Optical Sensors Based on Hybrid Aptamer/Conjugated Polymer Complexes

A Perspective Looking Backward and Forward on the 25th Anniversary of Conjugated Polyelectrolytes

Conjugated polyelectrolytes are π-conjugated polymers that contain ionic charged groups such as sulfonate (R-SO3-), carboxylate (R-COO-), or ammonium (R-NR3+) combined with a π-conjugated backbone. This perspective provides a summary review of the key developments in the field, starting from the first reports of their synthesis and properties to application-focused developments. The applications include optical sensors for molecular and biomolecular targets, organic electronic applications, and specific biological applications including cellular imaging and photodynamic therapy. This perspective concludes with a discussion of where the field of conjugated polyelectrolytes is expected to lead in the coming years.

Conjugated Polymers for Aptasensing Applications

Rapid and specific assaying of molecules that report on a pathophysiological condition, environmental pollution, or drug concentration is pivotal for establishing efficient and accurate diagnostic systems. One of the main components required for the construction of these systems is the recognition element (receptor) that can identify target analytes. Oligonucleotide switching structures, or aptamers, have been widely studied as selective receptors that can precisely identify targets in different analyzed matrices with minimal interference from other components in an antibody-like recognition process. These aptasensors, especially when integrated into sensing platforms, enable a multitude of sensors that can outperform antibody-based sensors in terms of flexibility of the sensing strategy and ease of deployment to areas with limited resources. Research into compounds that efficiently enhance signal transduction and provide a suitable platform for conjugating aptamers has gained huge momentum over the past decade. The multifaceted nature of conjugated polymers (CPs), notably their versatile electrical and optical properties, endows them with a broad range of potential applications in optical, electrical, and electrochemical signal transduction. Despite the substantial body of research demonstrating the enhanced performance of sensing devices using doped or nanostructure-embedded CPs, few reviews are available that specifically describe the use of conjugated polymers in aptasensing. The purpose of this review is to bridge this gap and provide a comprehensive description of a variety of CPs, from a historical viewpoint, underpinning their specific characteristics and demonstrating the advances in biosensors associated with the use of these conjugated polymers.

Recent Advances in Conjugated Polymer-Based Biosensors for Virus Detection

Nowadays, virus pandemics have become a major burden seriously affecting human health and social and economic development. Thus, the design and fabrication of effective and low-cost techniques for early and accurate virus detection have been given priority for prevention and control of such pandemics. Biosensors and bioelectronic devices have been demonstrated as promising technology to resolve the major drawbacks and problems of the current detection methods. Discovering and applying advanced materials have offered opportunities to develop and commercialize biosensor devices for effectively controlling pandemics. Along with various well-known materials such as gold and silver nanoparticles, carbon-based materials, metal oxide-based materials, and graphene, conjugated polymer (CPs) have become one of the most promising candidates for preparation and construction of excellent biosensors with high sensitivity and specificity to different virus analytes owing to their unique π orbital structure and chain conformation alterations, solution processability, and flexibility. Therefore, CP-based biosensors have been regarded as innovative technologies attracting great interest from the community for early diagnosis of COVID-19 as well as other virus pandemics. For providing precious scientific evidence of CP-based biosensor technologies in virus detection, this review aims to give a critical overview of the recent research related to use of CPs in fabrication of virus biosensors. We emphasize structures and interesting characteristics of different CPs and discuss the state-of-the-art applications of CP-based biosensors as well. In addition, different types of biosensors such as optical biosensors, organic thin film transistors (OTFT), and conjugated polymer hydrogels (CPHs) based on CPs are also summarized and presented.

A Label-Free, Mix-and-Detect ssDNA-Binding Assay Based on Cationic Conjugated Polymers

The accurate, simple, and efficient measurement of the concentration of single-stranded DNA (ssDNA) is important for many analytical applications, such as DNA adsorption, biosensor design, and disease diagnosis, but it is still a challenge. Herein, we studied a cationic conjugated polymer (CCP)-based ssDNA assay taking advantage of the obvious fluorescence change of CCPs upon binding ssDNA. Poly(3-(3'-N,N,N-triethylamino-1'-propyloxy)-4-methyl-2,5-thiophene hydrochloride) (PMNT) achieved an apparent dissociation constant (K_d) of 57 ± 4 nM for ssDNA, indicating a very high binding affinity between PMNT and ssDNA. This allowed us to develop a CCP-based ssDNA biosensor with a detection limit of 0.6 nM, similar to the fluorescence-dye-based method using SYBR Green I and SYBR Gold. Our CCP-based biosensor produced smaller differences among ssDNA samples with different base compositions. In addition, the existence of double-stranded DNA (dsDNA) at different concentrations did not interfere with the fluorescence of PMNT, indicating that our CCP-based biosensor was more suitable for the measurement of ssDNA. Compared with fluorescence-intensity-based quantification, our CCP system allowed ratiometric quantification, which made the calibration easier and more robust. We then applied our method to the quantification of ssDNA on AuNPs using both unmodified and thiolated ssDNA, and the accurate quantification of ssDNA was achieved without any fluorophore modification. This method provides an alternative approach for the measurement of ssDNA.

