DNA can stabilize silver nanoclusters (Ag N -DNAs) whose atomic sizes and diverse fluorescence colors are selected by nucleobase sequence. These programmable nanoclusters hold promise for sensing, ...bioimaging, and nanophononics. However, DNA’s vast sequence space challenges the design and discovery of Ag N -DNAs with tailored properties. In particular, Ag N -DNAs with bright near-infrared luminescence above 800 nm remain rare, placing limits on their applications for bioimaging in the tissue transparency windows. Here, we present a design method for near-infrared emissive Ag N -DNAs. By combining high-throughput experimentation and machine learning with fundamental information from Ag N -DNA crystal structures, we distill the salient DNA sequence features that determine Ag N -DNA color, for the entire known spectral range of these nanoclusters. A succinct set of nucleobase staple features are predictive of Ag N -DNA color. By representing DNA sequences in terms of these motifs, our machine learning models increase the design success for near-infrared emissive Ag N -DNAs by 12.3 times as compared to training data, nearly doubling the number of known Ag N -DNAs with bright near-infrared luminescence above 800 nm. These results demonstrate how incorporating known structure–property relationships into machine learning models can enhance materials study and design, even for sparse and imbalanced training data.
Stroke is one of the leading causes of death and disability worldwide. Tremendous improvements have been achieved in the acute care of stroke patients with the implementation of stroke units, ...thrombolytic drugs, and endovascular trombectomies. However, stroke survivors with neurological deficits require long periods of neurorehabilitation, which is the only approved therapy for poststroke recovery. With this scenario, more treatments are urgently needed, and only the understanding of the mechanisms of brain recovery might contribute to identify new therapeutic agents. Fortunately, brain injury after stroke is counteracted by the birth and migration of several populations of progenitor cells towards the injured areas, where angiogenesis and vascular remodeling play a key role providing trophic support and guidance during neurorepair. Endothelial progenitor cells (EPCs) constitute a pool of circulating bone-marrow derived cells that mobilize after an ischemic injury with the potential to incorporate into the damaged endothelium, to form new vessels, or to secrete trophic factors stimulating vessel remodeling. The circulating levels of EPCs are altered after stroke, and several subpopulations have proved to boost brain neurorepair in preclinical models of cerebral ischemia. The goal of this review is to discuss the current state of the neuroreparative actions of EPCs, focusing on their paracrine signaling mechanisms thorough their secretome and released extracellular vesicles.
DNA-stabilized silver nanoclusters (AgN-DNAs) are known to have one or two DNA oligomer ligands per nanocluster. Here, we present the first evidence that AgN-DNA species can possess additional ...chloride ligands that lead to increased stability in biologically relevant concentrations of chloride. Mass spectrometry of five chromatographically isolated near-infrared (NIR)-emissive AgN-DNA species with previously reported X-ray crystal structures determines their molecular formulas to be (DNA)2Ag16Cl28+. Chloride ligands can be exchanged for bromides, which red-shift the optical spectra of these emitters. Density functional theory (DFT) calculations of the 6-electron nanocluster show that the two newly identified chloride ligands were previously assigned as low-occupancy silvers by X-ray crystallography. DFT also confirms the stability of chloride in the crystallographic structure, yields qualitative agreement between computed and measured UV–vis absorption spectra, and provides interpretation of the 35Cl-nuclear magnetic resonance spectrum of (DNA)2Ag16Cl28+. A reanalysis of the X-ray crystal structure confirms that the two previously assigned low-occupancy silvers are, in fact, chlorides, yielding (DNA)2Ag16Cl28+. Using the unusual stability of (DNA)2Ag16Cl28+ in biologically relevant saline solutions as a possible indicator of other chloride-containing AgN-DNAs, we identified an additional AgN-DNA with a chloride ligand by high-throughput screening. Inclusion of chlorides on AgN-DNAs presents a promising new route to expand the diversity of AgN-DNA structure–property relationships and to imbue these emitters with favorable stability for biophotonics applications.
