Bio-recognitive photonics of a DNA-guided organic semiconductor

Accumulated in-situ spectral information analysis of room-temperature phosphorescence with time-gated bioimaging

This study introduces the time-gated analysis of room-temperature phosphorescence (RTP) for the in-situ analysis of the visible and spectral information of photons. Time-gated analysis is performed using a microscopic system consisting of a spectrometer, which is advantageous for in-situ analysis since it facilitates the real-time measurement of luminescence signal changes. An RTP material hybridized with a DNA aptamer that targets a specific protein enhances the intensity and lifetime of phosphorescence after selective recognition with the target protein. In addition, time-gated analysis allows for the millisecond-scale imaging of phosphorescence signals, excluding autofluorescence, and improves the signal-to-background ratio (SBR) through the accumulation of signals. While collecting the time-gated images and spectra of RTP and autofluorescent materials simultaneously, we develop a method for obtaining phosphorescence signals by means of selective exclusion of autofluorescence signals in simulated or real cell conditions. It is confirmed that the accumulated time-gated analysis can provide ample information about luminescence signals for bioimaging and biosensing applications.

Simultaneous enhancement in phosphorescence and its lifetime of PtOEP-peptide assembly triggered by protein interaction

We fabricated hybrid nanoparticles consisting of organic semiconducting material with peptide sequence to reflect the target protein interaction. A phosphorescent OLED material, platinum octaethylporphyrin (PtOEP) was self-assembled by reprecipitation with the A17 peptide (YCAYYSPRHKTTF) selected as a probe ligand in order to recognize heat shock protein 70 (HSP70). The phosphorescence intensity of the PtOEP-A17 assembly was enhanced by 125 % after treatment with HSP70. The specificity of the protein interaction was confirmed in both solution and solid states of the PtOEP-A17 assembly against to BSA and nucleolin. We figured out that the phosphorescence lifetime of PtOEP-A17 assembly after exposed to HSP70 increased significantly to 153 ns from initial 115 ns. These simultaneous enhancements in phosphorescence and lifetime triggered by the specific protein interaction would open new applications of PtOEP, a representative material of light-emitting device fields.

Crystal structure of poly[(aceto-nitrile-κN)(μ3-7-{[bis-(pyridin-2-ylmeth-yl)amino]-meth-yl}-8-hy-droxy-quinoline-5-sulfonato-κ4N,O:O':O'')sodium]

In the title compound, [Na(C22H19N4O4S)(CH3CN)]n, the NaI atom adopts a distorted square-pyramidal coordination geometry, formed by one N and one O atom of the qunolinol moiety in the ligand, two O atoms of sulfonate moieties of two adjacent ligands and the N atom of the coordinated aceto-nitrile solvent. The NaI atom is located well above the mean basal plane of the square-based pyramid. The apical position is occupied by a sulfonate O atom of a neighboring ligand. Three N atoms of the bis-(pyridin-2-ylmeth-yl)amine moiety in the ligand are not coordinated by the sodium atom. The mol-ecule forms an intra-molecular bifurcated O-H⋯[N(tertiary amine),N(pyridine)] hydrogen bond, generating S(6) and S(5) rings. In the crystal, four mol-ecules are linked by four Na-O(sulfonato) bridged coordination bonds, forming a supra-molecular centrosymmetric tetra-mer unit comprising an eight-membered ring, and generating a two-dimensional network sheet. The mol-ecules of different sheets form inter-molecular C-H⋯O hydrogen bonds, and thereby a three-dimensional network structure.

Triple-Peak Photoluminescence of DNA-Hybrid Alq3 Crystals Emitting a Depressed Single Peak upon Bio-Recognition

The green organic semiconductor, tris-(8-hydroxyquinoline)aluminum (Alq₃), was hybridized with DNA growing in the shape of hexagonal prismatic crystals. In this study, we applied hydrodynamic flow to the fabrication of Alq₃ crystals doped with DNA molecules. The hydrodynamic flow in the Taylor-Couette reactor induced nanoscale pores in the Alq₃ crystals, especially at the side part of the particles. The particles exhibited distinctly different photoluminescence emissions divided into three parts compared to common Alq₃-DNA hybrid crystals. We named this particle a "three-photonic-unit". After treatment with complementary target DNA, the three-photonic-unit Alq₃ particles doped with DNAs were found to emit depressed luminescence from side parts of the particles. This novel phenomenon would expand the technological value of these hybrid crystals with divided photoluminescence emissions toward a wider range of bio-photonic applications.