A facile aptamer-based sensing strategy for dopamine detection through the fluorescence energy transfer between dye and single-wall carbon nanohorns

Dopamine (DBA) as an important biomarker, plays a crucial role in disease diagnosis. In this study, we have developed a fast and simple aptamer-based fluorescence strategy which used single-wall carbon nanohorns (SWCNHs) as a quencher for dopamine detection. SWCNHs were negatively charged after pretreated, which improved its dispersion in solution. 5-carboxy-fluorescein (FAM) was used to label dopamine aptamer. In the absence of dopamine, FAM-modified aptamer could be absorbed onto the SWCNHs surface due to π-π interaction, resulting in the fluorescence intensity decreased. Dopamine could specifically bind with FAM-DNA to form G-quadruplex, which could not be absorbed onto the surface of SWCNHs. Hence, the fluorescence of FAM-DNA recovered, and the fluorescent intensity as a function of different concentrations of dopamine was measured. We obtained a detection limit of 5 μM for this detection system with a linear detection range of 0.02-2.20 mM. Furthermore, the feasibility of the innovative detection system has been verified by detecting dopamine in spiked serum samples.

Bioactive Composite Nanoparticles for Effective Microenvironment Regulation, Neuroprotection, and Cell Differentiation

Brain injuries typically result in neural tissue damage and trigger a permanent neurologic deficit. Current methods exhibit limited effects due to the harsh microenvironment of injury regions rich in reactive oxygen species (ROS). Herein, a microenvironment regulation combined with cellular differentiation strategy is designed for repairing injured nerves. We prepare PMNT/F@D-NP nanoparticles comprising a bioactive polythiophene derivative (PMNT) and fullerenol as a multifunctional theranostic nanoplatform. PMNT/F@D-NPs can significantly reduce the accumulation of ROS in the simulated ischemic brain injury trial and inhibit cell apoptosis due to the effective free radical scavenging ability of fullerenol. Interestingly, the bioactive PMNT/F@D-NPs can promote the proliferation and differentiation of neurons, confirmed by immunofluorescence and western blotting studies. This newly developed strategy exhibits a combinatorial therapeutic effect by promoting nerve cell survival and differentiation while improving the microenvironment in the damaged area, which paves the way for the rational design of multifunctional agents for brain injury therapy.

A Perspective on Polythiophenes as Conformation Dependent Optical Reporters for Label-Free Bioanalytics

Poly(3-alkylthiophene) (PT)-based conjugated polyelectrolytes (CPEs) constitute an important class of responsive polymers with excellent optical properties. The electrostatic interactions between PTs and target analytes trigger complexation and concomitant conformational changes of the PT backbones that produce distinct optical responses. These conformation-induced optical responses of the PTs enable them to be utilized as reporters for detection of various analytes by employing simple UV-vis spectrophotometry or the naked eye. Numerous PTs with unique pendant groups have been synthesized to tailor their interactions with analytes such as nucleotides, ions, surfactants, proteins, and bacterial and viral pathogens. In this perspective, we discuss PT-target analyte complexation for bioanalytical applications and highlight recent advancements in point-of-care and field deployable assays. Subsequently, we highlight a few areas of critical importance for future applications of PTs as reporters, including (i) design and synthesis of specific PTs to advance the understanding of the mechanisms of interaction with target analytes, (ii) using arrays of PTs and linear discriminant analysis for selective and specific detection of target analytes, (iii) translation of conventional homogeneous solution-based assays into heterogeneous membrane-based assay formats, and finally (iv) the potential of using PT as an alternative to conjugated polymer nanoparticles and dots in bioimaging.

DNA-Based Biosensors for the Biochemical Analysis: A Review

In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.

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.

Aptamer Switches Regulated by Post-Transition/Transition Metal Ions

We introduced an aptamer switch design that relies on the ability of post-transition/transition metal ions to trigger, through their coordination to nucleobases, substantial DNA destabilization. In the absence of molecular target, the addition of one such metal ion to usual aptamer working solutions promotes the formation of an alternative, inert DNA state. Upon exposure to the cognate compound, the equilibrium is shifted towards the competent DNA form. The switching process was preferentially activated by metal ions of intermediate base over phosphate complexation preference (i.e. Pb²⁺ , Cd²⁺ ) and operated with diversely structured DNA molecules. This very simple aptamer switch scheme was applied to the detection of small organics using the fluorescence anisotropy readout mode. We envision that the approach could be adapted to a variety of signalling methods that report on changes in the surface charge density of DNA receptors.

Architectures and Applications of BODIPY-Based Conjugated Polymers

Conjugated polymers generally contain conjugated backbone structures with benzene, heterocycle, double bond, or triple bond, so that they have properties similar to semiconductors and even conductors. Their energy band gap is very small and can be adjusted via chemical doping, allowing for excellent photoelectric properties. To obtain prominent conjugated materials, numerous well-designed polymer backbones have been reported, such as polyphenylenevinylene, polyphenylene acetylene, polycarbazole, and polyfluorene. 4,4'-Difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY)-based conjugated polymers have also been prepared owing to its conjugated structure and intriguing optical properties, including high absorption coefficients, excellent thermal/photochemical stability, and high quantum yield. Most importantly, the properties of BODIPYs can be easily tuned by chemical modification on the dipyrromethene core, which endows the conjugated polymers with multiple functionalities. In this paper, BODIPY-based conjugated polymers are reviewed, focusing on their structures and applications. The forms of BODIPY-based conjugated polymers include linear, coiled, and porous structures, and their structure-property relationship is explored. Also, typical applications in optoelectronic materials, sensors, gas/energy storage, biotherapy, and bioimaging are presented and discussed in detail. Finally, the review provides an insight into the challenges in the development of BODIPY-based conjugated polymers.

