Pyrene excimer signaling molecular beacons for probing nucleic acids

Nanoscale covalent organic frameworks for enhanced photocatalytic hydrogen production

Nanosizing confers unique functions in materials such as graphene and quantum dots. Here, we present two nanoscale-covalent organic frameworks (nano-COFs) that exhibit exceptionally high activity for photocatalytic hydrogen production that results from their size and morphology. Compared to bulk analogues, the downsizing of COFs crystals using surfactants provides greatly improved water dispersibility and light-harvesting properties. One of these nano-COFs shows a hydrogen evolution rate of 392.0 mmol g-1 h-1 (33.3 μmol h-1), which is one of the highest mass-normalized rates reported for a COF or any other organic photocatalysts. A reverse concentration-dependent photocatalytic phenomenon is observed, whereby a higher photocatalytic activity is found at a lower catalyst concentration. These materials also show a molecule-like excitonic nature, as studied by photoluminescence and transient absorption spectroscopy, which is again a function of their nanoscale dimensions. This charts a new path to highly efficient organic photocatalysts for solar fuel production.

Chemical Control of Fluorescence Lifetime towards Multiplexing Imaging

Fluorescence lifetime imaging has been a powerful tool for biomedical research. Recently, fluorescence lifetime-based multiplexing imaging has expanded imaging channels by using probes that harbor the same spectral channels and distinct excited state lifetime. While it is desirable to control the excited state lifetime of any given fluorescent probes, the rational control of fluorescence lifetimes remains a challenge. Herein, we chose boron dipyrromethene (BODIPY) as a model system and provided chemical strategies to regulate the fluorescence lifetime of its derivatives with varying spectral features. We find electronegativity of structural substituents at the 8' and 5' positions is important to control the lifetime for the green-emitting and red-emitting BODIPY scaffolds. Mechanistically, such influences are exerted via the photo-induced electron transfer and the intramolecular charge transfer processes for the 8' and 5' positions of BODIPY, respectively. Based on these principles, we have generated a group of BODIPY probes that enable imaging experiments to separate multiple targets using fluorescence lifetime as a signal. In addition to BODIPY, we envision modulation of electronegativity of chemical substituents could serve as a feasible strategy to achieve rational control of fluorescence lifetime for a variety of small molecule fluorophores.

Cell-resistant wavelength-shifting molecular beacons made of L-DNA and a clickable L-configured uridine

Wavelength-shifting molecular beacons were prepared from L-DNA. The clickable anchor for the two dyes, Cy3 and Cy5, was 2'-O-propargyl-L-uridine and was synthesized from L-ribose. Four clickable molecular beacons were prepared and double-modified with the azide dyes by a combination of click chemistry on a solid support for Cy3 during DNA synthesis and postsynthetic click chemistry for Cy5 in solution. Cy3 and Cy5 successfully formed a FRET pair in the beacons, and the closed form (red fluorescence) and the open form (green fluorescence) can be distinguished by the two-color fluorescence readout. Two molecular beacons were identified to show the greatest fluorescence contrast in temperature-dependent fluorescence measurements. The stability of the L-configured molecular beacons was demonstrated after several heating and cooling cycles as well as in the cell lysate. In comparison, D-configured molecular beacons showed a rapid decrease of fluorescence contrast in the cell lysate, which is caused by the opening of the beacons, probably due to degradation. This was confirmed in cell experiments using confocal microscopy. The L-configured molecular beacons are potential intracellular thermometers for future applications.

Unraveling the Origin of Multichannel Circularly Polarized Luminescence in a Pyrene-Functionalized Topologically Chiral [2]Catenane

Mechanically interlocked molecules (MIMs) are promising platforms for developing functionalized artificial molecular machines. The construction of chiral MIMs with appealing circularly polarized luminescence (CPL) properties has boosted their potential application in biomedicine and the optical industry. However, there is currently little knowledge about the CPL emission mechanism or the emission dynamics of these related MIMs. Herein, we demonstrate that time-resolved circularly polarized luminescence (TRCPL) spectroscopy combined with transient absorption (TA) spectroscopy offers a feasible approach to elucidate the origins of CPL emission in pyrene-functionalized topologically chiral [2]catenane as well as in a series of pyrene-functionalized chiral molecules. For the first time, direct evidence differentiating the chiroptical signals originating from either topological (local state emission) or Euclidean chirality (excimer state emission) in these pyrene-functionalized chiral molecules has been discovered. Our work not only establishes a novel and ideal approach to study CPL mechanism, but also provides a theoretical foundation for the rational design of novel chiral materials in the future.

