Programmable Metal/Semiconductor Nanostructures for mRNA-Modulated Molecular Delivery

Cytotoxic chemotherapeutics are important tools for the clinical treatment of a variety of solid tumors. However, their use is often complicated by multidrug resistance that can develop in patients, limiting the potencies of these agents. New strategies are needed to provide versatile systems that can respond to and disable resistance mechanisms. We demonstrate the use of a new family of materials, programmable metal/semiconductor nanostructures, for drug delivery and mRNA sensing in drug-resistant cells. These materials are composed of a central core gold nanoparticle surrounded by a layer of DNA-capped quantum dots. The modularity of these "core-satellite" assemblies allows for the construction of superstructures with controlled size and the incorporation of multiple functionalities for drug delivery. The DNA sequence within the nanoparticle specifically binds to an mRNA encoding an important drug resistance factor, MRP1, inside cancer cells, releasing a potent anticancer drug doxorubicin. This event triggers a turn-on fluorescence emission along with a downregulation of the MRP1 drug efflux pump, a main resistance factor for doxorubicin, yielding a remarkable improvement in therapeutic efficacy against drug-resistant cancer cells. This work paves the way for the development of programmable materials with multiple synergistic functionalities for biomedical applications.

Compositional and orientational control in metal halide perovskites of reduced dimensionality

Reduced-dimensional metal halide perovskites (RDPs) have attracted significant attention in recent years due to their promising light harvesting and emissive properties. We sought to increase the systematic understanding of how RDPs are formed. Here we report that layered intermediate complexes formed with the solvent provide a scaffold that facilitates the nucleation and growth of RDPs during annealing, as observed via in situ X-ray scattering. Transient absorption spectroscopy of RDP single crystals and films enables the identification of the distribution of quantum well thicknesses. These insights allow us to develop a kinetic model of RDP formation that accounts for the experimentally observed size distribution of wells. RDPs exhibit a thickness distribution (with sizes that extend above n = 5) determined largely by the stoichiometric proportion between the intercalating cation and solvent complexes. The results indicate a means to control the distribution, composition and orientation of RDPs via the selection of the intercalating cation, the solvent and the deposition technique.

Curvature-Mediated Surface Accessibility Enables Ultrasensitive Electrochemical Human Methyltransferase Analysis

The development of new tools for tracking the activity of human DNA methyltransferases is an important goal given the role of this enzyme as a cancer biomarker and epigenetic modulator. However, analysis of the human DNA (cytosine-5)-methyltransferase 1 (Dnmt1) activity is challenging, especially in crude samples, because of the low activity and large size of the enzyme. Here, we report a new approach to Dnmt analysis that combines nanostructured electrodes with a digest-and-amplify strategy that directly monitors Dnmt1 activity with high sensitivity. Nanostructured electrodes are required for the function of the assay to promote the accessibility of the electrode for human Dnmt1. Moreover, DNA-templated deposition of silver nanoparticles (for signal amplification) is combined with DNA Exonuclease I digestion to yield optimal target-to-control signals. We achieve high sensitivity for the detection of human Dnmt1, and particularly Dnmt1 from crude cell lysates. Specifically, the detection limit of our electrochemical assay is 20 pM, which is 2 orders of magnitude lower than previously reported methods. In crude lysates, we detected Dnmt1 from as few as five colorectal cancer cells (HCT116). With biopsy samples, we were able to distinguish colorectal tumor tissue from healthy adjacent tissue using only 10 μg of sample. The strategy enables analysis of an important marker underlying the epigenetic basis of cancerous transformation.

Metal-Organic Framework Thin Films on High-Curvature Nanostructures Toward Tandem Electrocatalysis

In tandem catalysis, two distinct catalytic materials are interfaced to feed the product of one reaction into the next one. This approach, analogous to enzyme cascades, can potentially be used to upgrade small molecules such as CO₂ to more valuable hydrocarbons. Here, we investigate the materials chemistry of metal-organic framework (MOF) thin films grown on gold nanostructured microelectrodes (AuNMEs), focusing on the key materials chemistry challenges necessary to enable the applications of these MOF/AuNME composites in tandem catalysis. We applied two growth methods-layer-by-layer and solvothermal-to grow a variety of MOF thin films on AuNMEs and then characterized them using scanning electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. The MOF@AuNME materials were then evaluated for electrocatalytic CO₂ reduction. The morphology and crystallinity of the MOF thin films were examined, and it was found that MOF thin films were capable of dramatically suppressing CO production on AuNMEs and producing further-reduced carbon products such as CH₄ and C₂H₄. This work illustrates the use of MOF thin films to tune the activity of an underlying CO₂RR catalyst to produce further-reduced products.