Screening, Post-SELEX Optimization and Application of DNA Aptamers Specific for Tobramycin

Tobramycin (TOB) is an aminoglycoside antibiotic. The residue of TOB in animal-derived foods and environment will be harmful to human health, and therefore the specific detection of TOB residue in food and water is of great importance. Herein, through magnetic beads-based SELEX, overall 37 ssDNA aptamers specific for TOB were screened after ten rounds of selection. The affinity and specificity of these aptamers were evaluated, among which No. 32 aptamer (Ap 32) exhibits excellent performance. Then a post-SELEX optimization of Ap 32 was carried out based on rational design, through which a truncated aptamer with the length of 34 nucleotides (Ap 32-2) was identified as the best aptamer for TOB. Finally, the application of the screened aptamer was explored. A colorimetric assay of TOB was established based on the aptamer-modified gold nanoparticles (AuNPs). In the range from 100 to 1400 nM, the absorbance of AuNPs solution at 520 nm was linearly decreased with the increased concentration of TOB. The detection limit was estimated to be 37.9 nM. The assay was applied to detect TOB residue in honey samples.

A fluorometric and colorimetric approach for the rapid detection of berberine hydrochloride based on an anionic polythiophene derivative

In this report, we develop a dual-output sensor with fluorometric and colorimetric responses, for the rapid and simple detection of berberine hydrochloride (BRH) in 100% aqueous solution based on an anionic polythiophene derivative, poly(2-(2-(4-methylthiophen-3-yloxy)-ethyl) malonic acid) (PTMA). The sensing performance and mechanism were carefully examined by absorption and emission spectra. It can be applied to quantitatively detect BRH in aqueous solution with a detection limit 0.27 μM. The appealing performance of the sensor was demonstrated to originate from the electrostatic and π-π interactions between PTMA and BRH, which promoted the conformational change and aggregation of the PTMA backbone. Moreover, this method allowed rapid detection of BRH in urine samples and BRH tablets with high accuracy.

Smart materials for point-of-care testing: From sample extraction to analyte sensing and readout signal generator

The last decade has seen a surge of technical developments in the field on point-of-care testing (POCT). While these developments are extremely diverse, the common aim is to implement improved methods for quick, reliable and inexpensive diagnosis of patients within the clinical setting. While examples of successful introduction and use of POCT techniques are growing, further developments are still necessary to create POCT devices with better portability, usability and performance. Advances in smart materials emerge as potentially valuable know-hows to provide a competitive edge to the development of next generation POCT devices. This review describes the key advantages of adopting smart material-based technologies at different analytical stages of a POCT platform. Under these analytical stages which involves sample pre-treatment, analyte sensing and readout signal generator, several concepts and approaches from contemporary research work in using smart material-based technologies will be the major focus in this review. Lastly, challenges and potential outlook in implementing materials technologies from the application point of view for POCT will be discussed.

DNA Tetrahedra Modules as Versatile Optical Sensing Platforms for Multiplexed Analysis of miRNAs, Endonucleases, and Aptamer-Ligand Complexes

The sensing modules for analyzing miRNAs or the endonucleases consist of tetrahedra functionalized with three different fluorophore-quencher pairs in spatially quenched configurations and hairpin units acting as recognition elements for the analytes. Three different miRNAs (miRNA-21, miRNA-221, and miRNA-155) or three different endonucleases (Nt.BbvCI, EcoRI, and HindIII) uncage the respective hairpins, leading to the switched-on fluorescence of the respective fluorophores and to the multiplex detection of the respective analytes. In addition, a tetrahedron module for the multiplexed analysis of aptamer ligand complexes (ligands = ATP, thrombin, VEGF) is introduced. The module includes edges modified with three spatially separated fluorophore-quencher pairs that were stretched by the respective aptamer strands to yield a switched-on fluorescent state. Formation of the respective aptamer ligands reconfigures the edges into fluorophore-quenched caged-hairpin structures that enable the multiplexed analysis of the aptamer-ligand complexes. The facile permeation of the tetrahedra structures into cells is used for the imaging of MCF-7 and HepG2 cancer cells and their discrimination from normal epithelial MCF-10A breast cells.

