Zero-Background Small-Molecule Sensors for Near-IR Fluorescent Imaging of Biomacromolecular Targets in Cells.

In this study, we report a general approach to the design of a new generation of small-molecule sensors that produce a zero background but are brightly fluorescent in the near-IR spectral range upon selective interaction with a biomolecular target. We developed a fluorescence turn-on/-off mechanism based on the aggregation/deaggregation of phthalocyanine chromophores. As a proof of concept, we designed, prepared, and characterized sensors for in-cell visualization of epidermal growth factor receptor (EGFR) tyrosine kinase. We established a structure/bioavailability correlation, determined conditions for the optimal sensor uptake and imaging, and demonstrated binding specificity and applications over a wide range of treatment options involving live and fixed cells. The new approach enables high-contrast imaging and requires no in-cell chemical assembly or postexposure manipulations (i.e., washes). The general design principles demonstrated in this work can be extended toward sensors and imaging agents for other biomolecular targets.

Pyrene-Benzimidazole Derivatives as Novel Blue Emitters for OLEDs.

Three novel small organic heterocyclic compounds: 2-(1,2-diphenyl)-1H-benzimidazole-7-tert-butylpyrene (compound A), 1,3-di(1,2-diphenyl)-1H-benzimidazole-7-tert-butylpyrene (compound B), and 1,3,6,8-tetra(1,2-diphenyl)-1H-benzimidazolepyrene (compound C) were synthesized and characterized for possible applications as blue OLED emitters. The specific molecular design targeted decreasing intermolecular aggregation and disrupting crystallinity in the solid-state, in order to reduce dye aggregation, and thus obtain efficient pure blue photo- and electroluminescence. Accordingly, the new compounds displayed reasonably high spectral purity in both solution- and solid-states with average CIE coordinates of (0.160 ± 0.005, 0.029 ± 0.009) in solution and (0.152 ± 0.007, 0.126 ± 0.005) in solid-state. These compounds showed a systematic decrease in degree of crystallinity and intermolecular aggregation due to increasing steric hindrance, as revealed using powder X-ray diffraction analysis and spectroscopic studies. An organic light-emitting diode (OLED) prototype fabricated using compound B as the non-doped emissive layer displayed an external quantum efficiency (EQE) of 0.35 (±0.04)% and luminance 100 (±6) cd m-2 at 5.5 V with an essentially pure blue electroluminescence corresponding to CIE coordinates of (0.1482, 0.1300). The highest EQE observed from this OLED prototype was 4.3 (±0.3)% at 3.5 V, and the highest luminance of 290 (±10) cd m-2 at 7.5 V. These values were found comparable to characteristics of the best pure blue OLED devices based on simple fluorescent small-molecule organic chromophores.

Rational design of guiding elements to control folding topology in i-motifs with multiple quadruplexes.

Nucleic acids are versatile scaffolds that accommodate a wide range of precisely defined operational characteristics. Rational design of sensing, molecular computing, nanotechnology, and other nucleic acid devices requires precise control over folding conformations in these macromolecules. Here, we report a new approach that empowers well-defined conformational transitions in DNA molecular devices. Specifically, we develop tools for precise folding of multiple DNA quadruplexes (i-motifs) within the same oligonucleotide strand. To accomplish this task, we modify a DNA strand with kinetic control elements (hairpins and double stranded stems) that fold on a much faster timescale and consequently guide quadruplexes toward the targeted folding topology. To demonstrate that such guiding elements indeed facilitate formation of the targeted folding topology, we thoroughly characterize the folding/unfolding transitions through a combination of thermodynamic techniques, size exclusion chromatography (SEC) and small-angle X-ray scattering (SAXS). Furthermore, we extend SAXS capabilities to produce a direct insight on the shape and dimensions of the folded quadruplexes by computing their electron density maps from solution scattering data.

Photochemistry with Plane-Polarized Light: Controlling Photochemical Reactivity via Spatially Selective Excitation.

