inside. Moreover, the diameter of the capillaries is 3.96 ± 0.89 μm. Interestingly, meningeal primo vessels in the central nervous system of mice is imaged with the diameter of 4.18 ± 1.18 μm, which has not been reported previously. It is worth mentioning that we found that orthotopic xenografts of brain tumors caused the appearance of corneal neovascularization and morphological changes in optic nerve microvessels. In conclusion, our work provides an effective Pdots-based imaging method for follow-up research on meningeal vascular-related diseases, and illustrates that the eye can serve as a window for the prevention and diagnosis of brain diseases.

An Atom-Precise Understanding of DNA-Stabilized Silver Nanoclusters

ConspectusDNA-stabilized silver nanoclusters (AgN-DNAs) are sequence-encoded fluorophores. Like other noble metal nanoclusters, the optical properties of AgN-DNAs are dictated by their atomically precise sizes and shapes. What makes AgN-DNAs unique is that nanocluster size and shape are controlled by nucleobase sequence of the templating DNA oligomer. By choice of DNA sequence, it is possible to synthesize a wide range of AgN-DNAs with diverse emission colors and other intriguing photophysical properties. AgN-DNAs hold significant potential as "programmable" emitters for biological imaging due to their combination of small molecular-like sizes, bright and sequence-tuned fluorescence, low toxicities, and cost-effective synthesis. In particular, the potential to extend AgN-DNAs into the second near-infrared region (NIR-II) is promising for deep tissue imaging, which is a major area of interest for advancing biomedical imaging. Achieving this goal requires a deep understanding of the structure-property relationships that govern AgN-DNAs in order to design AgN-DNA emitters with sizes and geometries that support NIR-II emission.In recent years, major advances have been made in understanding the structure and composition of AgN-DNAs, enabling new insights into the correlation of nanocluster structure and photophysical properties. These advances have hinged on combined innovations in mass characterization and crystallography of compositionally pure AgN-DNAs, together with combinatorial experiments and machine learning-guided design. A combined approach is essential due to the major challenge of growing suitable AgN-DNA crystals for diffraction and to the labor-intensive nature of preparing and solving the molecular formulas of atomically precise AgN-DNAs by mass spectrometry. These approaches alone are not feasibly scaled to explore the large sequence space of DNA oligomer templates for AgN-DNAs.This account describes recent fundamental advances in AgN-DNA science that have been enabled by high throughput synthesis and fluorimetry together with detailed analytical studies of purified AgN-DNAs. First, short introductions to nanocluster chemistry and AgN-DNA basics are presented. Then, we review recent large-scale studies that have screened thousands of DNA templates for AgN-DNAs, leading to discovery of distinct classes of these emitters with unique cluster core compositions and ligand chemistries. In particular, the discovery of a new class of chloride-stabilized AgN-DNAs enabled the first ab initio calculations of AgN-DNA electronic structure and present new approaches to stabilize these emitters in biologically relevant conditions. Near-infrared (NIR) emissive AgN-DNAs are also found to exhibit diverse structures and properties. Finally, we conclude by highlighting recent proof-of-principle demonstrations of NIR AgN-DNAs for targeted fluorescence imaging. Continued efforts may future push AgN-DNAs into the tissue transparency window for fluorescence imaging in the NIR-II tissue transparency window.

Fluorescence Screening of DNA-AgNCs with Pulsed White Light Excitation

DNA-stabilized silver nanoclusters (DNA-AgNCs) are a class of fluorophores with interesting photophysical properties dominated by the choice of DNA sequence. Screening methods with ultraviolet excitation and steady state well plate readers have previously been used for deepening the understanding between DNA sequence and emission color of the resulting DNA-AgNCs. Here, we present a new method for screening DNA-AgNCs by using pulsed white light excitation (λex ≈ 490-900 nm). By subtraction and time gating we are able to circumvent the dominating scatter of the white excitation light and extract both temporally and spectrally resolved emission of DNA-AgNCs over the visible to near-infrared range. Additionally, we are able to identify weak long-lived emission, which is often buried underneath the intense nanosecond fluorescence. This new approach will be useful for future screening of DNA-AgNCs (or other novel emissive materials) and aid machine-learning models by providing a richer training data set.