DNA oligomers are known to serve as stabilizing ligands for silver nanoclusters (Ag N -DNAs) with rod-like nanocluster geometries and nanosecond-lived fluorescence. Here, we report two AgN-DNAs that ...possess distinctly different structural properties and are the first to exhibit only microsecond-lived luminescence. These emitters are characterized by significant broadband downconversion from the ultraviolet/visible to the near-infrared region. Circular dichroism spectroscopy shows that the structures of these two Ag N -DNAs differ significantly from previously reported Ag N -DNAs. We find that these nanoclusters contain eight valence electrons, making them the first reported DNA-stabilized luminescent quasi-spherical superatoms. This work demonstrates the important role that nanocluster composition and geometry play in dictating luminescence properties of Ag N -DNAs and significantly expands the space of structure–property relations that can be achieved for Ag N -DNAs.
Cancer cells thrive when embedded in a fine-tuned cellular and extracellular environment or tumour microenvironment (TME). There is a general understanding of a co-evolution between cancer cells and ...their surrounding TME, pointing at a functional connection between cancer cells characteristics and the perturbations induced in their surrounding tissue. However, it has never been formally proven whether this functional connection needs to be set from the start or if aggressive cancer cells always dominate their microenvironmental any point in time. This would require a dedicated experimental setting where malignant cells are challenged to grow in a different TME from the one they would naturally create. Here we generated an experimental setting where we transiently perturb the secretory profile of aggressive breast cancer cells without affecting their intrinsic growth ability, which led to the initial establishment of an atypical TME. Interestingly, even if initially tumours are formed, this atypical TME evolves to impair long term in vivo cancer growth. Using a combination of in vivo transcriptomics, protein arrays and in vitro co-cultures, we found that the atypical TME culminates in the infiltration of macrophages with STAT1high activity. These macrophages show strong anti-tumoural functions which reduce long-term tumour growth, despite lacking canonical M1 markers. Importantly, gene signatures of the mesenchymal compartment of the TME, as well as the anti-tumoural macrophages, show striking prognostic power that correlates with less aggressive human breast cancers.
•Uncoupling breast cancer cell intrinsic potential from TME activation results in impaired tumour growth.•Long term impairment of growth is due to early differences in tumour microenvironment.•Fibroblasts and non-canonical macrophages are crucial for limiting tumour growth.•We define a specific tumour microenvironment with strong prognostic features for breast cancer patients.
DNA-stabilized silver clusters (Ag
N
-DNAs) exhibit diverse sequence-programmed fluorescence, making these tunable nanoclusters promising sensors and bioimaging probes. Recent advances in the ...understanding of Ag
N
-DNA structures and optical properties have largely relied on detailed characterization of single species isolated by chromatography. Because most Ag
N
-DNAs are unstable under chromatography, such studies do not fully capture the diversity of these clusters. As an alternative method, we use high-throughput synthesis and spectroscopy to measure steady state Stokes shifts of hundreds of Ag
N
-DNAs. Steady state Stokes shift is of interest because its magnitude is determined by energy relaxation processes which may be sensitive to specific cluster geometry, attachment to the DNA template, and structural engagement of solvent molecules. We identify 305 Ag
N
-DNA samples with single-peaked emission and excitation spectra, a characteristic of pure solutions and single emitters, which thus likely contain a dominant emissive Ag
N
-DNA species. Steady state Stokes shifts of these samples vary widely, are in agreement with values reported for purified clusters, and are several times larger than for typical organic dyes. We then examine how DNA sequence selects Ag
N
-DNA excitation energies and Stokes shifts, comment on possible mechanisms for energy relaxation processes in Ag
N
-DNAs, and discuss how differences in Ag
N
-DNA structure and DNA conformation may result in the wide distribution of optical properties observed here. These results may aid computational studies seeking to understand the fluorescence process in Ag
N
-DNAs and the relations of this process to Ag
N
-DNA structure.
We present a high-throughput study of the steady state Stokes shifts of >300 fluorescent DNA-stabilized silver clusters and the correlations of DNA sequence with the optical properties of these fluorophores.
We present chemical synthesis strategies for DNA-stabilized silver nanoclusters (Ag
N
-DNAs) with near-infrared (NIR) emission in the biological tissue transparency windows. Elevated temperatures can ...significantly increase chemical yield of near-infrared nanoclusters. In most cases, basic pH favors near-infrared nanoclusters while micromolar amounts of NaCl inhibit their formation.