2D Metal Oxyhalide-Derived Catalysts for Efficient CO2 Electroreduction

Electrochemical reduction of CO₂ is a compelling route to store renewable electricity in the form of carbon-based fuels. Efficient electrochemical reduction of CO₂ requires catalysts that combine high activity, high selectivity, and low overpotential. Extensive surface reconstruction of metal catalysts under high productivity operating conditions (high current densities, reducing potentials, and variable pH) renders the realization of tailored catalysts that maximize the exposure of the most favorable facets, the number of active sites, and the oxidation state all the more challenging. Earth-abundant transition metals such as tin, bismuth, and lead have been proven stable and product-specific, but exhibit limited partial current densities. Here, a strategy that employs bismuth oxyhalides as a template from which 2D bismuth-based catalysts are derived is reported. The BiOBr-templated catalyst exhibits a preferential exposure of highly active Bi ( 11¯0 ) facets. Thereby, the CO₂ reduction reaction selectivity is increased to over 90% Faradaic efficiency and simultaneously stable current densities of up to 200 mA cm^-2 are achieved-more than a twofold increase in the production of the energy-storage liquid formic acid compared to previous best Bi catalysts.

Dynamic CTC phenotypes in metastatic prostate cancer models visualized using magnetic ranking cytometry

Tumors can shed thousands of cells into the circulation daily. These circulating tumor cells (CTCs) are heterogeneous, and their phenotypes change dynamically. Real-time monitoring of CTC phenotypes is crucial to elucidate the role of CTCs in the metastatic cascade. Here, we monitor phenotypic changes in CTCs in mice xenografted with tumors with varying aggressiveness during cancer progression and a course of chemotherapy to study the metastatic potential of CTCs and changes in the properties of these cells in response to treatment. A new device that enables magnetic ranking cytometry (MagRC) is employed to profile the phenotypic properties of CTCs. Overall, CTCs from metastatic xenografts in mice display dynamic and heterogeneous profiles while non-metastatic models had static profiles. Decreased heterogeneity followed by a reduction in metastasis incidence was observed after a course of chemotherapy administered to highly metastatic xenografts. Phenotypic profiling of CTCs could be employed to monitor disease progression and predict therapeutic responses.

A fully-integrated and automated testing device for PCR-free viral nucleic acid detection in whole blood

Integrated devices for automated nucleic acid testing (NAT) are critical for infectious disease diagnosis to be performed outside of centralized laboratories. The gold standard methods for NAT are enzymatic amplification methods like the polymerase chain reaction that typically require expensive equipment and highly-trained personnel, limiting use in low-resource settings. A low-cost, integrated, rapid, portable and user-friendly point-of-care (POC) nucleic acid diagnostic device will improve the accessibility of NAT. Here, we present a fully integrated and simple-to-use POC device operated by a passive fluidic method that is able to perform a sequential multi-step assay to detect viral nucleic acids in blood. This simple device enabled the rapid detection of hepatitis C virus in blood in approximately 30 minutes with minimal sample handling by the user.

A Multifunctional Chemical Probe for the Measurement of Local Micropolarity and Microviscosity in Mitochondria

The measurement of physicochemical parameters in living cells can provide information on individual cellular organelles, helping us to understand subcellular function in health and disease. While organelle-specific chemical probes have allowed qualitative evaluation of microenvironmental variations, the simultaneous quantification of mitochondrial local microviscosity (η_m ) and micropolarity (ϵ_m ), along with concurrent structural variations, has remained an unmet need. Herein, we describe a new multifunctional mitochondrial probe (MMP) for simultaneous monitoring of η_m and ϵ_m by fluorescence lifetime and emission intensity recordings, respectively. The MMP enables highly precise measurements of η_m and ϵ_m in the presence of a variety of agents perturbing cellular function, and the observed changes can also be correlated with alterations in mitochondrial network morphology and motility. This strategy represents a promising tool for the analysis of subtle changes in organellar structure.