Photochemical reactions are intrinsically difficult to control because they involve high-energy excited-state species. Herein we report a novel approach toward controlling photochemical reactions via using the spatially selective excitation of specific electronic transitions. This can be performed using photochemical irradiation with the plane-polarized light of a photoreactive compound uniformly aligned in a nematic liquid-crystalline (LC) medium. Having chosen cyclopropenone photodecarbonylation as a proof-of-concept reaction, we demonstrated that it could be controlled via changing an angle between the incident light polarization plane and the LC director. We showed that two specific partially forbidden electronic transitions were mostly responsible for this photochemical reaction. We envision that this simple general method can be useful in experimental studies of the fundamental details of various photochemical processes and can help to increase the selectivity of photochemical transformations.

Impact of Local Stiffness on Entropy Driven Microscopic Dynamics of Polythiophene.

We exploited the high temporal and spatial resolution of neutron spin echo spectroscopy to investigate the large-scale dynamics of semiflexible conjugated polymer chains in solutions. We used a generalized approach of the well-established Zimm model of flexible polymers to describe the relaxation mode spectra of locally stiff polythiophene chains. The Zimm mode analysis confirms the existence of beads with a finite length that corresponds to a reduced number of segmental modes in semiflexible chains. Irrespective of the temperature and the molecular weight of the conjugated polymer, we witness a universal behavior of the local chain stiffness and invariability of the bead length. Our experimental findings indicate possibly minor role of the change in π-electron conjugation length (and therefore conjugated backbone planar to non-planar conformational transition) in the observed thermochromic behavior of polythiophene but instead point on the major role of chain dynamics in this phenomenon. We also obtained the first experimental evidence of an existence of a single-chain glass state in conjugated polymers.

Design of Turn-On Near-Infrared Fluorescent Probes for Highly Sensitive and Selective Monitoring of Biopolymers.

Simple, sensitive, and selective detection of specific biopolymers is critical in a broad range of biomedical and technological areas. We present a design of turn-on near-infrared (NIR) fluorescent probes with intrinsically high signal-to-background ratio. The fluorescent signal generation mechanism is based on the aggregation/de-aggregation of phthalocyanine chromophores controlled by selective binding of small-molecule "anchor" groups to a specific binding site of a target biopolymer. As a proof-of-concept, we demonstrate a design of a sensor for EGFR tyrosine kinase-an important target in cancer research. The universality of the fluorescent signal generation mechanism, as well as the dependence of the response selectivity on the choice of the small-molecule "anchor" group, make it possible to use this approach to design reliable turn-on NIR fluorescent sensors for detecting specific protein targets present in the low-nanomolar concentration range.

Multidimensional Tunability of Nucleic Acids Enables Sensing over Unknown Backgrounds.

A longstanding challenge in quantitative analysis is the relationship between a sensor's dynamic range and a background: the response range must align with the target's background value. If this condition is not met, a reliable measurement is impossible. The requirement is especially critical for sensing systems displaying sharp responses. In this work, we have solved the problem of response range/background misalignment via design of sensing systems that adjust their response to actual unknown backgrounds. The sensing systems are based on nucleic acid scaffolds: due to an intrinsic trait of multidimensional tunability, the sensors can assess the actual background and adjust response range accordingly. We established a general methodology and demonstrated, as a proof-of-concept, a practically meaningful example of detecting very small changes in proton concentrations over unknown aqueous backgrounds using a DNA i-motif sensor. Owing to multidimensional tunability of a DNA i-motif, this sensor could reliably measure changes in proton concentration that are 3 orders of magnitude below currently available methodologies.

Pyrenylpyridines: Sky-Blue Emitters for Organic Light-Emitting Diodes.