Colorimetric Urinalysis for On-Site Detection of Metabolic Biomarkers

Over the past few decades, colorimetric assays have been developed for cost-effective and rapid on-site urinalysis. Most of these assays were employed for detection of biomarkers such as glucose, uric acid, ions, and albumin that are abundant in urine at micromolar to millimolar levels. In contrast, direct assaying of urinary biomarkers such as glycated proteins, low-molecular-weight reactive oxygen species, and nucleic acids that are present at significantly lower levels (nanomolar to picomolar) remain challenging due to the interferences from the urine sample matrix. State-of-the-art assays for detection of trace amounts of urinary biomarkers typically utilize time-consuming and equipment-dependent sample pretreatment or clean-up protocols prior to assaying, which limits their applicability for on-site analysis. Herein, we report a colorimetric assay for on-site detection of trace amount of generic biomarkers in urine without involving tedious sample pretreatment protocols. The detection strategy is based on monitoring the changes in optical properties of poly(3-(4-methyl-3'-thienyloxy)propyltriethylammonium bromide) upon interacting with an aptamer or a peptide nucleic acid in the presence and absence of target biomarkers of relevance for the diagnosis of metabolic complications and diabetes. As a proof of concept, this study demonstrates facile assaying of advanced glycation end products, 8-hydroxy-2'-deoxyguanosine and hepatitis B virus DNA in urine samples at clinically relevant concentrations, with limits of detection of ∼850 pM, ∼650 pM, and ∼ 1 nM, respectively. These analytes represent three distinct classes of biomarkers: (i) glycated proteins, (ii) low-molecular-weight reactive oxygen species, and (iii) nucleic acids. Hence, the proposed methodology is applicable for rapid detection of generic biomarkers in urine, without involving sophisticated equipment and skilled personnel, thereby enabling on-site urinalysis. At the end of the contribution, we discuss the opportunity to translate the homogeneous assay into a paper-based format.

Lab-on-a-Chip Systems for Aptamer-Based Biosensing

Aptamers are oligonucleotides or peptides that are selected from a pool of random sequences that exhibit high affinity toward a specific biomolecular species of interest. Therefore, they are ideal for use as recognition elements and ligands for binding to the target. In recent years, aptamers have gained a great deal of attention in the field of biosensing as the next-generation target receptors that could potentially replace the functions of antibodies. Consequently, it is increasingly becoming popular to integrate aptamers into a variety of sensing platforms to enhance specificity and selectivity in analyte detection. Simultaneously, as the fields of lab-on-a-chip (LOC) technology, point-of-care (POC) diagnostics, and personal medicine become topics of great interest, integration of such aptamer-based sensors with LOC devices are showing promising results as evidenced by the recent growth of literature in this area. The focus of this review article is to highlight the recent progress in aptamer-based biosensor development with emphasis on the integration between aptamers and the various forms of LOC devices including microfluidic chips and paper-based microfluidics. As aptamers are extremely versatile in terms of their utilization in different detection principles, a broad range of techniques are covered including electrochemical, optical, colorimetric, and gravimetric sensing as well as surface acoustics waves and transistor-based detection.

Performance Enhancement of a Quartz Tuning Fork Sensor Using a Cellulose Nanocrystal-Reinforced Nanoporous Polymer Fiber

A cellulose nanocrystal (CNC)-reinforced polymethylmethacrylate (PMMA) fiber was obtained via electrospinning, and then attached between the two tines of a quartz tuning fork (QTF). The change in the resonance frequency of the CNC/PMMA composite fiber-coated QTF (CP-QTF) was measured upon being exposed to various concentrations of ethanol vapor. The frequency decreased as the ethanol vapor concentration increased, because the modulus of the composite fiber decreased due to the adsorption of the ethanol vapor. The composite fiber obtained at a high relative humidity (RH; 60% RH, CP60 fiber) produced a highly porous structure as a result of the moisture adsorption-induced phase separation of PMMA. The porosity of the CP60 fiber was higher than that of a CNC/PMMA composite fiber obtained at 30% RH (CP30 fiber) or that of a plain PMMA fiber obtained at 60% RH (P60 fiber), because hygroscopic CNCs promote moisture adsorption. The CP60 fiber-coated QTF (CP60-QTF) exhibited a greater frequency change and faster response time than P60-QTF and CP30-QTF upon exposure to ethanol vapor at the same concentration. The enhanced performance of CP60-QTF was attributed to its higher surface area and larger fiber modulus.

Gel Trapping Enables Optical Spectroscopy of Single Solvated Conjugated Polymers in Equilibrium

Single-molecule studies have provided a wealth of insight into the photophysics of conjugated polymers in the solid and desolvated state. Desolvating conjugated chains, e.g., by their embedding in inert solid matrices, invariably leads to chain collapse and the formation of intermolecular aggregates, which have a pronounced effect on their properties. By contrast, the luminescent properties of individual semiconducting polymers in their solvated and thermodynamic state remain largely unexplored. In this paper, we demonstrate a versatile gel trapping technique that enables the chemistry-free immobilization and interrogation of individual conjugated macromolecules, which retain a fully equilibrated conformation by contrast to conventional solid-state immobilization methods. We show how the technique can be used to record full luminescence spectra of single chains, to evaluate their time-resolved fluorescence, and to probe their photodynamics. Finally, we explore how the photophysics of different conjugated polymers is strongly affected by desolvation and chain collapse.

