Optical detection of DNA and proteins with cationic polythiophenes

Sensing, Imaging, and Therapeutic Strategies Endowing by Conjugate Polymers for Precision Medicine

Conjugated polymers (CPs) have promising applications in biomedical fields, such as disease monitoring, real-time imaging diagnosis, and disease treatment. As a promising luminescent material with tunable emission, high brightness and excellent stability, CPs are widely used as fluorescent probes in biological detection and imaging. Rational molecular design and structural optimization have broadened absorption/emission range of CPs, which are more conductive for disease diagnosis and precision therapy. This review provides a comprehensive overview of recent advances in the application of CPs, aiming to elucidate their structural and functional relationships. The fluorescence properties of CPs and the mechanism of detection signal amplification are first discussed, followed by an elucidation of their emerging applications in biological detection. Subsequently, CPs-based imaging systems and therapeutic strategies are illustrated systematically. Finally, recent advancements in utilizing CPs as electroactive materials for bioelectronic devices are also investigated. Moreover, the challenges and outlooks of CPs for precision medicine are discussed. Through this systematic review, it is hoped to highlight the frontier progress of CPs and promote new breakthroughs in fundamental research and clinical transformation.

Vibronic coupling and ultrafast relaxation dynamics in the first five excited singlet electronic states of bithiophene

The vibronic structure and nuclear dynamics in the first five excited singlet electronic states of bithiophene (2T) are investigated here. Specifically, considerations are given to comprehend the first two structureless and broad electronic absorption bands and the role of nonadiabatic coupling in the excited state relaxation mechanism of 2T in the gas phase. Associated potential energy surfaces (PESs) are established by constructing a model vibronic coupling Hamiltonian using 18 vibrational degrees of freedom and extensive ab initio electronic structure calculations. The topographies of these PESs are critically examined, and multiple conical intersections are established. The nuclear dynamics calculations are performed by propagating wave packets on the coupled electronic manifold. The present theoretical results are in good agreement with the experimental observations. It is found that strong nonadiabatic coupling between the S1-S4 and S1-S5 states along totally symmetric modes is predominantly responsible for the structureless and broad first absorption band, and overlapping S2, S3, S4, and S5 states form the second absorption band. Photorelaxation from the highly excited S5 to the lowest S1 state takes place through a cascade of diabatic population transfers among the S1-S4-S5 electronic manifold within the first ∼100 fs. Totally symmetric C=C stretching, C-S stretching, C-H wagging, ring puckering, and inter-ring bending modes collectively drive such relaxation dynamics.

Correlating Molar Mass, π-Conjugation, and Optical Properties of Narrowly Distributed Anionic Polythiophenes in Aqueous Solutions

Polythiophene-based conjugated polyelectrolytes (CPE) are attracting increasing attention as sensor or interface materials in chemistry and biology. While cationic polythiophenes are better understood, limited structural information is available on their anionic counterparts. Limited access to well-defined polymers has made the study of structure-property relationships difficult and clear correlations have remained elusive. By combining controlled Kumada catalyst transfer polymerization with a polymer-analog substitution, regioregular and narrowly distributed poly(6-(thiophen-3-yl)hexane-1-sulfonate)s (PTHS) with tailored chain length are prepared. Analysis of their aqueous solution structures by small-angle neutron scattering (SANS) revealed a cylindrical conformation for all polymers tested, with a length close to the contour length of the polymer chains, while the estimated radii remain too small (<1.5 nm) for extensive π-stacking of the chains. The latter is particularly interesting as the longest polymer exhibits a concentration-independent structured absorption typical of crystalline polythiophenes. Increasing the ionic strength of the solution diminishes these features as the Coulomb repulsion between the charged repeat units is shielded, allowing the polymer to adopt a more coiled conformation. The extended π-conjugation, therefore, appears to be a key parameter for these unique optical features, which are not present in the corresponding cationic polythiophenes.