Sculpting photoproducts with DNA origami

Natural light-harvesting systems spatially organize densely packed dyes in different configurations to either transport excitons or convert them into charge photoproducts, with high efficiency. In contrast, artificial photosystems like organic solar cells and light-emitting diodes lack this fine structural control, limiting their efficiency. Thus, biomimetic multi-dye systems are needed to organize dyes with the sub-nanometer spatial control required to sculpt resulting photoproducts. Here, we synthesize 11 distinct perylene diimide (PDI) dimers integrated into DNA origami nanostructures and identify dimer architectures that offer discrete control over exciton transport versus charge separation. The large structural-space and site-tunability of origami uniquely provides controlled PDI dimer packing to form distinct excimer photoproducts, which are sensitive to interdye configurations. In the future, this platform enables large-scale programmed assembly of dyes mimicking natural systems to sculpt distinct photophysical products needed for a broad range of optoelectronic devices, including solar energy converters and quantum information processors.

A Stimuli-Responsive Dual-Emitting Covalent Organic Framework Shows Selective Sensing of Highly Corrosive Acidic Media via Fluorescence Turn-On Signal with White Light Emission

Luminescent covalent organic frameworks (LCOFs) have been employed as platforms for sensing analytes. Judicial incorporation of appropriate functional units inside the framework leads to the different electronic states in the presence of external stimuli, e.g., temperature, pH, etc. We report herein a new COF (TPEPy) as a solid-state acid sensor specific for the highly acidic environments that range from pH ∼0.5 to ∼3.0. This COF shows a protonation-induced reversible color change from bright yellow to deep red upon decreasing the pH from 3 to 0.5 and vice versa. No visual color change was, however, observed above pH 3.0. Photoluminescence (PL) studies show that the intrinsic emission peak of the TPEPy COF at 530 nm is shifted to 420 nm owing to the N-protonation of the imine nitrogen of COF within this pH range. Extensive studies demonstrate that the protonation behavior of the COF is counterion dependent. This was revealed when different acids, e.g., HCl, HNO3, HBr, and HI, were employed. The intensity of the proton-induced emission peak at 420 nm depends significantly upon the counterions with the order of HCl > HNO3 > HBr > HI. These anions interact with the protonated TPEPy COF by cation-anion and H-bonding interactions. Further, the pristine COF showed near white light emission at a particular pH of 2.5 (CIE coordinates 0.27, 0.32). From the PL spectrophotometric titrations, the deprotonation pKa was experimentally found to be 1.8 ± 0.02 for the TPEPy COF. The sensor reported herein is reversible, reusable, and regenerable and is useful for assessing pH fluctuations within a strongly acidic range via digital signaling.

Time-resolved Fluorescence DNA-based Sensors for Reducing Background Fluorescence of Environment

The fluorescence assay is one of the popular methods that is applied for detection of different targets. However, this method may show low sensitivity and high background in biological samples due to the natural fluorescence of different compounds in complicated samples. In addition, it inevitably affects the detection results accuracy. A fundamental solution to this problem is the use of the time-resolved fluorescence technique (TRF). The main component of this technique is the use of long fluorescence lifetime reagents. In this review, various time-resolved fluorescent reagents such as complexes of lanthanide ions, lanthanide-doped inorganic nanoparticles; Mn-doped ZnS quantum dots (QDs) and pyrene excimer are introduced. Moreover, TRF sensors, especially TRF aptasensors (DNA-based sensors) are discussed. This review will give new ideas for researchers to develop novel high-sensitive TRF sensors that can remove or decrease background fluorescence and use them for the detection of various targets in complicated samples without treatment.

High-Throughput Analysis of Bacterial Toxic Lipopolysaccharide in Water by Dual-Wavelength Monitoring Using a Ratiometric Fluorescent Chemosensor

Lipopolysaccharide (LPS) is a bacterial toxin that causes fever in humans. Our small-molecule chemosensor named Zn-dpa-C2OPy shows rapid ratiometric fluorescence response to LPS in water with a detection limit of 11 pM, which is lower than that of our previously reported sensor. Spectroscopic measurements (fluorescence, absorbance, 1H NMR, and fluorescence lifetime), dynamic light scattering measurements, and transmission electron microscopy observations revealed that the fluorescence response was induced by the changes in the aggregation state via multi-point recognition of LPS through hydrophobic and electrostatic interactions, in addition to the coordination between the zinc(II)-dipicolylamine moiety of the chemosensor and the phosphate group of LPS. The proposed Zn-dpa-C2OPy chemosensor was applied to an original flow injection analysis (FIA) system with a self-developed dual-wavelength fluorophotometer, and a high throughput of 36 samples per hour was achieved. These results demonstrate the feasibility of this unique methodology combining a ratiometric fluorescent chemosensor and FIA for continuous online monitoring of LPS in water.