A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding

Therapeutic and diagnostic nucleic acid aptamers are designed to bind tightly and specifically to their target. The combination of structural and kinetic analyses of aptamer interactions has gained increasing importance. Here, we present a fluorescence-based switchSENSE aptasensor for the detailed kinetic characterization of aptamer-analyte interaction and aptamer folding, employing the thrombin-binding aptamer (TBA) as a model system. Thrombin-binding aptamer folding into a G-quadruplex and its binding to thrombin strongly depend on the type and concentration of ions present in solution. We observed conformational changes induced by cations in real-time and determined the folding and unfolding kinetics of the aptamer. The aptamer's affinity for K⁺ was found to be more than one order of magnitude higher than for other cations (K⁺ > NH₄⁺ >> Na⁺ > Li⁺). The aptamer's affinity to its protein target thrombin in the presence of different cations followed the same trend but differed by more than three orders of magnitude (K_D = 0.15 nM to 250 nM). While the stability (k_OFF) of the thrombin-TBA complex was similar in all conditions, the cation type strongly influenced the association rate (k_ON). These results demonstrated that protein-aptamer binding is intrinsically related to the correct aptamer fold and, hence, to the presence of stabilizing ions. Because fast binding kinetics with on-rates exceeding 10⁸ M^-1s^-1 can be quantified, and folding-related phenomena can be directly resolved, switchSENSE is a useful analytical tool for in-depth characterization of aptamer-ion and aptamer-protein interactions.

An aptamer-based hook-effect-recognizable three-line lateral flow biosensor for rapid detection of thrombin

In this paper, a three-line LFB was successfully developed by adding a thrombin line to a conventional two-line LFB for the detection of thrombin in a wide range of human serum. We introduced a thrombin line between the test line and the control line. The concentration of thrombin in the sample was quantitatively related to the signal formation on the three lines of the LFB. We can make use of signal on three lines to quantitative determinate the thrombin by data processing. The detection range of thrombin concentrations measured in 10 min was 1 nM to 100 μM and the LOD was 0.85 nM. Our approach paves way for rapid and sensitive thrombin detection and a superior device for testing in a wide range of physiological concentrations, which also can be used in other hook-effect-limited aptamers or antibodies based sandwich LFBs, and has a high accuracy even within the range of the hook-effect.

Lateral Flow Aptasensor for Simultaneous Detection of Platelet-Derived Growth Factor-BB (PDGF-BB) and Thrombin

Here we report a lateral flow aptasensor (LFA) for the simultaneous detection of platelet-derived growth factor-BB (PDGF-BB) and thrombin. Two pairs of aptamers, which are specific against PDGF-BB and thrombin, respectively, were used to prepare the LFA. Thiolated aptamers were immobilized on a gold nanoparticle (AuNP) surface and biotinylated aptamers were immobilized on the test zones of an LFA nitrocellulose membrane. The assay involved the capture of PDGF-BB and thrombin simultaneously in sandwich-type formats between the capture aptamers on the test zones of LFA and AuNP-labeled detection aptamers. AuNPs were thus captured on the test zones of the LFA and gave red bands to enable the visual detection of target proteins. Quantitative results were obtained by reading the test band intensities with a portable strip reader. By combining the highly specific molecular recognition properties of aptamers with the unique properties of lateral flow assay (low-cost, short assay time and a user-friendly format), the optimized aptasensor was capable of simultaneously detecting 1.0 nM of PDGF-BB and 1.5 nM of thrombin in association with a 10-min assay time. The biosensor was also successfully applied to detect PDGF-BB and thrombin in spiked human serum samples. The LFA shows great promise for the development of aptamer-based lateral flow strip biosensors for point-of-care or for the in-field detection of disease-related protein biomarkers.

Intermolecular distance measurement with TNT suppressor on the M13 bacteriophage-based Förster resonance energy transfer system

An M13 bacteriophage-based Förster resonance energy transfer (FRET) system is developed to estimate intermolecular distance at the nanoscale using a complex of CdSSe/ZnS nanocrystal quantum dots, genetically engineered M13 bacteriophages labeled with fluorescein isothiocyanate and trinitrotoluene (TNT) as an inhibitor. In the absence of trinitrotoluene, it is observed that a significant spectral shift from blue to green occur, which represents efficient energy transfer through dipole-dipole coupling between donor and acceptor, or FRET-on mode. On the other hand, in the presence of trinitrotoluene, the energy transfer is suppressed, since the donor-to-acceptor intermolecular distance is detuned by the specific capturing of TNT by the M13 bacteriophage, denoted as FRET-off mode. These noble features are confirmed by changes in the fluorescence intensity and the fluorescence decay curve. TNT addition to our system results in reducing the total energy transfer efficiency considerably from 16.1% to 7.6% compared to that in the non-TNT condition, while the exciton decay rate is significantly enhanced. In particular, we confirm that the energy transfer efficiency satisfies the original intermolecular distance dependence of FRET. The relative donor-to-acceptor distance is changed from 70.03 Å to 80.61 Å by inclusion of TNT.

Thioflavin T specifically brightening “Guanine Island” in duplex-DNA: a novel fluorescent probe for single-nucleotide mutation

Here, we found that Thioflavin T (ThT) could specifically bind with a G-GGG unit (named as “Guanine Island”) in double stranded DNA (ds-DNA).

