Label-free detection of bacterial RNA using polydiacetylene-based biochip

Sustainable colorimetric/luminescent sensors enabled by armored lipid nanoparticles

In this study, we developed a highly stable polymeric vesicle using a nanosilica-armor membrane to achieve a sustainable colorimetric/luminescent response. The silica armor can be grown directly as ~ 5 nm spherical nanoparticles on the surface of the diacetylene (DA) vesicle with liposomal structure. This can be accomplished via the modified Stöber reaction in pure water on a layer of amine linkers deposited on the vesicles. Once formed, the structural stability of the DA vesicles dramatically increased and remained so even in a dried powder form that could be stored for a period of approximately 6 months. Then, redispersed in water, the armored vesicles did not agglomerate because of the electric charge of the silica armor. After polymerization, the polydiacetylene (PDA) vesicles maintained an average of 87.4% their sensing capabilities compared to unstored vesicles. Furthermore, the silica membrane thickness can be controlled by reiteration of the electrostatic layer-by-layer approach and the direct hydrolysis of silica. As the number of silica armor membranes increases, the passage of the stimuli passing through the membranes becomes longer. Consequently, three layers of silica armor gave the PDA vesicles size-selective recognition to filter out external stimuli. These discoveries are expected to have large-scale effects in the chemo- and biosensor fields by applying protective layers to organic nanomaterials.

Structures and strategies for enhanced sensitivity of polydiacetylene(PDA) based biosensor platforms

Polydiacetylene (PDA) is a versatile polymer that has been studied in numerous fields because of its unique optical properties derived from alternating multiple bonds in the polymer backbone. The conjugated structure in the polymer backbone enables PDA to possess the ability of blue-red colorimetric transition when π-π interactions in the PDA backbone chain are disturbed by the external environment. The chromatic property of PDA disturbed by external stimuli can also emit fluorescence in the red region. Owing to the unique characteristics of PDA, it has been widely studied in facile and label-free sensing applications based on colorimetric or fluorescence signals for several decades. Among the various PDA structures, membrane structures assembled by amphiphilic molecules are widely used as a versatile platform because facile modification of the synthetic membrane provides extensive applications, such as receptor-ligand interactions, resulting in potent biosensors. To use PDA as a sensory material, several methods have been studied to endow the specificity to PDA molecules and to amplify the signal from PDA supramolecules. This is because selective and sensitive detection of target materials is required at an appropriate level corresponding to each material for applicable sensor applications. This review focuses on factors that affect the sensitivity of PDA composites and several strategies to enhance the sensitivity of the PDA sensor to various structures. Owing to these strategies, the PDA sensor system has achieved a higher level of sensitivity and selectivity, enabling it to detect multiple target materials for a full field of application.

Visual Simultaneous Detection and Real-Time Monitoring of Cadmium Ions Based on Conjugated Polydiacetylenes

We prepared the monomer PCDA-HP composed of 5-hydroxy-N ¹,N ³-bis(pyridin-2-ylmethyl)isophthalamide (HP) as a cadmium ion tweezer and then polymerized them to form a polydiacetylene (PDA)-based sensor (PDA-HP), which displayed selective and sensitive colorimetric and fluorometric change upon addition of a cadmium ion (Cd²⁺) at both pH 7.4 and 6.8. The PDA-HP polymer was highly selective for Cd²⁺ over other metal ions with colorimetric change. In addition, the PDA-HP chemosensor also showed a red fluorescence change in the presence of Cd²⁺ at both pH 7.4 and 6.8. Naked-eye detection of Cd²⁺ was accomplished in an aqueous solution through a PDA-based sensor system. Finally, the lowest energy structure of an HP chelator was obtained by the crystal structure and density functional theory (DFT) calculations.

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.

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.

Responsive Polydiacetylene Vesicles for Biosensing Microorganisms

Polydiacetylene (PDA) inserted in films or in vesicles has received increasing attention due to its property to undergo a blue-to-red colorimetric transition along with a change from non-fluorescent to fluorescent upon application of various stimuli. In this review paper, the principle for the detection of various microorganisms (bacteria, directly detected or detected through the emitted toxins or through their DNA, and viruses) and of antibacterial and antiviral peptides based on these responsive PDA vesicles are detailed. The analytical performances obtained, when vesicles are in suspension or immobilized, are given and compared to those of the responsive vesicles mainly based on the vesicle encapsulation method. Many future challenges are then discussed.

Biomolecule-Functionalized Smart Polydiacetylene for Biomedical and Environmental Sensing

Polydiacetylene (PDA) has attracted interest for use as a sensing platform in biomedical, environmental, and chemical engineering applications owing to its capacity for colorimetric and fluorescent transition in response to external stimuli. Many researchers have attempted to develop a tailor-made PDA sensor via conjugation of chemical or biological substances to PDA. Here, we review smart bio-conjugates of PDA with various biomolecules such as carbohydrates, lipids, nucleic acids, and proteins. In addition, materialization and signal amplification strategies to improve handling and sensitivity are described.