Synthesis and Characterizations of Polythiophene Networks with Nonplanar BN Lewis Pair Building Blocks

Doping the boron (B) element endowed organic π-conjugated polymers (OCPs) with intriguing optoelectronic properties. Herein, we introduce a new series of thienylborane-pyridine (BN) Lewis pairs via the facile reactions between thienylborane and various pyridine derivatives. Particularly, we developed a "one-pot" synthetic protocol to access BN2 with an unstable 4-bromopyridine moiety. Polycondensations between the BN Lewis pairs and distannylated thiophene afforded a new series of BN-cross-linked polythiophenes (BN-PTs). Experiments revealed that BN-PTs exhibited highly uniform chemical structures, particularly the uniform chemical environment of B-centers. BN-PTs showed good stability in the solid state. PBN2 even maintained the uniform B-center under high temperature or moisture conditions. The studies further suggested that the presence of topological BN structures endowed the polymers with strong intramolecular charge separation character. As a proof of concept, a representative BN-PT was tested as the catalyst for photocatalytic hydrogen evolution.

Self-Immolative Polythiophene for Sunlight Inactivation of Harmful Cyanobacteria

Harmful cyanobacterial blooms and the released microcystins (MCs) caused serious environmental and public health concerns to drinking water safety. Photo-oxidation is an appealing treatment option and alternative to conventional flocculation and microbial antagonists, but the performances of current photosensitizers (either inorganic or organic) are unsatisfactory. Here, a polythiophene photosensitizer (PT10) with both high yield of reactive oxygen species (ROS) production (mainly ¹O₂, Φ_Δ = 0.51, > 8 h continuous generation) and moderate photostability was used as a powerful algaecide to inhibit Microcystis aeruginosa. Due to the positive charge of PT10, the algal cells were quickly flocculated, followed by efficient inactivation in 4 h under white light irradiation (96.7%, 10 mW/cm²). Meanwhile, PT10 was self-immolated in about 6 h. Upon biosafety evaluation with adult zebrafish, the low toxicity of PT10 and the degradation products of PT10 and algae (early logarithmic growth stage) were confirmed. In addition, microcystin-LR (MC-LR), a toxic microcystin that will be released during the destruction of the algal cells, was also degraded. Therefore, PT10-based photoinactivation of M. aeruginosa featured both high performance and low secondary pollution. In real-world aquatic systems, PT10 was confirmed to be capable of sunlight-assisted inactivation of M. aeruginosa and prevent algal blooms, thus making it appealing for environmental remediation.

CRISPR/Cas-Based MicroRNA Biosensors

As important post-transcriptional regulators, microRNAs (miRNAs) play irreplaceable roles in diverse cellular functions. Dysregulated miRNA expression is implicated in various diseases including cancers, and thus miRNAs have become the valuable biomarkers for disease monitoring. Recently, clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) system has shown great promise for the development of next-generation biosensors because of its precise localization capability, good fidelity, and high cleavage activity. Herein, we review recent advance in development of CRISPR/Cas-based biosensors for miRNA detection. We summarize the principles, features, and performance of these miRNA biosensors, and further highlight the remaining challenges and future directions.

Stille type P-C coupling polycondensation towards phosphorus-crosslinked polythiophenes with P-regulated photocatalytic hydrogen evolution

Recently, exploring new type polymerization protocols has been a major driving force in advancing organic polymers into highly functional materials. Herein we report a new polycondensation protocol to implant the phosphorus (P) atom in the main backbone of crosslinked polythiophenes. The polycondensation harnesses a Stille phosphorus-carbon (P-C) coupling reaction between phosphorus halides and aryl stannanes that has not been reported previously. Mechanistic studies uncovered that the P-electrophile makes the reactivity of a catalytic Pd-center highly sensitive towards the chemical structures of aryl stannanes, which is distinct from the typical Stille carbon-carbon coupling reaction. The efficient P-C polycondensation afforded a series of P-crosslinked polythiophenes (PC-PTs). Leveraging on the direct P-crosslinking polymerization, solid-state ³¹P NMR studies revealed highly uniform crosslinking environments. Efficient post-polymerization P-chemistry was also applied to the PC-PTs, which readily yielded the polymers with various P-environments. As a proof of concept, new PC-PTs were applied as the photocatalysts for H₂ evolution under visible light irradiation. PC-PTs with an ionic P(Me)-center exhibit a H₂ evolution rate up to 2050 μmol h^-1 g^-1, which is much higher than those of PC-PTs with a P(O)-center (900 μmol h^-1 g^-1) and P(iii)-center (155 μmol h^-1 g^-1). For the first time, the studies reveal that regulating P-center environments can be an effective strategy for fine tuning the photocatalytic H₂ evolution performance of organic polymers.