Structure-Based Design of Versatile Biosensors for Small Molecules Based on the PAS Domain of a Thermophilic Histidine Kinase

The development of biosensors for in vitro quantification of small molecules such as metabolites or man-made chemicals is still a major challenge. Here we show that engineered variants of the sensory PAS domain of the histidine kinase CitA of the thermophilic bacterium Geobacillus thermoleovorans represent promising alternatives to established biorecognition elements. By combining binding site grafting and rational design we constructed protein variants binding l-malate, ethylmalonate, or the aromatic compound phthalate instead of the native ligand citrate. Due to more favorable entropy contributions, the wild-type protein and its engineered variants exhibited increased (nano- to micromolar) affinities and improved enantioselectivity compared to CitA homologues of mesophilic organisms. Ligand binding was directly converted into an optical signal that was preserved after immobilization of the protein. A fluorescently labeled variant was used to quantify ethylmalonate, an urinary biomarker for ethylmalonic encephalopathy, in synthetic urine, thereby demonstrating the applicability of the sensor in complex samples.

A Label-free Resonance Rayleigh Scattering Sensor for Detection of Thrombin Based on Aptamer Recognizing

The interaction between thrombin binding aptamer (TBA) and thrombin (TB) was studied by resonance Rayleigh scattering (RRS). In neutral medium, TBA is present in a balanced form between a G-quadruplex structure and a random coil structure, and the TBA can be induced by metal ions to form a G-quadruplex structure. Upon addition of thrombin, the G-quadruplex selectively bound to TB, which resulted in enhanced resonance Rayleigh scattering. The scattering intensities increased proportionally with the concentration of TB from 10 to 50 nM. The method had very high sensitivity and good selectivity, and the detection limit (3δ/s) was 1 nM. In this work, the spectral characteristics of RRS, the optimum conditions of the reaction, and influencing factors for the RRS intensities were investigated. Furthermore, the structure of the TBA-TB complex and the sensing mechanism were explored. The TB sensor was applied to a diluted human serum sample with satisfactory results, indicating the potential of this method to be applied to biological samples. A selective and simple RRS sensor for the detection of trace amounts of TB is proposed based on conformational change of TBA.

Optoelectronic Properties of Self-Assembled Nanostructures of Polymer Functionalized Polythiophene and Graphene

In this Feature Article, we discuss the variation of optoelectronic properties with the aggregation style of polythiophene (PT) graft copolymers and polymer-modified graphene systems. Grafting of flexible polymers on a PT chain exhibits several self-organized patterns under various conditions, causing different optical and electronic properties, arising from the different conformational states of the conjugated chain. Graphene, a zero band gap material, is functionalized with polymers both covalently and noncovalently to create a finite band gap importing new optoelectronic properties. The polymer-triggered self-assembled nanostructures of PT and graphene-based materials bring unique optical/electronic properties suitable for sensing toxic ions, nitroaromatics, and surfactants, for drug delivery, and also for fabricating molecular logic gates, electronic rectifiers, photocurrent devices, etc.

A photoelectrochemical aptasensor constructed with core-shell CuS-TiO2 heterostructure for detection of microcystin-LR

In this work, a CuS-TiO₂ heterojunction composite was prepared by dispersedly depositing CuS nanoparticles on TiO₂ nanospheres surface with a hydrothermal method, and was then used to construct a photoelectrochemical (PEC) aptasensor for sensitive detection of microcystin-LR (MC-LR) in aquatic environment. The energy bands of CuS nanoparticles and spherical anatase TiO₂ were well matched, which enhanced the photo-to-current conversion efficiency. The composite exhibited the enhanced visible light absorption, the improved separation of photo-generated charges, and the reduced self-aggregation of CuS nanoparticles, leading to the enhanced photocurrent response. The PEC aptasensor was constructed by immobilizing CuS-TiO₂ composite on ITO electrode with chitosan film that further covalently bound aminated aptamer. After the target, microcystin-LR (MC-LR) as an analyte model, was captured by the aptamer on the aptasensor, it could be oxidized by the photo-generated hole to impede the electron-hole recombination and further amplify the photocurrent. The PEC aptasensor showed superior analytical performance for MC-LR with a linear range of 5.0 × 10^-5 nM to 250 nM and a detection limit of 2.0 × 10^-5 nM. The detection results with the aptasensor for practical water samples indicated its promising application in environmental monitoring.

Application of DNA Machineries for the Barcode Patterned Detection of Genes or Proteins

The study introduces an analytical platform for the detection of genes or aptamer-ligand complexes by nucleic acid barcode patterns generated by DNA machineries. The DNA machineries consist of nucleic acid scaffolds that include specific recognition sites for the different genes or aptamer-ligand analytes. The binding of the analytes to the scaffolds initiate, in the presence of the nucleotide mixture, a cyclic polymerization/nicking machinery that yields displaced strands of variable lengths. The electrophoretic separation of the resulting strands provides barcode patterns for the specific detection of the different analytes. Mixtures of DNA machineries that yield, upon sensing of different genes (or aptamer ligands), one-, two-, or three-band barcode patterns are described. The combination of nucleic acid scaffolds acting, in the presence of polymerase/nicking enzyme and nucleotide mixture, as DNA machineries, that generate multiband barcode patterns provide an analytical platform for the detection of an individual gene out of many possible genes. The diversity of genes (or other analytes) that can be analyzed by the DNA machineries and the barcode patterned imaging is given by the Pascal's triangle. As a proof-of-concept, the detection of one of six genes, that is, TP53, Werner syndrome, Tay-Sachs normal gene, BRCA1, Tay-Sachs mutant gene, and cystic fibrosis disorder gene by six two-band barcode patterns is demonstrated. The advantages and limitations of the detection of analytes by polymerase/nicking DNA machineries that yield barcode patterns as imaging readout signals are discussed.