Recent Advances in Excimer-Based Fluorescence Probes for Biological Applications

The fluorescent probe is a powerful tool for biological sensing and optical imaging, which can directly display analytes at the molecular level. It provides not only direct visualization of biological structures and processes, but also the capability of drug delivery systems regarding the target therapy. Conventional fluorescent probes are mainly based on monomer emission which has two distinguishing shortcomings in practice: small Stokes shifts and short lifetimes. Compared with monomer-based emission, excimer-based fluorescent probes have large Stokes shifts and long lifetimes which benefit biological applications. Recent progress in excimer-based fluorescent sensors (organic small molecules only) for biological applications are highlighted in this review, including materials and mechanisms as well as their representative applications. The progress suggests that excimer-based fluorescent probes have advantages and potential for bioanalytical applications.

Dumbbell-type triplex molecular switch-based logic molecular assays of SARS-CoV-2

Accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of great importance to control the COVID-19 pandemic. The gold standard assays for COVID-19 diagnostics are mainly based on separately detecting open reading frame 1ab (ORF1ab) and nucleoprotein (N) genes by RT-PCR. However, the current approaches often obtain false positive-misdiagnose caused by cross-contamination or undesired amplification. To address this issue, herein, we proposed a dumbbell-type triplex molecular switch (DTMS)-based, logic-gated strategy for high-fidelity SARS-CoV-2 RNA detection. The DTMS consists of a triple-helical stem region and two-loop regions for recognizing the ORF1ab and N genes of SARS-CoV-2. Only when the ORF1ab and N gene are concurrent, DTMS experiences a structural rearrangement, thus, bringing the two pyrenes into spacer proximity and leading to a new signal readout. This strategy allows detecting SARS-CoV-2 RNA with a detection limit of 1.3 nM, independent of nucleic acid amplification, holding great potential as an indicator probe for screening of COVID-19 and other population-wide epidemics.

Three's a crowd - stabilisation, structure, and applications of DNA triplexes

DNA is a strikingly flexible molecule and can form a variety of secondary structures, including the triple helix, which is the subject of this review. The DNA triplex may be formed naturally, during homologous recombination, or can be formed by the introduction of a synthetic triplex forming oligonucleotide (TFO) to a DNA duplex. As the TFO will bind to the duplex with sequence specificity, there is significant interest in developing TFOs with potential therapeutic applications, including using TFOs as a delivery mechanism for compounds able to modify or damage DNA. However, to combine triplexes with functionalised compounds, a full understanding of triplex structure and chemical modification strategies, which may increase triplex stability or in vivo degradation, is essential - these areas will be discussed in this review. Ruthenium polypyridyl complexes, which are able to photooxidise DNA and act as luminescent DNA probes, may serve as a suitable photophysical payload for a TFO system and the developments in this area in the context of DNA triplexes will also be reviewed.

Fluorescence ratiometric DNA detection by peptide nucleic acid-pyrene binary probes

We developed a method for detecting DNA by excimer fluorescence from two peptide nucleic acids (PNAs) modified with a pyrene (Pyr). The two PNA-Pyr probes were prepared by solid-phase peptide synthesis, and we assessed fluorescence from the mixture of probes with DNA. From the results, excimer fluorescence derived from the two PNA-Pyr probes forming hybrids with the complementary DNA was observed, and the two probes showed the maximum excimer/monomer ratio when the probes and DNA were hybridized at a 1:1:1 ratio, indicating that the PNA-Pyr probes can detect target DNA. Furthermore, we adjusted the spatial arrangement between the two PNA-Pyr hybrids formed on the DNA to promote optimal excimer formation. As a result, optimal excimer formation was achieved by spacing the two nucleobases between the formed two hybrids and further inserting a hexamethylene linker (C6) between the PNA and Pyr of the PNA-Pyr probe on one side.