Reusable, Ultrasensitive, Patterned Conjugated Polyelectrolyte-Surfactant Complex Film with a Wide Detection Range for Copper Ion Detection

Conjugated polyelectrolytes (CPEs) are emerging as promising materials in the sensor field because they enable high-sensitivity detection of various substances in aqueous media. However, most CPE-based sensors have serious problems in real-world application because the sensor system is operated only when the CPE is dissolved in aqueous media. Here, the fabrication and performance of a water-swellable (WS) CPE-based sensor driven in the solid state are demonstrated. The WS CPE films are prepared by immersing a water-soluble CPE film in cationic surfactants of different alkyl chain lengths in a chloroform solution. The prepared film exhibits rapid, limited water swellability despite the absence of chemical crosslinking. The water swellability of the film enables the highly sensitive and selective detection of Cu²⁺ in water. The fluorescence quenching constant and the detection limit of the film are 7.24 × 10⁶ L mol^-1 and 4.38 nM (0.278 ppb), respectively. Moreover, the film is reusable via a facile treatment. Furthermore, various fluorescent patterns introduced by different surfactants are successfully fabricated by a simple stamping method. By integrating the patterns, Cu²⁺ detection in a wide concentration range (nM-mM) can be achieved.

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.

Synthesis and characterization of some novel polythiophene derivatives containing pyrazoline

Eight polythiophene derivatives containing pyrazoline side groups were synthesized by a chemical oxidative coupling polymerization using FeCl₃. The crystal structures of four monomers were determined which confirm the almost perpendicular orientation of the thiophene and pyrazoline rings, while the other substituents are more coplanar. Analyses of IR, ¹H-NMR, Raman and UV-Vis spectra demonstrated that the suggested polymerization was successful to generate the synthesized polythiophenes with the expected structures. The morphology of the synthesized polythiophenes was studied by SEM. The different substituents attached to the 1- and 3-positions of the pyrazoline side chain led to differences in optical properties, electrical conductivity, and thermal stability of the synthesized polythiophenes. By adding a pyrazoline side chain to polythiophenes, some polymers achieve good solubility, electrical conductivity of about 1.3 × 10^–6 S/cm, high fluorescence intensity (above 40,000 a.u.) at 505–550 nm and thermal stability up to 590°C in the air.

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.

Enhancement of charge-assisted hydrogen bond capabilities due to O-alkylation proximity in alkoxy cationic polythiophenes: solution- and solid-state evidence via EPR, AFM and surface free energy

Despite the array of applications for cationic polythiophenes (CPTs), there is still a need for structure-function guidelines and mechanistic understanding of their solution- and solid-state properties. This work presents a solution- and solid-state investigation of the effect of O-alkylation proximity on the hydrogen bonding (H-bonding) capabilities of alkoxy-CPTs, based on comparing an imidazolium alkoxy CPT with strong cation-pi, pi+ and positive charge-assisted hydrogen bonding (+CAHB) capabilities (PIMa), with two isothiouronium alkoxy CPTs with two-point +CAHB capabilities (PT1 & PT2), which have short and long alkoxy side chains, respectively. Our results show that a closer proximity of O-alkylation strengthens the +CAHB capabilities of PT1: in aqueous solutions, PT2 aggregates have a stronger interaction with cationic EPR spin probes than aggregates of PIMa and PT1, which in turn show a similar extent of repulsion towards the cationic spin probes. In solid-state, atomic force microscopy (AFM) shows that PIMa generates dendritic structures onto mica, with features of diffusion-limited aggregation (DLA), indicating strong interactions with the anionic substrate due to a high configurational entropy during spreading, regardless of being drop-casted from water or 1,4-dioxane-water (W-DI), despite the latter disturbing H-bonding due to selective solvation. PT1 is also capable of generating dendritic structures resembling ballistic aggregation (BA). However, this occurs only when casting from water, since W-DI generates island-like aggregates resembling attachment limited aggregation (ALA), which is the morphology generated by PT2 regardless of the solvent. Finally, spin-coated films of PIMa and PT1 show similar dispersivity of the surface free energy (SFE), which in turn is larger than that in PT2 films, which are also more affected when casted from W-DI, presenting much larger decreases of dispersivity. These results constitute a novel empirical structure-function guideline that could be useful for optimal design and/or processing of alkoxy CPTs. For example, dendritic patterns have recently gained attention since the colloidal droplet drying is related to engineering applications including inkjet printing, biosensing, and functional material design, while the SFE is relevant for opto- and bio-electronic applications of conjugated polyelectrolytes (CPEs). This information could also be useful when analyzing previous results obtained from alkoxy CPTs with different side chain lengths.