Electron-phonon interaction in efficient perovskite blue emitters

Low-dimensional perovskites have-in view of their high radiative recombination rates-shown great promise in achieving high luminescence brightness and colour saturation. Here we investigate the effect of electron-phonon interactions on the luminescence of single crystals of two-dimensional perovskites, showing that reducing these interactions can lead to bright blue emission in two-dimensional perovskites. Resonance Raman spectra and deformation potential analysis show that strong electron-phonon interactions result in fast non-radiative decay, and that this lowers the photoluminescence quantum yield (PLQY). Neutron scattering, solid-state NMR measurements of spin-lattice relaxation, density functional theory simulations and experimental atomic displacement measurements reveal that molecular motion is slowest, and rigidity greatest, in the brightest emitter. By varying the molecular configuration of the ligands, we show that a PLQY up to 79% and linewidth of 20 nm can be reached by controlling crystal rigidity and electron-phonon interactions. Designing crystal structures with electron-phonon interactions in mind offers a previously underexplored avenue to improve optoelectronic materials' performance.

2D matrix engineering for homogeneous quantum dot coupling in photovoltaic solids

Colloidal quantum dots (CQDs) are promising photovoltaic (PV) materials because of their widely tunable absorption spectrum controlled by nanocrystal size^1,2. Their bandgap tunability allows not only the optimization of single-junction cells, but also the fabrication of multijunction cells that complement perovskites and silicon ³ . Advances in surface passivation^2,4-7, combined with advances in device structures ⁸ , have contributed to certified power conversion efficiencies (PCEs) that rose to 11% in 2016 ⁹ . Further gains in performance are available if the thickness of the devices can be increased to maximize the light harvesting at a high fill factor (FF). However, at present the active layer thickness is limited to ~300 nm by the concomitant photocarrier diffusion length. To date, CQD devices thicker than this typically exhibit decreases in short-circuit current (J_SC) and open-circuit voltage (V_OC), as seen in previous reports^3,9-11. Here, we report a matrix engineering strategy for CQD solids that significantly enhances the photocarrier diffusion length. We find that a hybrid inorganic-amine coordinating complex enables us to generate a high-quality two-dimensionally (2D) confined inorganic matrix that programmes internanoparticle spacing at the atomic scale. This strategy enables the reduction of structural and energetic disorder in the solid and concurrent improvements in the CQD packing density and uniformity. Consequently, planar devices with a nearly doubled active layer thicknesses (~600 nm) and record values of J_SC (32 mA cm^-2) are fabricated. The V_OC improved as the current was increased. We demonstrate CQD solar cells with a certified record efficiency of 12%.

Activated Electron-Transport Layers for Infrared Quantum Dot Optoelectronics

Photovoltaic (PV) materials such as perovskites and silicon are generally unabsorptive at wavelengths longer than 1100 nm, leaving a significant portion of the IR solar spectrum unharvested. Small-bandgap colloidal quantum dots (CQDs) are a promising platform to offer tandem complementary IR PV solutions. Today, the best performing CQD PVs use zinc oxide (ZnO) as an electron-transport layer. However, these electrodes require ultraviolet (UV)-light activation to overcome the low carrier density of ZnO, precluding the realization of CQD tandem photovoltaics. Here, a new sol-gel UV-free electrode based on Al/Cl hybrid doping of ZnO (CAZO) is developed. Al heterovalent doping provides a strong n-type character while Cl surface passivation leads to a more favorable band alignment for electron extraction. CAZO CQD IR solar cell devices exhibit, at wavelengths beyond the Si bandgap, an external quantum efficiency of 73%, leading to an additional 0.92% IR power conversion efficiency without UV activation. Conventional ZnO devices, on the other hand, add fewer than 0.01 power points at these operating conditions.

DNA Polymerase θ Increases Mutational Rates in Mitochondrial DNA

Replication and maintenance of mitochondrial DNA (mtDNA) is essential for cellular function, yet few DNA polymerases are known to function in mitochondria. Here, we conclusively demonstrate that DNA polymerase θ (Polθ) localizes to mitochondria and explore whether this protein is overexpressed in patient-derived cells and tumors. Polθ appears to play an important role in facilitating mtDNA replication under conditions of oxidative stress, and this error-prone polymerase was found to introduce mutations into mtDNA. In patient-derived cells bearing a pathogenic mtDNA mutation, Polθ expression levels were increased, indicating that the oxidative conditions in these cells promote higher expression levels for Polθ. Heightened Polθ expression levels were also associated with elevated mtDNA mutation rates in a selected panel of human tumor tissues, suggesting that this protein can influence mutational frequencies in tumors. The results reported indicate that the mitochondrial function of Polθ may have relevance to human disease.