Luminescent Device for the Detection of Oxidative Stress Biomarkers in Artificial Urine

A luminescent paper-based device for the visual detection of oxidative stress biomarkers is reported. The device consists of a polyvinylidene fluoride membrane impregnated with poly(3-alkoxy-4-methylthiophene) (PT) for colorimetric detection. 8-hydroxy-2'-deoxyguanosine (8-OHdG), a biomarker associated with oxidative stress, is used as a model system for validating the proposed methodology. The detection strategy is based on monitoring the changes in optical properties of PT associated with its conformational changes upon interaction with an aptamer in the presence and in the absence of 8-OHdG. Fluorometric and colorimetric monitoring revealed linear responses for 8-OHdG concentrations between 50 pM and 500 nM (∼14 pg/mL to 140 ng/mL), with limits of detection of ∼300 pM and  ∼350 pM, respectively for ( n = 3). Colorimetric responses in artificial urine ascertained rapid, sensitive, and selective detection of 8-OHdG at clinically relevant (pM to nM) concentration levels. Furthermore, the proposed methodology enables point-of-care diagnostics for oxidative stress without requiring sophisticated instrumentation.

A high brightness probe of polymer nanoparticles for biological imaging

Conjugated polymer nanoparticles (CPNs) with high brightness in long wavelength region were prepared by the nano-precipitation method. Based on fluorescence resonance energy transfer (FRET) mechanism, the high brightness property of the CPNs was realized by four different emission polymers. Dynamic light scattering (DLS) and scanning electron microscopy (SEM) displayed that the CPNs possessed a spherical structure and an average diameter of ~75nm. Analysis assays showed that the CPNs had excellent biocompatibility, good photostability and low cytotoxicity. The CPNs were bio-modified with a cell penetrating peptide (Tat, a targeted element) through covalent link. Based on the entire wave fluorescence emission, the functionalized CPNs1-4 can meet multichannel and high throughput assays in cell and organ imaging. The contribution of the work lies in not only providing a new way to obtain a high brightness imaging probe in long wavelength region, but also using targeted cell and organ imaging.

Polydopamine-Functionalized CA-(PCL-ran-PLA) Nanoparticles for Target Delivery of Docetaxel and Chemo-photothermal Therapy of Breast Cancer

Current limitations of cancer therapy include the lack of effective strategy for target delivery of chemotherapeutic drugs, and the difficulty of achieving significant efficacy by single treatment. Herein, we reported a synergistic chemo-photothermal strategy based on aptamer (Apt)-polydopamine (pD) functionalized CA-(PCL-ran-PLA) nanoparticles (NPs) for effective delivery of docetaxel (DTX) and enhanced therapeutic effect. The developed DTX-loaded Apt-pD-CA-(PCL-ran-PLA) NPs achieved promising advantages, such as (i) improved drug loading content (LC) and encapsulation efficiency (EE) initiated by star-shaped copolymer CA-(PCL-ran-PLA); (ii) effective target delivery of drugs to tumor sites by incorporating AS1411 aptamers; (iii) significant therapeutic efficacy caused by synergistic chemo-photothermal treatment. In addition, the pD coating strategy with simple procedures could address the contradiction between targeting modification and maintaining formerly excellent bio-properties. Therefore, with excellent bio-properties and simple preparation procedures, the DTX-loaded Apt-pD-CA-(PCL-ran-PLA) NPs effectively increased the local drug concentration in tumor sites, minimized side effects, and significantly eliminated tumors, indicating the promising application of these NPs for cancer therapy.

Influence of Hofmeister I- on Tuning Optoelectronic Properties of Ampholytic Polythiophene by Varying pH and Conjugating with RNA

A significant tuning of optoelectronic properties of polythiophene (PT) chains due to Hofmeister iodide (I^-) ion is demonstrated in ampholytic polythiophene [polythiophene-g-poly{(N,N,N-trimethylamino iodide)ethyl methacrylate-co-methacrylic acid}, APT] at different pHs. In acidic medium, the absorption and emission signals of PT chromophore exhibit appreciable blue shift in the presence of I^- as counteranion only. The cooperative effect of undissociated -COOH and quaternary ammonium groups immobilize I^- near the apolar PT chain causing threading of grafted chains and hence twisting of the backbone attributing to the blue shift. As medium pH is increased, dethreading of the PT backbone occurs due to ionization of -COOH group, releasing quencher iodide ions from the vicinity of the PT chains resulting in a red shift in absorption and a sharp hike in fluorescence intensity (390 times) for an increase of excitons lifetime. With an increase of pH, morphology changes from a multivesicular aggregate with vacuoles to smaller size vesicles and finally to nanofibrillar network structure. Dethreading is also found when APT interacts with RNA showing a significant hike of fluorescence (22 times) for displacing iodide ions forming a nanofibrillar network morphology. Threading and dethreading also affect the resistance, capacitance, and Warburg impedance values of APT. Molecular dynamics simulation of a model APT chain in a water box supports the threading at lower pH where the iodide ions pose nearer to the PT chain than that at higher pH causing dethreading. So the influence of Hofmeister I^- ion is established for tuning the optoelectronic properties of a novel PT based polyampholyte by changing pH or by conjugating with RNA.