Molecular doping of nucleic acids into light emitting crystals driven by multisite-intermolecular interaction

We reveal the fundamental understanding of molecular doping of DNAs into organic semiconducting tris (8-hydroxyquinoline) aluminum (Alq₃) crystals by varying types and numbers of purines and pyrimidines constituting DNA. Electrostatic, hydrogen bonding, and π-π stacking interactions between Alq₃ and DNAs are the major factors affecting the molecular doping. Longer DNAs induce a higher degree of doping due to electrostatic interactions between phosphate backbone and Alq₃. Among four bases, single thymine bases induce the multisite interactions of π-π stacking and hydrogen bonding with single Alq₃, occurring within a probability of 4.37%. In contrast, single adenine bases form multisite interactions, within lower probability (1.93%), with two-neighboring Alq₃. These multisite interactions facilitate the molecular doping into Alq₃ particles compared to cytosines or guanines only forming π-π stacking. Thus, photoluminescence and optical waveguide phenomena of crystals were successfully tailored. This discovery should deepen our fundamental understanding of incorporating DNAs into organic semiconducting crystals.

Antibacterial activity of the micro and nanostructures of the optical material tris(8-hydroxyquinoline)aluminum and its application as an antimicrobial coating

Although tris(8-hydroxyquinoline)aluminum (Alq3), a fluorescent optical organometallic material, is known for its applications in optoelectronics, it has only few and limited applications in the biological field. In this study, the antibacterial activity of Alq3 micro and nanostructures was investigated. We prepared Alq3 nanostructures. We prepared nanosized Alq3 as rice-like structures that assembled into flower shapes with an α-crystal phase. Then, Alq3 micro and nanostructure antibacterial activities were estimated against seven human pathogenic bacterial strains. Besides, we compared their antibacterial activities with those of standard antibiotics. The minimal inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and IC50 were evaluated. Alq3 micro and nanostructure antibacterial activity showed considerable values compared to standard antibiotics. Besides, the obtained data revealed that the antibacterial activity of Alq3 in nanostructures with a new morphology is more than that in microstructures. The antibacterial activity of Alq3 nanostructures was attributed to their more surface interactions with the bacterial cell wall. The molecules of 8-hydroxyquinoline in the Alq3 structure could play crucial roles in its antibacterial activity. To apply the achieved results, Alq3 was incorporated with polystyrene (PS) in a ratio of 2% to fabricate a PS/Alq3 composite and used to coat glass beakers, which showed inhibition in the bacterial growth reduced to 65% compared with non-coated beakers. The finding of this study showed that Alq3 could be used as a promising antimicrobial coating.

Microbe-Assisted Nanocomposite Anodes for Aqueous Li-Ion Batteries

With the rapid increase in the use of lithium-ion batteries (LIBs), the development of safe LIBs has become an important social issue. Replacing flammable organic liquid electrolytes in current LIBs with water can be an alternative route to resolve this safety concern. The water-in-salt (WIS) electrolytes received great attention as next-generation electrolytes due to their large electrochemical stability window. However, their high cathodic limit remains as a challenge, impeding the use of low-potential anodes. Here, we report the first biodirected synthesis of carbonaceous layers on anodes to use them as interlayers that prevent a direct contact of water molecules to anode particles. High-aspect ratio microbes are utilized as precursors of carbonaceous layers on TiO₂ nanoparticles (m-TiO₂) to enhance the conductivity and to reduce the electrolysis of WIS electrolytes. We selected the cylindrical shape of microbes that offers geometric diversity, providing us a toolkit to investigate the effect of microbe length in forming the network in binary composites and their impacts on the battery performance with WIS electrolytes. Using microbes with varying aspect ratios, the optimal microbe size to maximize the battery performance is determined. The effects of storage time on microbe size are also studied. Compared to uncoated TiO₂ anodes, m-TiO₂ exhibited 49% higher capacity at the 40th cycle and enhanced the cycle life close to anodes made with a conventional carbon precursor while using an 11% less amount of carbon. We performed density functional theory calculations to unravel the underlying mechanism of the performance improvement using microbe-derived carbon layers. Computational results show that high amounts of pyridinic nitrogen present in the peptide bonds in microbes are expected to slow down the water diffusion. Our findings provide key insights into the design of an interlayer for WIS anodes and open an avenue to fabricate energy storage materials using biomaterials.