Colorimetric and Fluorometric Profiling of Advanced Glycation End Products

Profiling of advanced glycation end products (AGEs) is an emerging area of clinical significance for disease diagnosis and prognosis. Typically, concentrations of AGEs are estimated in laboratories by trained personnel using sophisticated equipment. Herein, a facile approach for colorimetric and fluorometric profiling of AGEs is reported for rapid and on-site analysis. The concentrations of AGE levels in plasma are estimated via changes in optical properties of polythiophenes (PTs) upon interaction with aptamers (Apts) in the presence and in the absence of AGEs. To validate the proposed approach, glyceraldehyde-derived AGEs (AGE class 1 [AGE1]), the biomarker associated with cardiovascular diseases and diabetes, are used as a model system. Colorimetric analysis yielded linear responses for AGE1 for clinically relevant concentration ranges between 1.5 and 300 μg/mL with a limit of detection (LOD) of ∼1.3 μg/mL. Subsequently, an approach utilizing PTs with four different pendant groups in conjunction with four different Apts is demonstrated for qualitative colorimetric profiling and for quantitative fluorometric profiling of up to four AGEs in clinical matrices. Principal component analysis (PCA) of fluorometric responses of AGE-spiked samples yielded distinct responses for the different AGEs tested. Thus, the proposed approach ascertains rapid profiling of spiked AGEs in plasma samples without the requirement of preanalytical processing and advanced instrumentation, thereby facilitating on-site diagnosis.

Cationic polythiophene-anionic fullerene pair in water and water-dioxane: studies on hydrogen bonding capabilities, kinetic and thermodynamic properties

Despite the vast array of solution- and solid-state bio-analytical, bioelectronic and optoelectronic applications of cationic polythiophenes (CPTs), the number of studies focused on the role of hydrogen bonding (H-bonding) between these and other molecules is scarce, regardless of whether H-bonding is expected to play an important role in several such applications. Also, despite the advantages of using cosolvents to systematically examine the molecular interactions, there are no such studies for CPTs to our knowledge. This work presents a steady-state UV-vis/fluorescence spectroscopic, kinetic and thermodynamic study on the H-bonding interactions between a water-soluble, cationic-anionic (isothiouronium-tetraphosphonate), polythiophene-fullerene donor-acceptor pair with two-point, charge-assisted H-bonding (CAHB) capabilities, tuned using water or a 1,4-dioxane-water mixture (W-DI). Both solvents generate photoinduced electron transfer (PET), fluorescence resonance energy transfer (FRET), spontaneous binding, H-bonding, ground-state complexing via multiple site binding, formation of micelle-like aggregates and equivalence points at a similar concentration of the quencher. However, in comparison with water, W-DI promotes less-ordered, less packed micellar aggregates, due to hydrophobic desolvation of the H-bond and larger solvent displacement during the PT1-4Fo complexation. This would decrease the extent of charge-transfer and the size of the sphere-of-quenching, mainly by displacements or rotations of the H-bonds, instead of elongations, together with a possible larger extent of diffusion-controlled static quenching. At [4Fo] larger than the equivalence point the micelles formed in water do not have available binding sites due to a tighter aggregation, causing a decrease in the quenching efficiency, while the micelles formed in W-DI start showing larger quenching efficiencies, possibly due to an increase in entropy that overcomes the desolvation of the H-bonding. These results could be useful when analyzing outputs from systems including CPTs with H-bonding capabilities, operating in (or casted from) solvents with clear differences in polarity and/or H-bonding capacity.