Single-cell mRNA cytometry via sequence-specific nanoparticle clustering and trapping

Cell-to-cell variation in gene expression creates a need for techniques that characterize expression at the level of individual cells. This is particularly true for rare circulating tumor cells (CTCs), in which subtyping and drug resistance are of intense interest. Here we describe a method for cell analysis – single-cell mRNA cytometry – that enables the isolation of rare cells from whole blood as a function of target mRNA sequences. This approach uses two classes of magnetic particles that are labelled to selectively hybridize with different regions of the target mRNA. Hybridization leads to the formation of large magnetic clusters that remain localized within the cells of interest, thereby enabling the cells to be magnetically separated. Targeting specific intracellular mRNAs enables sorting of CTCs from normal hematopoietic cells. No PCR amplification is required to determine RNA expression levels and genotype at the single-cell level, and minimal cell manipulation is required. To demonstrate this approach we use single-cell mRNA cytometry to detect clinically-important sequences in prostate cancer specimens.

Pore Shape Defines Paths of Metastatic Cell Migration

Invasion of dense tissues by cancer cells involves the interplay between the penetration resistance offered by interstitial pores and the deformability of cells. Metastatic cancer cells find optimal paths of minimal resistance through an adaptive path-finding process, which leads to successful dissemination. The physical limit of nuclear deformation is related to the minimal cross section of pores that can be successfully penetrated. However, this single biophysical parameter does not fully describe the architectural complexity of tissues featuring pores of variable area and shape. Here, employing laser nanolithography, we fabricate pore microenvironment models with well-controlled pore shapes, through which human breast cells (MCF10A) and their metastatic offspring (MCF10CA1a.cl1) could pervade. In these experimental settings, we demonstrate that the actual pore shape, and not only the cross section, is a major and independent determinant of cancer penetration efficiency. In complex architectures containing pores demanding large deformations from invading cells, tall and narrow rectangular openings facilitate cancer migration. In addition, we highlight the characteristic traits of the explorative behavior enabling metastatic cells to identify and select such pore shapes in a complex multishape pore environment, pinpointing paths of least resistance to invasion.

Combinatorial Probes for High-Throughput Electrochemical Analysis of Circulating Nucleic Acids in Clinical Samples

The analysis of circulating tumour nucleic acids (ctNAs) provides a minimally invasive way to assess the mutational spectrum of a tumour. However, effective and practical methods for analyzing this emerging class of markers are lacking. Analysis of ctNAs using a sensor-based approach has notable challenges, as it is vital to differentiate nucleic acids from normal cells from mutation-bearing sequences emerging from tumours. Moreover, many genes related to cancer have dozens of different mutations. Herein, we report an electrochemical approach that directly detects genes with mutations in patient serum by using combinatorial probes (CPs). The CPs enable detection of all of the mutant alleles derived from the same part of the gene. As a proof of concept, we analyze mutations of the EGFR gene, which has more than 40 clinically relevant alterations that include deletions, insertions, and point mutations. Our CP-based approach accurately detects mutant sequences directly in patient serum.

Synthetic Control over Quantum Well Width Distribution and Carrier Migration in Low-Dimensional Perovskite Photovoltaics

Metal halide perovskites have achieved photovoltaic efficiencies exceeding 22%, but their widespread use is hindered by their instability in the presence of water and oxygen. To bolster stability, researchers have developed low-dimensional perovskites wherein bulky organic ligands terminate the perovskite lattice, forming quantum wells (QWs) that are protected by the organic layers. In thin films, the width of these QWs exhibits a distribution that results in a spread of bandgaps in the material arising due to varying degrees of quantum confinement across the population. Means to achieve refined control over this QW width distribution, and to examine and understand its influence on photovoltaic performance, are therefore of intense interest. Here we show that moving to the ligand allylammonium enables a narrower distribution of QW widths, creating a flattened energy landscape that leads to ×1.4 and ×1.9 longer diffusion lengths for electrons and holes, respectively. We attribute this to reduced ultrafast shallow hole trapping that originates from the most strongly confined QWs. We observe an increased PCE of 14.4% for allylammonium-based perovskite QW photovoltaics, compared to 11-12% PCEs obtained for analogous devices using phenethylammonium and butylammonium ligands. We then optimize the devices using mixed-cation strategies, achieving 16.5% PCE for allylammonium devices. The devices retain 90% of their initial PCEs after >650 h when stored under ambient atmospheric conditions.

