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.

Monitoring Based on Narrow-Band Resonance Raman for "Phase-Shifting" π-Conjugated Polydiacetylene Vesicles upon Host-Guest Interaction and Thermal Stimuli.

The present study reports a quantified monitoring by means of in situ resonance Raman scattering that analyzes phase-shifting characteristics of π-systems upon interacting with target analytes. A chemo- and thermochromic polydiacetylene vesicular probe is evaluated with multiple-wavelength Raman scattering modes in resonance with its phases, respectively, and thus can trace the phase-shifts. This Raman scattering-based analytical quantification is also successful in monitoring host-guest recognition events by utilizing much narrower bands, compared to those in conventional absorption or photoluminescence (PL) methods. As one of the outcomes, the monitoring analysis overcomes the limitations based on widely used colorimetric response (%CR) or PL that failed in the case of interaction with a surfactant, CTAB.

Biodegradation of saline phenolic wastewater in a biological contact oxidation reactor with immobilized cells of Oceanimonas sp.

OBJECTIVE: To develop a method to treat saline phenolic wastewater in a biological contact oxidation reactor (BCOR) with immobilized cells of a marine microorganism, Oceanimonas sp., isolated from seawater. RESULTS: Cells were immobilized on fibre carriers in the BCOR. Saline wastewater with phenol at 1.5 g/l and NaCl at 6 % (w/v) was treated. In continuous assays, 99 % removal of phenol was achieved and a kinetic model for the phenol degradation is presented based on Monod's equation. CONCLUSION: The BOCR system using immobilized cells of Oceanimonas efficiently treats saline phenolic wastewaters without having decrease the salinity of the wastewater.

Protein Recognition by Phase Transition of Aptamer-Linked Polythiophene Single Nanowire.

A novel protein recognition platform is developed using aptamer-linked polythiophene nanowires. As the aptamer functionalized poly (3-methylthiophene) nanowire is treated by the specific protein, resonance Raman and photoluminescence signals are simultaneously enhanced. Statistical analyses deliver the capability of a single conjugated polymer nanowire with phase-transition characteristics in response to selectivity and concentration.

Controlled assembly of photosensitizers through directional interactions for effective photooxidation.

Despite the fact that effective photosensitizers (PSs) can be achieved through rational molecular design, controlling the hierarchical assemblies of individual PSs with distinct function and morphological nanoscopic architectures remains a challenge. Here, very ordered one-dimensional PS polymers and their hollow tubular structures are presented from aqueous assembly of organic PS-based di- or tri-blocked supramolecules. Di-blocked PSs were interdigitated into 1D fibrils, significantly quenching photooxidation. Meanwhile, tri-blocked PSs were tilted with respect to each other to generate hollow tubules, showing remarkable photo-activities as well as photo-stability, which are particularly suited for green chemistry due to their unusual rapid photo-oxidation.

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.

Heavy Metal Ions Trigger a Fluorescent Quenching in DNA-Organic Semiconductor Hybrid Assemblies.

The significance of DNA is no longer limited to its role as a biological information carrier; as a natural polymer, it also become in the field of materials. Single-stranded DNA (ssDNA) molecules with specific sequences can form a G-quadruplex or hairpin-shaped conformation with specific heavy metal ions through coordination bonds. In this study, ssDNA molecules of the four sequences were prepared into hybrid assemblies with one of the famous display materials, the tris-(8-hydroxyquinoline)aluminum (Alq3) semiconductor. Based on these hybrid assemblies, heavy metal ions, namely Pb2+, Hg2+, Cd2+ and As3+, were detected individually at the ppb level. Apart from this, in practical application, many samples containing heavy metal ions are digested with acid. By introducing MES buffer solution, the influence of acidity on the fluorescent signal of Alq3 was excluded. This strategy showed promising results in the practical application of detecting heavy metal ions in shrub branches and leaves.

Fluorescence switch in red-phase polydiacetylene films and vesicles upon thermal cycles.

The switch phenomena of thermochromism of red-phase polymerized PCDA (10,12-pentacosadiynoic acid) Langmuir-Schaefer (LS) films and vesicles were investigated in situ during repeated heating and cooling processes between 25 degrees C and 70 degrees C. During repeated thermal cycles, the solid-supported LS films exhibited switch phenomena in both the visible and fluorescent spectra, that is, the colorimetric response (CR) of the PCDA LS films was ca. 80% at 70 degrees C but is ca. 50-60% at 25 degrees C with an increase of fluorescent intensity in the cooling process and a decrease in the heating process. On the other hand, the PCDA vesicles exhibited such phenomenon only in the fluorescent spectra, that is, the CR of the PCDA vesicles was constant as ca. 100% after being stable red form with the same trend in the fluorescent intensity. The changes in molecular configuration revealed by in situ Fourier transform infrared (FTIR) were in good agreement with the trend of fluorescence emission upon repeated thermal stimuli rather than that of visible absorption.

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.

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.

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).

Photoluminescence Enhancement of Poly(3-methylthiophene) Nanowires upon Length Variable DNA Hybridization.

The use of low-dimensional inorganic or organic nanomaterials has advantages for DNA and protein recognition due to their sensitivity, accuracy, and physical size matching. In this research, poly(3-methylthiophene) (P3MT) nanowires (NWs) are electrochemically prepared with dopant followed by functionalization with probe DNA (pDNA) sequence through electrostatic interaction. Various lengths of pDNA sequences (10-, 20- and 30-mer) are conjugated to the P3MT NWs respectively followed with hybridization with their complementary target DNA (tDNA) sequences. The nanoscale photoluminescence (PL) properties of the P3MT NWs are studied throughout the whole process at solid state. In addition, the correlation between the PL enhancement and the double helix DNA with various lengths is demonstrated.

