Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum ...computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA HJ). Indolenine squaraines were chosen for their excellent spectral properties, stability, and diversity of chemical modifications. Six squaraines of varying hydrophobicity from highly hydrophobic to highly hydrophilic were assembled in two dimer configurations and a tetramer. In general, the examined squaraines demonstrated a propensity toward face-to-face aggregation behavior observed via steady-state absorption, fluorescence, and circular dichroism spectroscopies. Modeling based on the Kühn–Renger–May approach quantified the strength of excitonic coupling in the squaraine aggregates. The strength of excitonic coupling strongly correlated with squaraine hydrophobic region. Dimer aggregates of dichloroindolenine squaraine were found to exhibit the strongest coupling strength of 132 meV (1065 cm–1). In addition, we identified the sites for dye attachment in the DNA HJ that promote the closest spacing between the dyes in their dimers. The extracted aggregate geometries, and the role of electrostatic and steric effects in squaraine aggregation are also discussed. Taken together, these findings provide a deeper insight into how dye structures influence excitonic coupling in dye aggregates covalently templated via DNA, and guidance in design rules for exciton-based materials and devices.
Dye molecules that absorb light in the visible region are key components in many applications, including organic photovoltaics, biological fluorescent labeling, super-resolution microscopy, and ...energy transport. One family of dyes, known as squaraines, has received considerable attention recently due to their favorable electronic and photophysical properties. In addition, these dyes have a strong propensity for aggregation, which results in emergent materials properties, such as exciton delocalization. This will be of benefit in charge separation and energy transport along with fundamental studies in quantum information. Given the high structural tunability of squaraine dyes, it is possible that exciton delocalization could be tailored by modifying the substituents attached to the π-conjugated network. To date, limited theoretical studies have explored the role of substituent effects on the electronic and photophysical properties of squaraines in the context of DNA-templated dye aggregates and resultant excitonic behavior. We used
ab initio
theoretical methods to determine the effects of substituents on the electronic and photophysical properties for a series of nine different squaraine dyes. Solvation free energy was also investigated as an insight into changes in hydrophobic behavior from substituents. The role of molecular symmetry on these properties was also explored
via
conformation and substitution. We found that substituent effects are correlated with the empirical Hammett constant, which demonstrates their electron donating or electron withdrawing strength. Electron withdrawing groups were found to impact solvation free energy, transition dipole moment, static dipole difference, and absorbance more than electron donating groups. All substituents showed a redshift in absorption for the squaraine dye. In addition, solvation free energy increases with Hammett constant. This work represents a first step toward establishing design rules for dyes with desired properties for excitonic applications.
Squaraine dyes are candidates for DNA-templated excitonic interactions. This work presents substituent effects on the electronic and photophysicalproperties of squaraine dyes and a correlation between empirical Hammettconstant and those properties.
Advancements in DNA computation have unlocked molecular-scale information processing possibilities, utilizing the intrinsic properties of DNA for complex logical operations with transformative ...applications in biomedicine. DNA computation shows promise in molecular diagnostics, enabling precise and sensitive detection of genetic mutations and disease biomarkers. Moreover, it holds potential for targeted gene regulation, facilitating personalized therapeutic interventions with enhanced efficacy and reduced side effects. Herein, we have developed six DNAzyme-based logic gates able to process YES, AND, and NOT Boolean logic. The novelty of this work lies in their additional functionalization with a common DNA scaffold for increased cooperativity in input recognition. Moreover, we explored hierarchical input binding to multi-input logic gates, which helped gate optimization. Additionally, we developed a new design of an allosteric hairpin switch used to implement NOT logic. All DNA logic gates achieved the desired true-to-false output signal when detecting a panel of miRNAs, known for their important role in malignancy regulation. This is the first example of DNAzyme-based logic gates having all input-recognizing elements integrated in a single DNA nanostructure, which provides new opportunities for building DNA automatons for diagnosis and therapy of human diseases.
Researchers have developed a new riboswitch-based NOT gate, alongside various DNA logic gates, eachoptimized on a common scaffold. This advancement enhances performance and enables accurate detection of miRNAs on a molecular scale through DNA computing.