Organic Semiconductor-DNA Hybrid Assemblies

Organic semiconductors are photonic and electronic materials with high luminescence, quantum efficiency, color tunability, and size-dependent optoelectronic properties. The self-assembly of organic molecules enables the establishment of a fabrication technique for organic micro- and nano-architectures with well-defined shapes, tunable sizes, and defect-free structures. DNAs, a class of biomacromolecules, have recently been used as an engineering material capable of intricate nanoscale structuring while simultaneously storing biological genetic information. Here, the up-to-date research on hybrid materials made from organic semiconductors and DNAs is presented. The trends in photonic and electronic phenomena discovered in DNA-functionalized and DNA-driven organic semiconductor hybrids, comprising small molecules and polymers, are observed. Various hybrid forms of solutions, arrayed chips, nanowires, and crystalline particles are discussed, focusing on the role of DNA in the hybrids. Furthermore, the recent technical advances achieved in the integration of DNAs in light-emitting devices, transistors, waveguides, sensors, and biological assays are presented. DNAs not only serve as a recognizing element in organic-semiconductor-based sensors, but also as an active charge-control material in high-performance optoelectronic devices.

DNA Self-Switchable Microlaser

Advances in switchable microlasers have emerged as a building block with immense potential in controlling light-matter interactions and integrated photonics. Compared to artificially designed interfaces, a stimuli-responsive biointerface enables a higher level of functionalities and versatile ways of tailoring optical responses at the nanoscale. However, switching laser emission with biological recognition has yet to be addressed, particularly with reversibility and wavelength tunability over a broad spectral range. Here we demonstrate a self-switchable laser exploiting the biointerface between label-free DNA molecules and dye-doped liquid crystal matrix in a Fabry-Perot microcavity. Laser emission switching among different wavelengths was achieved by utilizing DNA conformation changes as the switching power, which alters the orientation of the liquid crystals. Our findings demonstrate that different concentrations of single-stranded DNA lead to different temporal switching of lasing wavelengths and intensities. The lasing wavelength could be reverted upon binding with the complementary sequence through DNA hybridization process. Both experimental and theoretical studies revealed that absorption strength is the key mechanism accounting for the laser shifting behavior. This study represents a milestone in achieving a biologically controlled laser, shedding light on the development of programmable photonic devices at the sub-nanoscale by exploiting the complexity and self-recognition of biomolecules.

Bio-Photonic Waveguide of a DNA-Hybrid Semiconductor Prismatic Hexagon

A successful identification of DNA-DNA recognition, based on the waveguide effect of a 1D hybrid prismatic hexagon crystal interfacing of DNA with an organic semiconductor is achieved. This bio-hybrid 1D crystal simultaneously discerns the complementary case at its one end against a 1-mer mismatch in 27-mer nucleic acid sequence at the other end. The loss coefficient value of this waveguide is estimated to be 0.159 µm^-1 for the perfect match, which is a stark discrepancy compared to 0.244 µm^-1 for the 1-mer mismatch, implying waveguide performance with a higher efficiency. These results demonstrate successfully that multiple biological interactions can be realized by the optical waveguide of the single 1D bio-hybrid-crystal and will push this class of materials into bio-related applications.

Photoluminescent Response of Poly(3-methylthiophene)-DNA Single Nanowire Correlating to Nucleotide-Mismatch Locus in DNA-DNA Hybridization

π-Conjugated polymers have become qualified candidates for biosensing owing to their unique optoelectronic properties and excellent biocompatibility. In this contribution, nucleotide mismatches in DNA hybridization, being variable in position, are reflected in a stark manner by poly(3-methylthiophene) (P3MT) nanowires (NWs), in which probe DNA sequence is properly functionalized. Selected as the systematic investigation are complementary target DNA (tDNA), random sequence DNA, and three kinds of 1-mer mismatched tDNAs with different mismatch loci away from the NW's surface. Nanoscale optical observation of the single P3MT NWs in solid states reveals that the more distant the mismatch position is from the surface, the higher the photoluminescence (PL) occurs, while the complementary sequence yields the highest but the random one remains the lowest. Hence, the PL intensity increases with the relative length of the DNA-DNA hybridization from the surface. These results deliver a new basis that π-conjugated polymers can be potentially applicable to detailed nucleotide analyses as in single nucleotide polymorphism.