Mitochondrial tyrosyl-DNA phosphodiesterase 2 and its TDP2S short isoform

Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs abortive topoisomerase II cleavage complexes. Here, we identify a novel short isoform of TDP2 (TDP2^S) expressed from an alternative transcription start site. TDP2^S contains a mitochondrial targeting sequence, contributing to its enrichment in the mitochondria and cytosol, while full-length TDP2 contains a nuclear localization signal and the ubiquitin-associated domain in the N-terminus. Our study reveals that both TDP2 isoforms are present and active in the mitochondria. Comparison of isogenic wild-type (WT) and TDP2 knockout (TDP2^-/-/-) DT40 cells shows that TDP2^-/-/- cells are hypersensitive to mitochondrial-targeted doxorubicin (mtDox), and that complementing TDP2^-/-/- cells with human TDP2 restores resistance to mtDox. Furthermore, mtDox selectively depletes mitochondrial DNA in TDP2^-/-/- cells. Using CRISPR-engineered human cells expressing only the TDP2^S isoform, we show that TDP2^S also protects human cells against mtDox. Finally, lack of TDP2 in the mitochondria reduces the mitochondria transcription levels in two different human cell lines. In addition to identifying a novel TDP2^S isoform, our report demonstrates the presence and importance of both TDP2 isoforms in the mitochondria.

Mixed-quantum-dot solar cells

Colloidal quantum dots are emerging solution-processed materials for large-scale and low-cost photovoltaics. The recent advent of quantum dot inks has overcome the prior need for solid-state exchanges that previously added cost, complexity, and morphological disruption to the quantum dot solid. Unfortunately, these inks remain limited by the photocarrier diffusion length. Here we devise a strategy based on n- and p-type ligands that judiciously shifts the quantum dot band alignment. It leads to ink-based materials that retain the independent surface functionalization of quantum dots, and it creates distinguishable donor and acceptor domains for bulk heterojunctions. Interdot carrier transfer and exciton dissociation studies confirm efficient charge separation at the nanoscale interfaces between the two classes of quantum dots. We fabricate the first mixed-quantum-dot solar cells and achieve a power conversion of 10.4%, which surpasses the performance of previously reported bulk heterojunction quantum dot devices fully two-fold, indicating the potential of the mixed-quantum-dot approach.

Enhancing the Potency of Nalidixic Acid toward a Bacterial DNA Gyrase with Conjugated Peptides

Quinolones and fluoroquinolones are widely used antibacterial agents. Nalidixic acid (NA) is a first-generation quinolone-based antibiotic that has a narrow spectrum and poor pharmacokinetics. Here, we describe a family of peptide-nalidixic acid conjugates featuring different levels of hydrophobicity and molecular charge prepared by solid-phase peptide synthesis that exhibit intriguing improvements in potency. In comparison to NA, which has a low level of potency in S. aureus, the NA peptide conjugates with optimized hydrophobicities and molecular charges exhibited significantly improved antibacterial activity. The most potent NA conjugate-featuring a peptide containing cyclohexylalanine and arginine-exhibited efficient bacterial uptake and, notably, specific inhibition of S. aureus DNA gyrase. A systematic study of peptide-NA conjugates revealed that a fine balance of cationic charge and hydrophobicity in an appendage anchored to the core of the drug is required to overcome the intrinsic resistance of S. aureus DNA gyrase toward this quinolone-based drug.

Characterization of Trypanosoma cruzi MutY DNA glycosylase ortholog and its role in oxidative stress response

Trypanosoma cruzi is a protozoan parasite and the causative agent of Chagas disease. Like most living organisms, it is susceptible to oxidative stress, and must adapt to distinct environments. Hence, DNA repair is essential for its survival and the persistence of infection. Therefore, we studied whether T. cruzi has a homolog counterpart of the MutY enzyme (TcMYH), important in the DNA Base Excision Repair (BER) mechanism. Analysis of T. cruzi genome database showed that this parasite has a putative MutY DNA glycosylase sequence. We performed heterologous complementation assays using this genomic sequence. TcMYH complemented the Escherichia coli MutY- strain, reducing the mutation rate to a level similar to wild type. In in vitro assays, TcMYH was able to remove an adenine that was opposite to 8-oxoguanine. We have also constructed a T. cruzi lineage that overexpresses MYH. Although in standard conditions this lineage has similar growth to control cells, the overexpressor is more sensitive to hydrogen peroxide and glucose oxidase than the control, probably due to accumulation of AP sites in its DNA. Localization experiments with GFP-fused TcMYH showed this enzyme is present in both nucleus and mitochondrion. QPCR and MtOX results reinforce the presence and function of TcMYH in these two organelles. Our data suggest T. cruzi has a functional MYH DNA glycosylase, which participates in nuclear and mitochondrial DNA Base Excision Repair.