Utilization of chromic polydiacetylene assemblies as a platform to probe specific binding between drug and RNA

Recognition of nucleic acids remains an important endeavor in biology. Nucleic acids adopt shapes ranging from A-form (RNA and GC rich DNA) to B-form (AT rich DNA). We show, in this contribution, shape-specific recognition of A-U rich RNA duplex by a neomycin (Neo)-polydiacetylene (PDA) complex. PDA assemblies are fabricated by using a well-known diacetylene (DA) monomer, 10,12-pentacosadiynoic acid (PCDA). The response of poly(PCDA) assemblies is generated by mixing with a modified neomycin-PCDA monomer (Neo-PCDA). The functionalization by neomycin moiety provides specific binding with homopolyribonucleotide poly (rA) - poly (rU) stimulus. Various types of alcohols are utilized as additives to enhance the sensitivity of poly(PCDA)/Neo-PCDA assemblies. A change of absorption spectra is clearly observed when a relatively low concentration of poly (rA)-poly (rU) is added into the system. Furthermore, poly(PCDA)/Neo-PCDA shows a clear specificity for poly (rA)-poly (rU) over the corresponding DNA duplex. The variation of linker between neomycin moiety and conjugated PDA backbone is found to significantly affect its sensitivity. We also investigate other parameters including the concentration of Neo-PCDA and the DA monomer structure. Our results provide here preliminary data for an alternative approach to improve the sensitivity of PDA utilized in biosensing and diagnostic applications.

Polydiacetylene/Anti-HBs Complexes for Visible and Fluorescent Detection of Hepatitis B Surface Antigen on a Nitrocellulose Membrane

The immunochromatographic assay (ICA) using a nitrocellulose (NC) membrane offers several advantages. This technique is a rapid and straightforward method in contrast to other immunoassays. Polydiacetylene (PDA) vesicles have unique optical properties, displaying red color and red fluorescence at the same time. In this system, red-phase PDA vesicles are used as a fluorescent dye as well as a surface for immobilized hepatitis B surface antibody (HBsAb). PDA has a remarkable stability compared with other fluorescent dyes. In this study, the most suitable PDA/HBsAb complexes are introduced for detecting hepatitis B surface antigen (HBsAg). Then, the PDA/HBsAb complexes affixed antibody is attached to NC membrane, which has two lines to confirm detection of HBsAg. The main advantage of this system is that the detection of HBsAg can be observed in both visible and fluorescent images due to the optical properties of polydiacetylene. Detection of HBsAg is observed up to 0.1 ng mL^-1 by fluorescent analysis and confirmed by red line on the NC membrane up to 1 ng mL^-1 (HBsAg) using the naked eye. Consequently, these results show that PDA/HBsAb complexes were successfully applied to ICA for the diagnosis of hepatitis B.

Colorimetric Polydiacetylene-Aerogel Detector for Volatile Organic Compounds (VOCs)

A new hybrid system comprising polydiacetylene (PDA), a chromatic conjugated polymer, embedded within aerogel pores has been constructed. The PDA-aerogel powder underwent dramatic color changes in the presence of volatile organic compounds (VOCs), facilitated through infiltration of the gas molecules into the highly porous aerogel matrix and their interactions with the aerogel-embedded PDA units. The PDA-aerogel composite exhibited rapid color/fluorescence response and enhanced signals upon exposure to low VOC concentrations. Encapsulation of PDA derivatives displaying different headgroups within the aerogel produced distinct VOC-dependent color transformations, forming a PDA-aerogel "artificial nose".

Selective and sensitive detection of MiRNA-21 based on gold-nanorod functionalized polydiacetylene microtube waveguide

Development of rapid, highly selective and sensitive miRNA detection in a complex biological environment has attracted considerable attention. Herein, we describe a novel two step method to construct gold-nanorod functionalized polydiacetylene (PDA) microtube for miRNA detection. In PDA microtube, with a one-dimensional (1D) waveguide nature, the excitation position and emission out-coupling position are far apart, thus helpful in reducing contribution of auto-fluorescence from biological sample. The use of specially designed toehold-mediated strand displacement reaction enables the reliable and selective discrimination of miRNA sequences with high sequence homology. Based on the condensing enrichment effect, the detection limit of the proposed PDA microtube system is as low as 0.01nM, and it can be applied directly to detect disease-specific miRNA targets in human serum. This PDA microtube waveguide system can be further integrated into the chip for the potential applications in minimally invasive, portable clinical diagnostic equipment.

Multiplex 16S rRNA-derived geno-biochip for detection of 16 bacterial pathogens from contaminated foods

Foodborne diseases caused by various pathogenic bacteria occur worldwide. To prevent foodborne diseases and minimize their impacts, it is important to inspect contaminated foods and specifically detect many types of pathogenic bacteria. Several DNA oligonucleotide biochips based on 16S rRNA have been investigated to detect bacteria; however, a mode of detection that can be used to detect diverse pathogenic strains and to examine the safety of food matrixes is still needed. In the present work, a 16S rRNA gene-derived geno-biochip detection system was developed after screening DNA oligonucleotide specific capture probes, and it was validated for multiple detection of 16 pathogenic strains that frequently occur with a signature pattern. rRNAs were also used as detection targets directly obtained from cell lysates without any purification and amplification steps in the bacterial cells separated from 8 food matrixes by simple pretreatments. Thus, the developed 16S rRNA-derived geno-biochip can be successfully used for the rapid and multiple detection of the 16 pathogenic bacteria frequently isolated from contaminated foods that are important for food safety.

Recent progress in stimuli-induced polydiacetylenes for sensing temperature, chemical and biological targets

Polydiacetylenes (PDAs) have received increasing attention as smart materials owing to their unique properties. Upon addition of various stimuli, blue PDAs can undergo a colorimetric transition from blue to red along with a change from non-fluorescent to fluorescent. The optical changes can be readily detected by the naked eye and by using absorption and fluorescence spectrometers. These properties make PDAs excellent materials for use in platforms for sensing chemical or biological targets. In recent years, a number of biosensors and chemosensors based on the optical responses of polydiacetylenes have been reported. In this review, recent advances made in this area were discussed following a format based on different cognizing targets, including temperature, metal ions, anions, surfactants, amines, water, gas, sugars, hydrocarbons, neomycin, heparin, virus, enzymes, bacteria, and cancers. Emphasis is given to the methods used to prepare PDA sensing systems as well as their sensing performance.

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.