More than double the fun with two-photon excitation microscopy

For generations researchers have been observing the dynamic processes of life through the lens of a microscope. This has offered tremendous insights into biological phenomena that span multiple orders of time- and length-scales ranging from the pure magic of molecular reorganization at the membrane of immune cells, to cell migration and differentiation during development or wound healing. Standard fluorescence microscopy techniques offer glimpses at such processes in vitro, however, when applied in intact systems, they are challenged by reduced signal strengths and signal-to-noise ratios that result from deeper imaging. As a remedy, two-photon excitation (TPE) microscopy takes a special place, because it allows us to investigate processes in vivo, in their natural environment, even in a living animal. Here, we review the fundamental principles underlying TPE aimed at basic and advanced microscopy users interested in adopting TPE for intravital imaging. We focus on applications in neurobiology, present current trends towards faster, wider and deeper imaging, discuss the combination with photon counting technologies for metabolic imaging and spectroscopy, as well as highlight outstanding issues and drawbacks in development and application of these methodologies.

Fluorescence Biosensing Based on Bifurcated DNA Scaffold-Aggregated Ag Nanocluster via Responsive Conformation Switch of Quasi-Molecular Beacon

To address the limitations of typical hairpin-structural molecular beacons, exploring the ability of a quasi-molecular beacon (qMB) to create label-free fluorescence biosensors is intriguing and remains a challenge. Herein, we propose the first example of modular qMB with the feature of a stimulation-responsive conformation switch to develop an aggregated Ag nanocluster (aAgNC) in a bifurcated DNA scaffold for fluorescently sensing a specific initiator (I*). This qMB was well designed to program four functional modules: I*-recognizable element adopting metastable stem-loop bihairpin structure and two DNA splits (exposed C3GT4 and locked C4AC4T) of aAgNC template that is separated by a tunable hairpin spacer for the customized combination of selective recognition and signaling readout. When presenting I* in an assay route, the specific hybridization induces the directional disassembly of the bihairpin unit, on which the qMB is configurationally switched to liberate the locked split. Thus, the bifurcated parent template pair of C3GT4/C4AC4T is proximal, affording in situ nucleation and clustering of emissive aAgNC. By collecting the fluorescence signal, the quantitative detection of I* is achieved. Benefiting from the ingenious programming of qMB, the recognizing and signaling integration actuates the construction of a facile and convenient fluorescent biosensor featuring rapid reaction kinetics, a wide linear range, high sensitivity, and specificity. This would provide a new paradigm to exploit versatile qMB-based biosensing platforms via stimulation-responsive conformation switches for developing various DNA-scaffolded Ag clusters.

Beyond nature's base pairs: machine learning-enabled design of DNA-stabilized silver nanoclusters

Sequence-encoded biomolecules such as DNA and peptides are powerful programmable building blocks for nanomaterials. This paradigm is enabled by decades of prior research into how nucleic acid and amino acid sequences dictate biomolecular interactions. The properties of biomolecular materials can be significantly expanded with non-natural interactions, including metal ion coordination of nucleic acids and amino acids. However, these approaches present design challenges because it is often not well-understood how biomolecular sequence dictates such non-natural interactions. This Feature Article presents a case study in overcoming challenges in biomolecular materials with emerging approaches in data mining and machine learning for chemical design. We review progress in this area for a specific class of DNA-templated metal nanomaterials with complex sequence-to-property relationships: DNA-stabilized silver nanoclusters (AgN-DNAs) with bright, sequence-tuned fluorescence colors and promise for biophotonics applications. A brief overview of machine learning concepts is presented, and high-throughput experimental synthesis and characterization of AgN-DNAs are discussed. Then, recent progress in machine learning-guided design of DNA sequences that select for specific AgN-DNA fluorescence properties is reviewed. We conclude with emerging opportunities in machine learning-guided design and discovery of AgN-DNAs and other sequence-encoded biomolecular nanomaterials.

Bioconjugation of a Near-Infrared DNA-Stabilized Silver Nanocluster to Peptides and Human Insulin by Copper-Free Click Chemistry

DNA-stabilized silver nanoclusters (DNA-AgNCs) are biocompatible emitters with intriguing properties. However, they have not been extensively used for bioimaging applications due to the lack of structural information and hence predictable conjugation strategies. Here, a copper-free click chemistry method for linking a well-characterized DNA-AgNC to molecules of interest is presented. Three different peptides and a small protein, human insulin, were tested as labeling targets. The conjugation to the target compounds was verified by MS, HPLC, and time-resolved anisotropy measurements. Moreover, the spectroscopic properties of DNA-AgNCs were found to be unaffected by the linking reactions. For DNA-AgNC-conjugated human insulin, fluorescence imaging studies were performed on Chinese hamster ovary (CHO) cells overexpressing human insulin receptor B (hIR-B). The specific staining of the CHO cell membranes demonstrates that DNA-AgNCs are great candidates for bioimaging applications, and the proposed linking strategy is easy to implement when the DNA-AgNC structure is known.