Conjugation of chemical handles and functional moieties to DNA during solid phase synthesis with sulfonyl azides

Labelling of oligonucleotides with dyes, targeting ligands, and other moieties has become ever more essential in life-sciences. Conventionally, modifications are introduced to oligonucleotides during solid phase synthesis by special phosphoramidites functionalised with a chemical handle or the desired functional group. In this work, we present a facile and inexpensive method to introduce modifications to oligonucleotides without the need for special phosphoramidites. Sulfonyl azides are applied to react with one or more selected phosphite intermediates during solid phase synthesis. We have prepared 11 sulfonyl azides with different chemical handles such as amine, azide, alkyne, and thiol, and we have further introduced functionalities such as pyrene, other dyes, photo-switchable azobenzenes, and a steroid. The method is compatible with current phosphoramidite-based automated oligonucleotide synthesis and serves as a simple alternative to the unstable and expensive special phosphoramidites currently used for conjugation to oligonucleotides.

Research progress of live-cell RNA imaging techniques

RNA molecules play diverse roles in many physiological and pathological processes as they interact with various nucleic acids and proteins. The various biological processes of RNA are highly dynamic. Tracking RNA dynamics in living cells is crucial for a better understanding of the spatiotemporal control of gene expression and the regulatory roles of RNA. Genetically encoded RNA-tagging systems include MS2/MCP, PP7/PCP, boxB/λN22 and CRISPR-Cas. The MS2/MCP system is the most widely applied, and it has the advantages of stable binding and high signal-to-noise ratio, while the realization of RNA imaging requires gene editing of the target RNA, which may change the characteristics of the target RNA. Recently developed CRISPR-dCas13 system does not require RNA modification, but the uncertainty in CRISPR RNA (crRNA) efficiency and low signal-to-noise ratio are its limitations. Fluorescent dye-based RNA-tagging systems include molecular beacons and fluorophore-binding aptamers. The molecular beacons have high specificity and high signal-to-noise ratio; Mango and Peppers outperform the other RNA-tagging system in signal-to-noise, but they also need gene editing. Live-cell RNA imaging allows us to visualize critical steps of RNA activities, including transcription, splicing, transport, translation (for message RNA only) and subcellular localization. It will contribute to studying biological processes such as cell differentiation and the transcriptional regulation mechanism when cells adapt to the external environment, and it improves our understanding of the pathogenic mechanism of various diseases caused by abnormal RNA behavior and helps to find potential therapeutic targets. This review provides an overview of current progress of live-cell RNA imaging techniques and highlights their major strengths and limitations.

In situ construction of a cobalt oxyhydroxide loaded pyrene-based fluorescent organic nanoprobe for bioimaging of endogenous ascorbic acid in living cells

A novel in situ strategy to fabricate CoOOH nanoflake-loaded pyrene-based FONs (denoted as PyFONs@CoOOH) as proof-of-concept of a sensing platform for direct bioimaging of endogenous AA in living cells.

Luminescent Covalent Organic Frameworks for Biosensing and Bioimaging Applications

Luminescent covalent organic frameworks (LCOFs) have attracted significant attention due to their tunability of structures and photophysical properties at molecular level. LCOFs are built to highly ordered and periodic 2D or 3D framework structures through covalently assembling with various luminophore building blocks. Recently, the advantages of LCOFs including predesigned properties of structure, unique photoluminescence, hypotoxicity and good biocompatibility and tumor penetration, broaden their applications in biorelated fields, such as biosensing, bioimaging, and drug delivery. A specific review that analyses the advances of LCOFs in the field of biosensing and bioimaging is thus urged to emerge. Here the construction of LCOFs is reviewed first. The synthetic chemistry of LCOFs highlights the key role of chemical linkages, which not only concrete the building blocks but also affect the optical properties and even can act as the responsive sites for potential sensing applications. How to brighten LCOFs are clarified through description of structure managements. The ability to utilize the luminescence of LCOFs for applications in biosensing and bioimaging is discussed using state-of-the-art examples of varied practical goals. A prospect finally addresses opportunities and challenges the development of LCOFs facing from chemistry, physics to the applications, according to their current progress.

Relationship Between Molecular Structure, Single crystal Packing and Self-Assembly Behavior: A Case Based on Pyrene Imide Derivatives

Development of new n-type one-dimensional (1D) self-assembly nanostructure and a clear understanding of the relationship between molecular structure and self-assembly behavior are important prerequisites for further designing and optimizing organic optoelectronic nanodevice. In this article, a series of n-type organic semiconductor materials based on pyrene imide were successfully synthesized through [4+2] cycloaddition reactions and their preliminary optical and electrochemical properties were studied. The simulated HOMO-LUMO bandgaps via DFT tallied with the experimental data well. The self-assembly of these materials showed needle or fiber-like morphologies, indicating that different conjugation degree or alkyl group had significant influence on their self-assembly behaviors. Furthermore, the single-crystal packing for these molecules were analyzed and it was found out that the changes of conjugated backbone and functional group would affect certain crystal lattice parameter significantly, such as the intermolecular packing distance and crystal size etc, which would further result in different self-assembly morphology.