A novel sky-blue-emitting tripyrenylpyridine derivative, 2,4,6-tri(1-pyrenyl)pyridine (2,4,6-TPP), has been synthesized using a Suzuki coupling reaction and compared with three previously reported isomeric dipyrenylpyridine (DPP) analogues (2,4-di(1-pyrenyl)pyridine (2,4-DPP), 2,6-di(1-pyrenyl)pyridine (2,6-DPP), and 3,5-di(1-pyrenyl)pyridine (3,5-DPP)). As revealed by single-crystal X-ray analysis and computational simulations, all compounds possess highly twisted conformations in the solid state with interpyrene torsional angles of 42.3°-57.2°. These solid-state conformations and packing variations of pyrenylpyridines could be correlated to observed variations in physical characteristics such as photo/thermal stability and spectral properties, but showed only marginal influence on electrochemical properties. The novel derivative, 2,4,6-TPP, exhibited the lowest degree of crystallinity as revealed by powder X-ray diffraction analysis and formed amorphous thin films as verified using grazing-incidence wide-angle X-ray scattering. This compound also showed high thermal/photo stability relative to its disubstituted analogues (DPPs). Thus, a nondoped organic light-emitting diode (OLED) prototype was fabricated using 2,4,6-TPP as the emissive layer, which displayed a sky-blue electroluminescence with Commission Internationale de L'Eclairage (CIE) coordinates of (0.18, 0.34). This OLED prototype achieved a maximum external quantum efficiency of 6.0 ± 1.2% at 5 V. The relatively high efficiency for this simple-architecture device reflects a good balance of electron and hole transporting ability of 2,4,6-TPP along with efficient exciton formation in this material and indicates its promise as an emitting material for design of blue OLED devices.

Amplifying fluorescent conjugated polymer sensor for singlet oxygen detection.

A "higher energy gap" concept was applied towards designing an efficient turn-on amplifying sensor for singlet oxygen - an important biomedical and environmental monitoring analytical target. The concept is based on modulation of intramolecular energy transfer in fluorescent conjugated polymers through the formation of a higher energy gap "roadblock" upon reaction with a target analyte. The polymer sensor incorporates 1,4-disubstituted tetracene units which act as reactive sites for singlet oxygen. The resulting polymer sensor demonstrates significant fluorescent signal amplification and a broader analyte detection range relative to a corresponding small-molecule sensor.

Influence of Anion Variations on Morphological, Spectral, and Physical Properties of the Propidium Luminophore.

Propidium iodide (3,8-diamino-5-[3-(diethylmethylammonio)propyl]-6-phenylphenanthridinium diiodide, [P][I]), is a well-known red fluorescent dye that is widely used for biological applications such as staining. In this study, we have replaced the iodide counteranion of [P][I] with three hydrophobic and bulky organic anions, trifluoromethanesulfonate/[TfO], bis(trifluoromethanesulfonyl)imide/[NTf2], and bis(perfluoroethylsulfonyl)imide/[BETI], and have thus obtained a propidium-derived group of uniform materials based on organic salts (PGUMBOS). The morphological, spectral, and physical properties of these materials were investigated in order to understand the impact of anion variations. While [P][I] is a crystalline solid, propidium salts with [BETI] or [NTf2] counteranions, i.e., [P][BETI] and [P][NTf2], have significantly lower crystallinity as reflected in powder X-ray diffraction data. In addition, [P][BETI] and [P][NTf2] exhibited improved photothermal stability as compared to [P][I] when examined using thermogravimetric analysis and time-dependent kinetic fluorescence experiments under the given experimental conditions. Spectral and electronic properties of the propidium luminophore were not significantly changed upon anion variations, although fluorescence lifetimes and quantum yields showed a systematic increase with decreasing solvent polarity. The experimental HOMO-LUMO energy gaps of these compounds were ∼2 eV with energies of HOMO and LUMO orbitals obtained as -5.15 (±0.08) and -3.19 (±0.08) eV.

Three-Dimensional Morphology Control Yielding Enhanced Hole Mobility in Air-Processed Organic Photovoltaics: Demonstration with Grazing-Incidence Wide-Angle X-ray Scattering.

Polymer organic photovoltaic (OPV) device performance is defined by the three-dimensional morphology of the phase-separated domains in the active layer. Here, we determine the evolution of morphology through different stages of tailored solvent vapor and thermal annealing techniques in air-processed poly(3-hexylthiophene-2,5-diyl)/phenyl-C61-butyric acid methyl ester-based OPV blends. A comparative evaluation of the effect of solvent type used for vapor annealing was performed using grazing-incidence wide-angle X-ray scattering, atomic force microscopy, and UV-vis spectroscopy to probe the active-layer morphology. A nonhalogenated orthogonal solvent was found to impart controlled morphological features within the exciton diffusion length scales, enhanced absorbance, greater crystallinity, increased paracrystalline disorder, and improved charge-carrier mobility. Low-boiling, fast-diffusing isopropanol allowed the greatest control over the nanoscale structure of the solvents evaluated and yielded a cocontinuous morphology with narrowed domains and enhanced paths for the charge carrier to reach the anode.