Chirality in polythiophenes: A review

Chiroptical polythiophene (PTh), as one of the most important chiral conductive polymers, is an emerging and hot topic in chiral materials, which shows great application potentials in fields as diverse as chiral sensing and separation, asymmetry catalysis, chiroptoelectronics, and even chiro-spintronics. This review summarizes progress in chiral polythiophenes (PThs) in the past 10 years, including the synthesis, properties and applications. Main focus is placed on the manner in which chirality is implemented and the optical activity of the chiral PThs. We showcase examples in which the chirality of PThs is induced by side chain substituents with point, planar, and axial chirality or arises from external chiral media. Application of chiral PThs is also included. Finally, perspectives for further development are offered.

Array-Based Biosensors for Bacteria Detection: From the Perspective of Recognition

Array-based biosensors have shown as effective and powerful tools to distinguish intricate mixtures with infinitesimal differences among analytes such as nucleic acids, proteins, microorganisms, and other biomolecules. In array-based bacterial sensing, the recognition of bacteria is the initial step that can crucially influence the analytical performance of a biosensor array. Bacteria recognition as well as the signal readout and mathematical analysis are indispensable to ensure the discrimination ability of array-based biosensors. Strategies for bacteria recognition mainly include the specific interaction between biomolecules and the corresponding receptors on bacteria, the noncovalent interaction between materials and bacteria, and the specific targeting of bacterial metabolites. In this review, recent advances in array-based bacteria sensors are discussed from the perspective of bacteria recognition relying on the characteristics of different bacteria. Principles of bacteria recognition and signal readout for bacteria detection are highlighted as well as the discussion on future trends in array-based biosensors.

Optical Biosensors for Virus Detection: Prospects for SARS-CoV-2/COVID-19

The recent pandemic of the novel coronavirus disease 2019 (COVID-19) has caused huge worldwide disruption due to the lack of available testing locations and equipment. The use of optical techniques for viral detection has flourished in the past 15 years, providing more reliable, inexpensive, and accurate detection methods. In the current minireview, optical phenomena including fluorescence, surface plasmons, surface-enhanced Raman scattering (SERS), and colorimetry are discussed in the context of detecting virus pathogens. The sensitivity of a viral detection method can be dramatically improved by using materials that exhibit surface plasmons or SERS, but often this requires advanced instrumentation for detection. Although fluorescence and colorimetry lack high sensitivity, they show promise as point-of-care diagnostics because of their relatively less complicated instrumentation, ease of use, lower costs, and the fact that they do not require nucleic acid amplification. The advantages and disadvantages of each optical detection method are presented, and prospects for applying optical biosensors in COVID-19 detection are discussed.

PCR-Free Methodology for Detection of Single-Nucleotide Polymorphism with a Cationic Polythiophene Reporter

This study presents a nonamplification-based nucleic acid assay for the detection of single-nucleotide polymorphism (SNP) associated with familial Mediterranean fever (FMF) besides polymerase chain reaction (PCR)-based methodologies. The major objective is to show the potential of the proposed assay for rapid screening of FMF in a Mediterranean region of 400 million population. The assay relies on binding difference of specially designed wild and mutant primers to the target genomic DNA, followed by determination of unbound primers by quick titration of a cationic polythiophene reporter. The fluorescent reporter exhibits signal transition from 525 to 580 nm in the presence of unbound primers, and it correlates the binding affinity of label-free primers to the homozygous wild and mutant genomes. As a proof of concept, 26 real samples are studied relying on the ON and OFF fluorescence signals of the cationic polythiophene reporter. The results are analyzed by principal component analysis (PCA), which provides clear separation of healthy and patient individuals. The further analysis by support vector machine (SVM) classification has revealed that our assay converges to 96% overall accuracy. These results support that the PCR-free nucleic acid assay has a significant potential for rapid and cost-effective screening of familial Mediterranean fever.