Novel indolenine based norsquaraine dyes, wherein the oxygen of the squaric acid bridge was substituted with a barbituric or a dicyanomethylene group, were synthesized and their molecular structure, ...spectral and luminescent properties were compared to those of analogous squaraine dyes. The molecular structure was investigated using X-ray analysis, NMR spectroscopy and ab initio DFT B3LYP/6-311G (d, p) simulations. The calculated populations of possible conformers and the barriers of internal rotations were found to be in good agreement with the experimental data. Norsquaraines absorb and emitt light within the same long-wavelength spectral range as the corresponding squaraines but due to intramolecular H-bonds and increased conformational rigidity they were less sensitive to solvent polarity and the presence of protein (BSA).
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•Novel, norsquaraine dyes were synthesized and compared to analogous squaraines.•Squaric oxygen was substituted with a barbituric and dicyanomethylene group.•The molecular structures were investigated using X-ray, NMR and ab initio.•Norsquaraine molecules are more flat, rigid and polar compared to squaraines.•Both dye classes are suitable for fluorescence based sensing applications.
This study focuses on health-related plant use among speakers of the critically endangered Naukan language (Inuit-Yupik-Unangan family) in the Russian Far East. The Naukan people were forced, in ...1958, under Soviet consolidation, to move from their original settlement on Cape Dezhnev, leading to significant changes in spiritual worldview, subsistence, social structure, and language proficiency in the years that followed. Here, we focus on changes that elders report in their edible, medicinal, and spiritual uses of local plant species since their childhood.
The authors worked from 2014 to 2016 in the villages of Lavrentiya, Lorino, and Uelen, in the Chukotskiy district of the Chukotka autonomous region, directly adjacent to the Bering Strait. We conducted structured interviews, using an oral history approach, along with participant observation and collection of voucher specimens from the local arctic tundra. Those with Naukan names and uses represent 42 species in 25 families.
Participants reported a decrease of 13% in the number of edible species that people currently harvest, from what they recall harvesting in their youth. On the other hand, the number of local species considered to be medicinal has actually increased by 225%. Current and past Naukan medicinal practices diverge in some notable ways from those of neighboring societies on the Alaskan side of the Bering Strait. Most of the spiritual significance of local plants species is remembered by only a few elders.
Naukan elders explained the large increase in use of medicinal plants by noting that their original concept of medicine emphasized prevention and that illnesses were often assigned a spiritual rather than physical cause. Increased integration with ethnic Russians after moving from Naukan led to the adoption not only of new plant uses, but also of an entirely different, more naturalistic way of viewing illness and treatment.
Novel pH-sensitive, water-soluble, long-wavelength fluorescent norsquaraine dyes and their barbituric and dicyanomethylene derivatives were synthesized and investigated. Some of these dyes contain a ...carboxylic functionality that was converted into an NHS ester to facilitate bio-conjugation. The absorption and emission spectra, fluorescence quantum yields, lifetimes, polarization, and photostabilities were measured free in solution and after binding to bovine serum albumin (BSA) and compared to those of conventional squaraines and the norcyanine dye CypHer5. Contrary to squaraines, norsquaraines are pH-sensitive but almost unaffected by the interaction with proteins. These dyes can potentially be used as fluorescent labels for biomedical applications, in particular for protein labeling, polarization-based assays, cell-based and pH-sensing measurements.
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•Novel pH-sensitive, water-soluble, fluorescent norsquaraine dyes were synthesized.•Squaric oxygen was substituted with a barbituric and dicyanomethylene group.•NHS esters of some of these dyes were synthesized to facilitate bio-conjugation.•Spectral and protolytic properties were investigated and compared to squaraines.•The dyes are suitable for protein labeling, polarization and pH-sensing assays.
Commercially available, near-infrared fluorescent squaraine dyes (Seta-635 and Seta-670) were covalently bound to antibodies and employed in surface enhanced immunoassay. From fluorescence intensity ...and lifetime changes determined for a surface which had been coated with silver nanoparticles as well as a non-coated glass surface, both labeled compounds exhibited a 15- to 20-fold enhancement of fluorescence on the silver-coated surface compared to that achieved on the non-coated surface. In addition, the fluorescence lifetime changed drastically for both labels in the case of silver-coated surfaces. The fluorescence signal enhancement obtained for the two dyes was greater than that previously recorded for Rhodamine Red-X and AlexaFluor-647 labels.