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.

Effect of bioflocculation on fouling-related biofoulants in a membrane bioreactor during saline wastewater treatments.

A membrane bioreactor (MBR) was operated in two modes; with and without the inoculation of marine Arthrobacter cells, to investigate the effect of bioflocculation on membrane biofouling during saline wastewater treatments. The MBR-Arthrobacter system showed a higher resistance to membrane fouling than the normal MBR system. Lower concentrations of the fouling-related components and higher removal efficiencies of COD and NH3-N were observed in the MBR-Arthrobacter system. The bioflocculation of Arthrobacter preferred to settle down the humic acid-like, fulvic acid-like and aromatic proteins components (larger biomolecules) rather than the soluble microbial by-product-like components (smaller biomolecules).

Capillary-Driven Sensor Fabrication of Polydiacetylene-on-Silica Plate in 30 Seconds: Facile Utilization of π-Monomers with C18- to C25-Long Alkyl Chain.

By utilizing the capillary-force-driven action, a novel polydiacetylene-based sensor on the porous silica plate was developed within 30 s for π-diacetylene monomers with variable chain lengths. This method enables one to utilize diacetylene monomers even with the shorter alkyl chain length of C18-C21, which has not been possible with conventional methods. The invented sensor platform employing shorter monomers was found to perform better, as was demonstrated for gaseous and aqueous analytes, i.e., ammonia gas and nucleic acids in aqueous phase. This new polydiacetylene platform opens up the development of quick and easy fabrication and the use of chemical and biochemical chips.

Real-time monitoring of biofoulants in a membrane bioreactor during saline wastewater treatment for anti-fouling strategies.

This work presents a novel, fast and simple monitoring-responding method at the very early stages of membrane bio-fouling in a membrane bioreactor (MBR) during saline wastewater treatment. The impacts of multiple environmental shocks on membrane fouling were studied. The transmembrane pressure exceeded the critical fouling pressure within 8days in the case of salinity shock or temperature shock. In the case of DO shock, the transmembrane pressure exceeded the critical fouling pressure after 16days, showing the lower impact of DO shock on the MBR. In another study, the membrane fouling was observed within 4days responding to mixed environmental shocks. To decrease the potential of membrane bio-fouling, another bioreactor was integrated immediately with the MBR as a quickly-responded countermeasure, when an early warning of membrane bio-fouling was provided. After the bioreactor enhancement, the time required for membrane fouling increased from 4 to 10days.

Cultivation of activated sludge using sea mud as seed to treat industrial phenolic wastewater with high salinity.

A technique is proposed to treat saline hazardous wastewater by using marine activated sludge, cultivated with sea mud as seed. Since the developed marine activated sludge had phenol-tolerant microorganisms (MAS-1, MAS-2 and MAS-3) which originated from the ocean, it was envisaged that these bacteria could survive and breakdown phenol in saline environments. In this work, typical phenol-tolerant microorganisms were isolated from the marine activated sludge and identified. After a hierarchical acclimation process, the marine activated sludge was used to treat the industrial phenolic wastewater with high salinity. The marine activated sludge was able to break down phenol and other organic components effectively and efficiently in treating the wastewater with salinity of 5.7% w/v. The results showed a high removal of phenol (99%), COD (80%) and NH3-N (68%).

Bio-recognitive photonics of a DNA-guided organic semiconductor.

Incorporation of duplex DNA with higher molecular weights has attracted attention for a new opportunity towards a better organic light-emitting diode (OLED) capability. However, biological recognition by OLED materials is yet to be addressed. In this study, specific oligomeric DNA-DNA recognition is successfully achieved by tri (8-hydroxyquinoline) aluminium (Alq3), an organic semiconductor. Alq3 rods crystallized with guidance from single-strand DNA molecules show, strikingly, a unique distribution of the DNA molecules with a shape of an 'inverted' hourglass. The crystal's luminescent intensity is enhanced by 1.6-fold upon recognition of the perfect-matched target DNA sequence, but not in the case of a single-base mismatched one. The DNA-DNA recognition forming double-helix structure is identified to occur only in the rod's outer periphery. This study opens up new opportunities of Alq3, one of the most widely used OLED materials, enabling biological recognition.

Oligonucleotide assisted light-emitting Alq3 microrods: energy transfer effect with fluorescent dyes.

Oligonucleotide assisted tri(8-hydroxyquinoline) aluminium (Alq3) microrods were prepared for the first time. When hybridized with oligonucleotide labeled by Cy3 fluorescent dye, a significant photoluminescence variation of the Alq3 microrods was observed due to Förster resonance energy transfer, unlike when Cy5-oligonucleotide was used. Versatile nucleotide manipulation would open up wider applications of Alq3-based materials, based on this fundamental observation.

Rapid analysis of barley straw before and after dilute sulfuric acid pretreatment by photoluminescence.

The fluorescence intensities (FIs) of raw and pretreated barley straws were measured by fluorescence microscopy, and the difference in the fluorescence intensity of barley straw before and after dilute acid pretreatment was analyzed by investigation of the major compounds of barley straw. The difference in fluorescence intensity was due to the difference in xylan content. Barley straw was pretreated using dilute sulfuric acid at various conditions and the correlation between the fluorescence intensity and glucose yield of barley straw was investigated. The coefficient of determination (R(2)) of the correlation was found to be 72.28%. Also the calibration of fluorescence intensity with the xylan content was performed. In addition, the absorption and emission spectra of the raw and the pretreated barley straw were examined to verify the proposed method. The absorption and emission wave lengths were 550 nm and 665 nm, respectively.