Effect of doped H, Br, Cu, Kr, Ge, As and Fe on structural features and bandgap of poly C13H8OS-X: a DFT calculation

Structural features such as the shape, the lattice constant, the bond length, the total energy per cell, and the energy bandgap (Eg) of C13H8OS-X are studied by the calculating Partial Density Of States (PDOS), and DOS package of the Material Studio (MS) software. Calculations show that the bond length and the bond angle between atoms insignificant change as 1.316 Å to 1.514 Å for C-C, 1.211 Å for C-O, 1.077 Å to 1.105 Å for C-H; bond angle of round one changes from 118.883° to 121.107° for C-C-C, from 117.199° to 122.635° for H-C-C, from 119.554° to 123.147° for C-C-O and from 109.956° to 117.537° for C-C-H. When C13H8OS-X doped in the order of -Br, -Cu, -Kr, -Ge, -As, and -Fe then bond lengths, bond angles between atoms have a nearly constant value. Particularly for links C-X, there is a huge change in value, respectively 1.876, 1.909, 10.675, 2.025, 2.016, 2.014 Å; the total energy change from Etot = -121,794 eV to Etot = -202,859 eV, and the energy band gap decreases from Eg = 2.001 eV to Eg = 0.915 eV. The obtained results are useful and serve as a basis for future experimental research.

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.

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.

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.

Sensitive Detection and Conjoint Analysis of Promoter Methylation by Conjugated Polymers for Differential Diagnosis and Prognosis of Glioma

Glioma is the most common primary tumor in the central nervous system (CNS) with the worst prognosis. Accurate pathological diagnosis has always been a challenge for optimal management of glioma. Promoter methylation is an important mechanism of epigenetic silencing tumor-suppressor genes and a potential biomarker for differential diagnosis and prognosis. Herein, using the cationic conjugated polymer (CCP)-based fluorescence resonance energy transfer (FRET) technique, we realized a highly sensitive detection of promoter methylation in clinical samples of minimal methylation degree (1.25%) and trace DNA quantity (10 ng/μL). Results for three glioma-related genes (MGMT, CDKN2A, and TERT) were combined in a diagnostic classifier to analyze the glioma-CpG island methylator phenotype (G-CIMP), which achieved a sensitivity of 80% at a maximum specificity of 100% for a glioma diagnosis. Kaplan-Meier survival curves and Pearson correlation analysis revealed that the prognosis of glioma patients with high G-CIMP scores (>5) was significantly better than those with low G-CIMP scores, especially in diffuse midline glioma and astrocytoma. This CCP-based FRET technique for determining G-CIMP status could provide patients with rapid and reasonably accurate diagnosis of glioma, as well as a valuable prognostic prediction that can guide individual treatment.

Conjoint Analysis of DNA Methylation for Tumor Differentiation Using Cationic Conjugated Polymers

Molecular biomarkers, especially DNA methylation, are crucial discoveries for early detection of cancer. Compared with a single biomarker detection mode, using the conjoint detection mode can allow researchers to easily assess the association of the biomarkers with specific cancer. In this paper, we calculated the methylation status of RASSF1A, APC, CDKN2A/p16, and TMEFF2 genes using cationic conjugated polymers (CCPs)-based fluorescence resonance energy transfer (FRET) technique and then explored the connection between the overall DNA methylation status of the four genes and the clinical parameters of lung cancer patients. After analysis, no association was found between the methylation status of any single gene and the grade of tumor differentiation among 159 lung cancer samples analyzed. However, for conjoint analysis using the four genes, a statistically significant difference was reached between methylation status and the grade of tumor differentiation. The methylation levels in a panel of the four genes were correlated with sex, age, smoking pack-years, and lymphatic metastasis. Therefore, the conjoint analysis of DNA methylation in specific cancer-related genes could be a useful diagnostic tool for clinical implementation.

Helical polymers for biological and medical applications

Helices are the most prevalent secondary structure in biomolecules and play vital roles in their activity. Chemists have been fascinated with mimicking this molecular conformation with synthetic materials. Research has now been devoted to the synthesis and characterization of helical materials, and to understand the design principles behind this molecular architecture. In parallel, work has been done to develop synthetic polymers for biological and medical applications. We now have access to materials with controlled size, molecular conformation, multivalency or functionality. As a result, synthetic polymers are being investigated in areas such as drug and gene delivery, tissue engineering, imaging and sensing, or as polymer therapeutics. Here, we provide a critical view of where these two fields, helical polymers and polymers for biological and medical applications, overlap. We have selected relevant polymer families and examples to illustrate the range of applications that can be targeted and the impact of the helical conformation on the performance. For each family of polymers, we briefly describe how they can be prepared, what helical conformations are observed and what parameters control helicity. We close this Review with an outlook of the challenges ahead, including the characterization of helicity through the process and the identification of biocompatibility.