Model System Study of Environmentally Persistent Free Radicals Formation in a Semiconducting Polymer Modified Copper Clay System at Ambient Temperature.

This paper systematically investigates how environmentally persistent free radicals (EPFRs) are formed in a phenol contaminated model soil. Poly-p-phenylene (PPP) modified and copper-loaded montmorillonite (MMT) clays were developed and used as models of soil organic matter and the clay mineral component, respectively, with phenol being employed as a precursor pollutant. The polymer modification of the clays was carried out via surface-confined Kumada catalyst-transfer chain-growth polymerization. The presence and location of the polymer were confirmed by a combination of thermogravimetric analysis (TGA), Raman spectroscopy, and X-ray diffraction data. EPFRs were formed by the Cu(II)-clay (Cu(II)CaMMT) and poly-p-phenylene-Cu(II)clay (PPP-Cu(II)CaMMT) composite systems under environmentally relevant conditions. The g-factor and concentration of EPFRs formed by the Cu(II)CaMMT and PPP-Cu(II)CaMMT systems were found to be 2.0034 and 1.22 × 1017 spins/g and 2.0033 and 1.58 × 1017spins/g, respectively. These g-factors are consistent with the formation of phenoxyl radicals. Extended X-Ray absorption fine structure (EXAFS) analysis shows that there are distinct differences in the local stuctures of the phenoxyl radicals associated with only the Cu(II) redox centers and those formed in the presences of the PPP polymer. X-ray absorption near edge spectroscopy (XANES) results provided evidence for the reduction of Cu(II) to Cu(I) in the EPFR forming process. The 1/e lifetimes of the formed EPFRs revealed a decay time of ~20 h for the Cu(II)CaMMT system and a two-step decay pattern for the PPP-Cu(II)CaMMT system with decay times of ~13.5 h and ~55.6 h. Finally, the generation of reactive oxygen species (hydroxyl radical; •OH) by these clay systems was also investigated, with higher concentrations of •OH detected for the phenol-dosed Cu(II)CaMMT and PPP-Cu(II)CaMMT systems, compared to the non-EPFR containing undosed PPP-Cu(II)CaMMT system.

Rational Control of Folding Cooperativity in DNA Quadruplexes.

Availability of basic tools for engineering molecular systems with precisely defined properties is crucial toward progress in development of new responsive materials. Among such materials are systems capable of generating an ultrasensitive response (i.e., large relative changes in output in response to small changes in input). Herein, we focus on a rational design of DNA quadruplex based structures as ultrasensitive response elements. In particular, we demonstrate how addition of allosteric guiding elements can be engineered into H(+)-responsive i-motif structure to yield maximized response sensitivity.

A dual input DNA-based molecular switch.

We have designed and characterized a DNA-based molecular switch which processes two physiologically relevant inputs: pH (i.e. alkalinisation) and enzymatic activity, and generates a chemical output (in situ synthesized oligonucleotide). The design, based on allosteric interactions between i-motif and hairpin stem within the DNA molecule, addresses such critical physiological system parameters as molecular simplicity, tunability, orthogonality of the two input sensing domains, and compatibility with intracellular operation/delivery.

Rational design of highly responsive pH sensors based on DNA i-motif.

Availability of strategies for molecular biosensing over a finely adjustable dynamic range is essential for understanding and controlling vital biological processes. Herein we report design principles of highly responsive pH sensors based on a DNA i-motif where both response sensitivity and transition midpoint can be tuned with high precision over the physiologically relevant pH interval. The tuning is accomplished via rational manipulations of an i-motif structure as well as incorporation of allosteric control elements. This strategy delivers molecular sensing systems with a transition midpoint tunable with 0.1 pH units precision and with a total response range as narrow as 0.2 pH units which can be adjusted to a variety of outputs (e.g., fluorescent readout). The potential of the presented approach is not limited by pH sensing but may extend toward manipulation of other quadruplex based structures or the development of ultraresponsive elements for artificial molecular machines and signaling systems.