Use of a small molecule as an initiator for interchain staudinger reaction: A new ATP sensing platform using product fluorescence

We demonstrated that a small molecule induced interchain Staudinger reaction can be employed for highly selective detection of adenosine triphosphate (ATP), an important energy-storage biomolecule. A designed ATP split aptamer (A1) was first functionalized with a weakly fluorescent coumarin derivative due to an azide group (azido-coumarin). The second DNA strand (A2) was covalently linked with triphenylphosphine, which could selectively and efficiently reduce azido to amino group through the Staudinger reaction. The A2 was then hybridized with a half of another designed longer DNA strand (T1). The second half of T1 was a split aptamer and selectively recognized ATP with A1 to form a sandwich structure. The specific interaction between ATP and the aptamers drew the two functionalized DNA strands (A1 and A2) together to initiate the interchain Staudinger reduction at fmol-nmol concentration level, hence produced fluorescent 7-aminocoumarin which could be used as an indicator for the presence of trace ATP. The reaction process had a concentration dependent manner with ATP in a large concentration range. Such a strategy of interchain Staudinger reaction can be extended to construct biosensors for other small functional molecules on the basis of judiciously designed aptamers.

Water-Soluble Conjugated Polymer as a Fluorescent Probe for Monitoring Adenosine Triphosphate Level Fluctuation in Cell Membranes during Cell Apoptosis and in Vivo

Adenosine triphosphate (ATP) is used as the energy source in cells and plays crucial roles in various cellular events. The cellular membrane is the protective barrier for the cytoplasm of living cells and involved in many essential biological processes. Many fluorescent probes for ATP have been successfully developed, but few of these probes were appropriate for visualizing ATP level fluctuation in cell membranes during the apoptotic cell death process. Herein, we report the synthesis of a new water-soluble cationic polythiophene derivative that can be utilized as a fluorescent sensor for detecting ATP in cell membranes. Poly((3-((4-methylthiophen-3-yl)oxy)propyl)triphenylphosphonium chloride) (PMTPP) exhibits high sensitivity and good selectivity to ATP, and the detection limit is 27 nM. The polymer shows low toxicity to live cells and excellent photostability in cell membranes. PMTPP was practically utilized for real-time monitoring of ATP levels in the cell membrane through fluorescence microscopy. We have demonstrated that the ATP levels in cell membranes increased during the apoptotic cell death process. The probe was also capable of imaging ATP levels in living mice.

A Nanoparticle-Decorated Biomolecule-Responsive Polymer Enables Robust Signaling Cascade for Biosensing

To meet the increasing demands for ultrasensitivity in monitoring trace amounts of low-abundance early biomarkers or environmental toxins, the development of a robust sensing system is urgently needed. Here, a novel signal cascade strategy is reported via an ultrasensitive polymeric sensing system (UPSS) composed of gold nanoparticle (gNP)-decorated polymer, which enables gNP aggregation in polymeric network and electrical conductance change upon specific aptamer-based biomolecular recognition. Ultralow concentrations of thrombin (10^-18 m) as well as a low molecular weight anatoxin (165 Da, 10^-14 m) are detected selectively and reproducibly. The biomolecular recognition induced polymeric network shrinkage responses as well as dose-dependent responses of the UPSS are validated using in situ real-time atomic-force microscopy, representing the first instance of real-time detection of biomolecular binding-induced polymer shrinkage in soft matter. Furthermore, in situ real-time confocal laser scanning microscopy imaging reveals the dynamic process of gNP aggregation responses upon biomolecular binding.

A colorimetric aptamer biosensor based on cationic polythiophene derivative as peroxidase mimetics for the ultrasensitive detection of thrombin

A colorimetric assay for the ultrasensitive determination of thrombin was presented, in which the cationic polythiophene derivative was used as catalyst of the 3,3',5,5'-tetramethylbenzidine (TMB)-H₂O₂ reaction and the thrombin-binding aptamer (TBA) was used as inducing polymer's different conformation elements. It was found the cationic polythiophene derivative, poly[3-(3'-N,N,N-triethylamino-1'-propyloxy)-4-methyl-2,5-t-hiophene hydrochloride] (PMNT), can catalyze the oxidation reaction of TMB in the presence of H₂O₂ to produce a blue color solution. The catalytic activity of PMNT on the TMB-H₂O₂ reaction was closely relevant to the conformation of PMNT. The absorbance of TMB-H₂O₂ was distinctly increased in the presence of TBA. With the addition of thrombin, TBA interacted with thrombin to form a G-quadruplex structure. The conformational change weakened the catalytic activity of PMNT and resulted in a decrease in the absorbance. The colorimetric sensor could detect thrombin down to 4pM with high selectivity against other interfering proteins. This work is not only of importance for a better understanding of the unique properties of cationic polythiophenes derivative but also have great potential for medical diagnostics and therapy for human health.