Synthesis yield of NIR-emissive DNA-stabilized silver nanoclusters is significantly enhanced by temperatures of 20 to 40 °C and basic pH.
Melanoma is a highly aggressive tumour that can metastasize very early in disease progression. Notably, melanoma can disseminate using amoeboid invasive strategies. We show here that high Myosin II ...activity, high levels of ki-67 and high tumour-initiating abilities are characteristic of invasive amoeboid melanoma cells. Mechanistically, we find that WNT11-FZD7-DAAM1 activates Rho-ROCK1/2-Myosin II and plays a crucial role in regulating tumour-initiating potential, local invasion and distant metastasis formation. Importantly, amoeboid melanoma cells express both proliferative and invasive gene signatures. As such, invasive fronts of human and mouse melanomas are enriched in amoeboid cells that are also ki-67 positive. This pattern is further enhanced in metastatic lesions. We propose eradication of amoeboid melanoma cells after surgical removal as a therapeutic strategy.
Endothelial progenitor cells (EPCs) have been pursued as a potential cellular therapy for stroke and central nervous system injury. However, their underlying mechanisms remain to be fully defined. ...Recent experimental studies suggest that mitochondria may be released and transferred between cells. In this proof‐of‐concept study, we asked whether beneficial effects of EPCs may partly involve a mitochondrial phenomenon as well. First, EPC‐derived conditioned medium was collected and divided into supernatant and particle fractions after centrifugation. Electron microscopy, Western blots, and flow cytometry showed that EPCs were able to release mitochondria. ATP and oxygen consumption assays suggested that these extracellular mitochondria may still be functionally viable. Confocal microscopy confirmed that EPC‐derived extracellular mitochondria can be incorporated into normal brain endothelial cells. Adding EPC particles to brain endothelial cells promoted angiogenesis and decreased the permeability of brain endothelial cells. Next, we asked whether EPC‐derived mitochondria may be protective. As expected, oxygen–glucose deprivation (OGD) increased brain endothelial permeability. Adding EPC‐derived mitochondria particles to the damaged brain endothelium increased levels of mitochondrial protein TOM40, mitochondrial DNA copy number, and intracellular ATP. Along with these indirect markers of mitochondrial transfer, endothelial tightness was also restored after OGD. Taken together, these findings suggest that EPCs may support brain endothelial energetics, barrier integrity, and angiogenic function partly through extracellular mitochondrial transfer. Stem Cells 2018;36:1404–1410
Endothelial progenitor cell (EPC)‐derived mitochondria particles to damaged brain endothelium after oxygen–glucose deprivation (OGD) increased levels of mitochondrial protein TOM40, mitochondrial DNA copy number, and intracellular ATP along with restoring endothelial tightness after OGD. These findings suggest that EPCs may support brain endothelial energetics, barrier integrity, and angiogenic function partly through extracellular mitochondrial transfer.
DNA serves as a versatile template for few-atom silver clusters and their organized self-assembly. These clusters possess unique structural and photophysical properties that are programmed into the ...DNA template sequence, resulting in a rich palette of fluorophores which hold promise as chemical and biomolecular sensors, biolabels, and nanophotonic elements. Here, we review recent advances in the fundamental understanding of DNA-templated silver clusters (Ag
N
-DNAs), including the role played by the silver-mediated DNA complexes which are synthetic precursors to Ag
N
-DNAs, structure-property relations of Ag
N
-DNAs, and the excited state dynamics leading to fluorescence in these clusters. We also summarize the current understanding of how DNA sequence selects the properties of Ag
N
-DNAs and how sequence can be harnessed for informed design and for ordered multi-cluster assembly. To catalyze future research, we end with a discussion of several opportunities and challenges, both fundamental and applied, for the Ag
N
-DNA research community. A comprehensive fundamental understanding of this class of metal cluster fluorophores can provide the basis for rational design and for advancement of their applications in fluorescence-based sensing, biosciences, nanophotonics, and catalysis.
DNA can stabilize silver clusters with sequence-tuned fluorescence. We review recent advances in understanding of the structures and properties of DNA-templated silver clusters, their rational design and ordered arrangement, and emerging challenges.
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