Highly selective detection of oil spill polycyclic aromatic hydrocarbons using molecularly imprinted polymers for marine ecosystems.

Im*plications due to oil spills on marine ecosystems have created a great interest toward developing more efficient and selective materials for oil spill toxins detection and remediation. This research paper highlights the application of highly efficient molecularly imprinted polymer (MIP) adsorbents based on a newly developed functional crosslinker (N,O-bismethacryloyl ethanolamine, NOBE) for detection of highly toxic polycyclic aromatic hydrocarbons (PAHs) in seawater. The binding capacity of MIP for oil spill toxin pyrene is 35 mg/g as compared to the value of 3.65 mg/g obtained using a non-imprinted polymer (NIP). The selectivity of all three high molecular weight PAHs (pyrene, chrysene and benzo[a]pyrene) on the NOBE-MIP shows an excellent selective binding with only 5.5% and 7% cross-reactivity for chrysene and benzo[a]pyrene, respectively. Not only is this particularly significant because the rebinding solvent is water, which is known to promote non-selective hydrophobic interactions; the binding remains comparable under salt-water conditions. These selective and high capacity adsorbents will find wide application in industrial and marine water monitoring/remediation.

Design and evaluation of an i-motif-based allosteric control mechanism in DNA-hairpin molecular devices.

Molecular devices designed to assess and manipulate biologically relevant conditions with required accuracy and precision play an essential role in life sciences research. Incorporating allosteric regulation mechanism is an attractive strategy toward more efficient artificial sensing and switching systems. Herein, we report on a new principle of regulating switching parameters of a DNA-based molecular device based on allosteric interaction between spatially separated hairpin stem and a tetraplexed fragment (i.e., i-motif). We characterized thermodynamic and kinetic effects arising from interaction between functional domains of the device and demonstrated the potential of applying the allosteric control principle for rational design of sensors and switches with precisely defined operational characteristics.

Thin-film ratiometric fluorescent chemosensors with tunable performance characteristics.

A simple method for tuning the performance characteristics of fluorescent ratiometric sensors based on surface-immobilized monolayers of π-conjugated molecules enabled gradual adjustment of the sensitivity and the analyte detection range of the sensor. This approach has been applied to fine-tune the sensing performance of a prototype ratiometric chemosensor for fluoride ions.

Development and screening of contrast agents for in vivo imaging of Parkinson's disease.

PURPOSE: The goal was to identify molecular imaging probes that would enter the brain, selectively bind to Parkinson's disease (PD) pathology, and be detectable with one or more imaging modalities. PROCEDURE: A library of organic compounds was screened for the ability to bind hallmark pathology in human Parkinson's and Alzheimer's disease tissue, alpha-synuclein oligomers and inclusions in two cell culture models, and alpha-synuclein aggregates in cortical neurons of a transgenic mouse model. Finally, compounds were tested for blood-brain barrier permeability using intravital microscopy. RESULTS: Several lead compounds were identified that bound the human PD pathology, and some showed selectivity over Alzheimer's pathology. The cell culture models and transgenic mouse models that exhibit alpha-synuclein aggregation did not prove predictive for ligand binding. The compounds had favorable physicochemical properties, and several were brain permeable. CONCLUSIONS: Future experiments will focus on more extensive evaluation of the lead compounds as PET ligands for clinical imaging of PD pathology.

Surface-immobilized monolayers of conjugated oligomers as a platform for fluorescent sensors design: the effect of exciton delocalization on chemosensing performance.

Surface-immobilized monolayers of fluorescent molecular sensors consisting of a short conjugated oligo(p-phenylene ethynylene) core end-capped with an acceptor fluorophore (analyte receptor) display significant signal amplification due to enhanced intermolecular energy transfer within the monolayer. This general phenomenon offers a superior platform for designing ratiometric fluorescent sensors. An example of how this can be used to convert a narrow-range threshold fluorescent pH indicator (fluorescein) to a broad-range ratiometric fluorescent chemosensor is described.