Ultrafast Excitation Transfer in Cy5 DNA Photonic Wires Displays Dye Conjugation and Excitation Energy Dependency

DNA scaffolds enable base-pair-specific positioning of fluorescent molecules, allowing for nanometer-scale precision in controlling multidye interactions. Expanding on this concept, DNA-based molecular photonic wires (MPWs) allow for light harvesting and directional propagation of photonic energy on the nanometer scale. The most common MPW examples exploit Förster resonance energy transfer (FRET), and FRET between the same dye species (HomoFRET) was recently shown to increase the distance and efficiency at which MPWs can function. Although increased proximity between adjacent fluorophores can be used to increase the energy transfer efficiency, FRET assumptions break down as the distance between the dye molecules becomes comparable to their size (∼2 nm). Here we compare dye conjugation with single versus dimer Cy5 dye repeats as HomoFRET MPW components on a double-crossover DNA scaffold. At room temperature (RT) under low-light conditions, end-labeled uncoupled dye molecules provide optimal transfer, while the Cy5 dimers show ultrafast (<100 ps) nonradiative decay that severely limits their functionality. Of particular interest is the observation that through increased excitation fluence as well as cryogenic temperatures, the dimeric MPW shows suppression of the ultrafast decay, demonstrating fluorescence lifetimes similar to the single Cy5 MPWs. This work points to the complex dynamic capabilities of dye-based nanophotonic networks, where dye positioning and interactions can become critical, and could be used to extend the lengths and complexities of such dye-DNA devices, enabling multiparameter nanophotonic circuitry.

In Situ Enhanced Raman and Photoluminescence of Bio-Hybrid Ag/Polymer Nanoparticles by Localized Surface Plasmon for Highly Sensitive DNA Sensors

We experimentally demonstrate the simultaneous enhancement of Raman and photoluminescence (PL) of core-shell hybrid nanoparticles consisting of Ag (core) and polydiacetylene (PDA, shell) through the assistance of localized surface plasmon (LSP) effect for the effective biosensor. Core-shell nanoparticles (NPs) are fabricated in deionized water through a sequential process of reprecipitation and self-assembly. The Raman signal of PDA on core-shell NPs is enhanced more than 100 times. Also, highly enhanced photoluminescence is observed on Ag/PDA hybrid NPs after coupling of the complementary t-DNA with p-DNA which are immobilized on PDA shell. This indicates that the core Ag affects the Raman and PL of PDA through the LSP resonance, which can be caused by the energy and/or charge transfer caused by the LSP coupling and the strong electromagnetic field near Ag NP surface. Only electrons present on the surface interact with the PDA shell, not involving the electrically neutral part of the electrons inside the Ag NP. Furthermore, this work shows that as prepared Ag/PDA NPs functionalized by probe DNA can sense the target DNA with an attomolar concentration (100 attomole).

Selective Immobilization of Fluorescent Proteins for the Fabrication of Photoactive Materials

The immobilization of fluorescent proteins is a key technology enabling to fabricate a new generation of photoactive materials with potential technological applications. Herein we have exploited superfolder green (sGFP) and red (RFP) fluorescent proteins expressed with different polypeptide tags. We fused these fluorescent proteins to His-tags to immobilize them on graphene 3D hydrogels, and Cys-tags to immobilize them on porous microparticles activated with either epoxy or disulfide groups and with Lys-tags to immobilize them on upconverting nanoparticles functionalized with carboxylic groups. Genetically programming sGFP and RFP with Cys-tag and His-tag, respectively, allowed tuning the protein spatial organization either across the porous structure of two microbeads with different functional groups (agarose-based materials activated with metal chelates and epoxy-methacrylate materials) or across the surface of a single microbead functionalized with both metal-chelates and disulfide groups. By using different polypeptide tags, we can control the attachment chemistry but also the localization of the fluorescent proteins across the material surfaces. The resulting photoactive material formed by His-RFP immobilized on graphene hydrogels has been tested as pH indicator to measure pH changes in the alkaline region, although the immobilized fluorescent protein exhibited a narrower dynamic range to measure pH than the soluble fluorescent protein. Likewise, the immobilization of Lys-sGFP on alginate-coated upconverting nanoparticles enabled the infrared excitation of the fluorescent protein to be used as a green light emitter. These novel photoactive biomaterials open new avenues for innovative technological developments towards the fabrication of biosensors and photonic devices.