Pixelated colorimetric nucleic acid assay

Conjugated polyelectrolytes (CPEs) have been widely used as reporters in colorimetric assays targeting nucleic acids. CPEs provide naked eye detection possibility by their superior optical properties however, as concentration of target analytes decrease, trace amounts of nucleic acid typically yield colorimetric responses that are not readily perceivable by naked eye. Herein, we report a pixelated analysis approach for correlating colorimetric responses of CPE with nucleic acid concentrations down to 1 nM, in plasma samples, utilizing a smart phone with an algorithm that can perform analytical testing and data processing. The detection strategy employed relies on conformational transitions between single stranded nucleic acid-cationic CPE duplexes and double stranded nucleic acid-CPE triplexes that yield distinct colorimetric responses for enabling naked eye detection of nucleic acids. Cationic poly[N,N,N-triethyl-3-((4-methylthiophen-3-yl)oxy)propan-1-aminium bromide] is utilized as the CPE reporter deposited on a polyvinylidene fluoride (PVDF) membrane for nucleic acid assay. A smart phone application is developed to capture and digitize the colorimetric response of the individual pixels of the digital images of CPE on the PVDF membrane, followed by an analysis using the algorithm. The proposed pixelated approach enables precise quantification of nucleic acid assay concentrations, thereby eliminating the margin of error involved in conventional methodologies adopted for interpretation of colorimetric responses, for instance, RGB analysis. The obtained results illustrate that a ubiquitous smart phone could be utilized for point of care colorimetric nucleic acids assays in complex matrices without requiring sophisticated software or instrumentation.

Electronic structure of polythiophene gas sensors for chlorinated analytes

Density functional theory studies are performed to investigate the response of polythiophene as a sensor for chlorinated gaseous analytes. Interaction of polythiophene with these analytes is studied from both H-side (dipole-dipole) and Cl-side (halogen bonding) of analyte to get the most stable interaction site. Inferences from interaction energy, natural bond orbital, and Mulliken charge analyses are in line with those from geometric analysis. Interaction energies reveal that polythiophene has specificity and selectivity towards chlorine. Interestingly, the halogen bond in PT-Cl₂ complexes is stronger than ion-dipole bond in the complexes of polythiophene with other analytes. The sensing of polythiophene towards these analytes is also measured by perturbing the electronic properties including ionization potential, electron affinity, λ_max, and H→L gap. The spectroscopic properties (UV absorption spectra) reveal the interaction behavior of polythiophene with these chlorinated analytes. All these parameters including orbital analysis and H→L energies indicate high sensitivity of polythiophene for chlorine. Graphical abstractInteraction of chlorinated gaseous analytes with polythiophene surface.

Advances in conjugated polymers for visualization of latent fingerprints: a critical perspective

Owing to unique photophysical and structural features conjugated polymers (CPs) have demonstrated high selectivity, specificity and enhanced imaging ability and are utilized for rapid latent fingerprint development using simple processing methods.

Water-Soluble Conjugated Organic Molecules as Optical and Electrochemical Materials for Interdisciplinary Biological Applications