Polythiophenboronic acid (PThBA) combines an affinity for saccharides with the unique properties of conducting polymers. This polymer was synthesized by enzymatic catalyzed oxidative polymerization, ...characterized by UV–vis spectroscopy in solvents of different polarity and by 1H NMR. A suspension of PThBA nanoparticles (PThBA NPs) was prepared by injecting a methanol solution of PThBA into an aqueous electrolyte. PThBA NPs were characterized by scanning electron microscopy. Nanoparticle tracking analysis and dynamic light scattering were used to study the concentration of the particles and the particle size distribution. The effect of pH on these properties was analyzed and an increase in nanoparticle size was observed at alkaline pH. This effect was explained by electrostatic swelling of the nanoparticles. Measurements of ζ-potentials in the wide pH range showed the presence of acidic groups with a pK a of 8.6; the value of the surface charge at the conditions of maximal deprotonation of these groups was estimated to be ∼70 mC/m2. Changes in the optical spectra of PThBA NPs due to variations in pH and additions of organic solvents indicate transformations between twisted and planar conformations of the polymer backbone. The binding of saccharides by PThBA NPs resulted in a decrease in the size and charge of the nanoparticles. Recently developed wide-field surface plasmon resonance microscopy (WF-SPRM) can simultaneously monitor every single nanoparticle among many thousands adsorbed on a surface. It was used for the first time to study chemosensitive nanoparticles. The described above effects of pH change and saccharide binding described above, monitor were confirmed by using integral techniques in monitoring individual nanoparticles, by WF-SPRM. The pH effects were shown to be reversible. An increase in the affinity of PThBA NPs for saccharides at a more alkaline pH was also observed. A fast recovery of polymer binding sites by a pH decrease was demonstrated. The synthesized and characterized PThBA NPs can be further used for various purposes including analytical assays, chemical sensors, or chemosensitive nanotechnological devices.
We describe the photophysical properties of Seta-633, a commercially available near-infrared (NIR) dye, and its use as a fluorescent label to study the interaction between low-molecular-weight ...analytes and proteins using fluorescence lifetime as the readout parameter. In a model assay, we demonstrate that a biotinylated Seta-633 tracer binds to antibiotin with high specificity. Importantly, the lifetime of Seta-633−biotin increases about 1.8-fold upon binding to a specific antibody (antibiotin, MW = 160 kDa), while the titration with bovine serum albumin (BSA) or nonspecific antibody does not result in a noticeable change in lifetime. This behavior is contrary to that of fluorescent tracers like Cy5 or Alexa 647, which typically exhibit much smaller lifetime changes upon binding to antibodies.
The applicability of the two newly commercial available squaraine labels Square-670-NHS and Seta-635-NHS to exploring protein-lipid interactions has been evaluated. The labels were conjugated to ...lysozyme (Lz) (squaraine-lysozyme conjugates below referred to as Square-670-Lz and Seta-635-Lz), a structurally well-characterized small globular protein displaying the ability to interact both, electrostatically and hydrophobically with lipids. The lipid component of the model systems was represented by lipid vesicles composed of zwitterionic lipids egg yolk phosphatidylcholine (PC) and 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine (SOPC), and their mixtures with anionic lipids either beef heart cardiolipin (CL) or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG), respectively. Fluorescence intensity of Square-670-Lz was found to decrease upon association with lipid bilayer, while the fluorescence intensity of Seta-635-Lz displayed more complex behavior depending on lipid-to-protein molar ratio. Covalent coupling of squaraine labels to lysozyme exerts different influence on the properties of dye-protein conjugate. It was suggested that Square-670-NHS covalent attachment to Lz molecule enhances protein propensity for self-association, while squaraine label Seta-635-NHS is sensitive to different modes of lysozyme-lipid interactions-within the L:P range 6-11, when hydrophobic protein-lipid interactions are predominant, an aggregation of membrane-bound protein molecules takes place, thereby decreasing the fluorescence intensity of Seta-635-Lz. At higher L:P values (from 22 to 148) when electrostatic interactions are enhanced fluorescence intensity of Seta-635-Lz increases with increasing lipid concentrations.
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