Mercury ion-DNA specificity triggers a distinctive photoluminescence depression in organic semiconductor probes guided with a thymine-rich oligonucleotide sequence

DNA strands have been recently found to play a role in crystallizing organic semiconductors as a substitute for conventional surfactants. Such DNA-guided organic semiconductor particles possessed the recognition ability to complementary target DNAs, resulting in "enhanced luminescence" due to the lesser degree of non-radiative dissipation. Apart from this, in this study we developed selective recognition of mercury ions by utilizing DNA probes having ion-specific thymine-rich motifs. Strikingly, the specific ion-DNA interaction triggered rather distinctive "depressed luminescence" emitting from the particles. The mercury ions were found to be present both at the surface and the inner regions, which were discovered to relate to the drastic morphological distortion of the particles as evidenced by elemental, electron microscopy, and confocal fluorescence microscopy analyses. This novel phenomenon discovered would expand the technological values of organic semiconductors conjugated with oligonucleotides toward a wider range of target-specific applications.

Facile Immobilization of Enzyme via Co-Electrospinning: A Simple Method for Enhancing Enzyme Reusability and Monitoring an Activity-Based Organic Semiconductor

The stability, reusability, and monitoring of enzyme activity have been investigated to improve their efficiency for successful utilization in a broad range of industrial and medical applications. Herein, we present a simple method for fabricating an electrospun fiber/enzyme scaffold via co-electrospinning. The characterization of soluble and immobilized α-amylases with regard to pH, thermal stability, and reusability were studied. An organic light emitting material tris(8-hydroxyquinoline)aluminum was incorporated to monitor the enzyme activity for several reuses.

Growth and Brilliant Photo-Emission of Crystalline Hexagonal Column of Alq₃ Microwires

We report the growth and nanoscale luminescence characteristics of 8-hydroxyquinolinato aluminum (Alq₃) with a crystalline hexagonal column morphology. Pristine Alq₃ nanoparticles (NPs) were prepared using a conventional reprecipitation method. Crystal hexagonal columns of Alq₃ were grown by using a surfactant-assisted self-assembly technique as an adjunct to the aforementioned reprecipitation method. The formation and structural properties of the crystalline and non-crystalline Alq₃ NPs were analyzed with scanning electron microscopy and X-ray diffraction. The nanoscale photoluminescence (PL) characteristics and the luminescence color of the Alq₃ single NPs and their crystal microwires (MWs) were evaluated from color charge-coupled device images acquired using a high-resolution laser confocal microscope. In comparison with the Alq₃ NPs, the crystalline MWs exhibited a very bright and sharp emission. This enhanced and sharp emission from the crystalline Alq₃ single MWs originated from effective π-π stacking of the Alq₃ molecules due to strong interactions in the crystalline structure.

Physical Modeling of Activation Energy in Organic Semiconductor Devices based on Energy and Momentum Conservations

Field effect mobility in an organic device is determined by the activation energy. A new physical model of the activation energy is proposed by virtue of the energy and momentum conservation equations. The dependencies of the activation energy on the gate voltage and the drain voltage, which were observed in the experiments in the previous independent literature, can be well explained using the proposed model. Moreover, the expression in the proposed model, which has clear physical meanings in all parameters, can have the same mathematical form as the well-known Meyer-Neldel relation, which lacks of clear physical meanings in some of its parameters since it is a phenomenological model. Thus it not only describes a physical mechanism but also offers a possibility to design the next generation of high-performance optoelectronics and integrated flexible circuits by optimizing device physical parameter.