Apart from the wide applications in the field of electronic and optoelectronic devices, conjugated molecules have been established as useful functional materials for biological applications. By introducing hydrophilic side chains to conjugated backbones, water-soluble conjugated polymers or oligomers (CPs or COs) inherit the attractive optical and electronic properties from conjugated molecules, while their water solubility ensures interaction with biological substrates such as biomacromolecules, microorganisms, and living cells for further biological applications. Benefiting from high brightness, large extinction coefficients, excellent photostability, low cytotoxicity, stability in bodily fluids, and versatile structural modifications, water-soluble conjugated polymers and oligomers have offered powerful alternatives in a variety of biological applications including biological and chemical sensors, fluorescence imaging, disease diagnostics, and therapy. This Account will focus on our recent advances in design, synthesis, and interdisciplinary biological applications of a series of new water-soluble CP and CO materials, starting with a brief introduction to water-soluble CPs and COs and various methods and strategies developed for the preparation of advanced water-soluble CPs and COs. Since their properties can be tuned by rational design and synthesis at the level of the conjugated repeat unit and versatile pendant groups, CPs and COs provide a diverse toolbox for satisfying interdisciplinary biological applications. The application of water-soluble CPs and COs in the past five years can be broadly categorized into four areas. Specifically, integrating the unique optoelectronic properties of water-soluble CPs and COs with self-assembly and supramolecular strategies, efficacy regulation of antibiotic and anticancer drugs has been achieved, meanwhile drug resistance could be overcome and drug resistant "superbacteria" can be inhibited. For applications regulating cellular functions and biological processes, we introduce CPs and COs with the ability to regulate intracellular oxidative stress, cell-cell communication, cellular proliferation, cell membrane permeability, and quorum sensing of bacteria cells. By covalent linkage of reactive groups upon CPs and COs, these molecules are endowed with abilities like disassembly of amyloid polypeptides, biased distribution in cells, selective imaging of organelles, and distinguished interactions with biomolecules. For photothermal therapy (PTT) applications, photothermal-responsive conjugated polymer materials have been utilized for remote control of gene expression in living cells and in vivo photothermal therapy of cancer. Beyond these applications, we have achieved new interdisciplinary applications of water-soluble CP and CO materials for biological optoelectronic devices including photosynthesis, photocatalysis, and bioenergy. Specific features or properties of water-soluble CPs and COs are leveraged to bring opportunities for each of these applications. These studies open a new frontier for development of new functional conjugated molecule materials and provide better understanding of their interactions with biological systems as well as structure/property relationships. Current limitations confronted by CPs and COs are raised, and developmental direction for the future is proposed.

Synthesis and optical studies of Y-shaped imidazole derivatives

A novel series Y-shaped π-expanded imidazole based chromophores was designed and synthesized. The series contains thirteen 2-aryl-4,5-bis[2-(aryl)vinyl)]-1H-imidazoles (6a-6m), which were characterized by spectroscopic analysis. The structures of compounds 6d and 6j were also confirmed by X-ray crystallographic analysis. The optical studies were investigated using absorption and emission measurements in dichloromethane. The fluorescence quantum yields were observed varying in 0.22-0.59 range, but the compounds with nitro substituent did not show the fluorescence. The absorption and emission study of the series helped us to understand the effect of substituents on the optical properties of compounds as well.

Precisely Defined Conjugated Oligoelectrolytes for Biosensing and Therapeutics

Conjugated oligoelectrolytes (COEs) are a relatively new class of synthetic organic molecules with, as of yet, untapped potential for use in organic optoelectronic devices and bioelectronic systems. COEs also offer a novel molecular approach to biosensing, bioimaging, and disease therapy. Substantial progress has been made in the past decade at the intersection of chemistry, materials science, and the biological sciences developing COEs and their polymer analogues, namely, conjugated polyelectrolytes (CPEs), into synthetic systems with biological and biomedical utility. CPEs have traditionally attracted more attention in arenas of sensing, imaging, and therapy. However, the precisely defined molecular structures and interactions of COEs offer potential key advantages over CPEs, including higher reliability and fluorescence quantum efficiency, larger diversity of subcellular targeting strategies, and improved selectivity to biomolecules. Here, the unique-and sometimes overlooked-properties of COEs are discussed and the noticeable progress in their use for biological sensing, imaging, and therapy is reviewed.

Synthesis of a one-handed helical polythiophene: a new approach using an axially chiral bithiophene with a fixed syn-conformation

An optically active polythiophene, which can fold into a one-handed helical conformation under good solvent conditions, has been developed.

We report an optically active polythiophene capable of forming a one-handed helically folded conformation without needing aggregate formation, poor solvent conditions, hydrogen-bonded ion-pair formation or guest addition. The target polythiophene (poly-T_R) with a static axial chirality in the main chain was synthesized via Stille coupling copolymerization of a glucose-linked chiral 5,5′-dibromobithiophene with 2,5-bis(stannyl)thiophene. Poly-T_R showed a characteristic circular dichroism and circularly polarized luminescence, which were completely different to those observed for an analogous polymer (poly-Ph_R) and the corresponding unimer/dimer model compounds. This chiroptical study, combined with the results of all-atom molecular dynamics simulations, revealed that poly-T_R can fold into a left-handed helical conformation under good solvent conditions. Partial conformational regulation derived from the fixed syn-conformation of the chiral bithiophene unit was considered a key factor in producing the one-handed helical polythiophene.