Design of Large Stokes Shift Fluorescent Proteins Based on Excited State Proton Transfer of an Engineered Photobase

The incredible potential for fluorescent proteins to revolutionize biology has inspired the development of a variety of design strategies to address an equally broad range of photophysical characteristics, depending on potential applications. Of these, fluorescent proteins that simultaneously exhibit high quantum yield, red-shifted emission, and wide separation between excitation and emission wavelengths (Large Stokes Shift, LSS) are rare. The pursuit of LSS systems has led to the formation of a complex, obtained from the marriage of a rationally engineered protein (human cellular retinol binding protein II, hCRBPII) and different fluorogenic molecules, capable of supporting photobase activity. The large increase in basicity upon photoexcitation leads to protonation of the fluorophore in the excited state, dramatically red-shifting its emission, leading to an LSS protein/fluorophore complex. Essential for selective photobase activity is the intimate involvement of the target protein structure and sequence that enables Excited State Proton Transfer (ESPT). The potential power and usefulness of the strategy was demonstrated in live cell imaging of human cell lines.

Nucleic Acid Tests for Clinical Translation

Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.

Achieving Organic Smart Fluorophores by Controlling the Balance between Intermolecular Interactions and External Stimuli

Organic smart fluorophores (OSFs) are highly desirable over the past decades because of their potential applications in advanced photonic devices. However, it is still difficult and challenging to obtain such materials with tunable photophysical properties and high emission efficiency based on robust construction strategies. Therefore, we proposed a simple and efficient strategy for constructing OSFs by balancing the competition between intermolecular interactions and external stimuli via molecular structure design. In this work, four pyrene derivatives (T1-Py, T4-Py, T12-Py, and S12-Py) with tunable stimuli-responsive properties were designed and synthesized. The tunable intermolecular interactions in solution states were successfully demonstrated by the molecular structure and solution concentration-dependent luminescence properties. The effect of alkyl chain length on molecular packing in solid states was investigated by polarized optical microscopy and powder and single-crystal X-ray diffraction; the results show that with the increase in molecular chain length, the molecular packing of the compounds gradually changed from π-π stacked compact mode to X-crossing stacked loose mode, which leads to different stimuli-responsive phenomena of these compounds. The strategy provided herein facilitates the construction of multistimuli-responsive (thermochromism, mechanochromism, and vapochromism) OSFs with adjustable emission color. Harnessing the heat-responsive luminescence properties and great solubility of T12-Py, the optical information anticounterfeiting based on temperature was demonstrated by printing different concentrations of T12-Py solution on filter papers. Much more, this research may provide broad implications for the design of organic smart materials based on intermolecular interactions.

Probing Transient DNA Conformation Changes with an Intercalative Fluorescent Excimer

Variation of DNA conformation is important in regulating gene expression and mediating drug-DNA interactions. However, directly probing transient DNA conformation changes is challenging owing to the dynamic nature of this process. We show a label-free fluorescence method to monitor transient DNA conformation changes in DNA structures with various lengths and shapes using a DNA intercalator, K21. K21 can form transient excimers on the surface of DNA; the ratiometric emission of monomer and excimer correlate to DNA transient conformation stability in numerous DNA structures, including i-motifs, G-quadruplex structures, and single nucleotide mutation at random position. We analyzed the conformation dynamics of a single plasmid before and after enzyme digestion with confocal fluorescence microscopy. This method provides a label-free fluorescence strategy to probe transient conformation changes of DNA structures and has potential in uncovering transient genomic processes in living cells.

Iridium-catalysed borylation of pyrene – a powerful route to novel optoelectronic materials

We summarized the Ir-catalysed borylation of PAHs, especially pyrene, and the optoelectronic materials generated by following this chemistry. The optoelectronic properties of pyrene derivatives have also been discussed.

Computer vision vs. spectrofluorometer-assisted detection of common nitro-explosive components with bola-type PAH-based chemosensors

Computer vision (CV) algorithms are widely utilized in imaging processing for medical and personal electronics applications. In sensorics CV can provide a great potential to quantitate chemosensors' signals. Here we wish to describe a method for the CV-assisted spectrofluorometer-free detection of common nitro-explosive components, e.g. 2,4-dinitrotoluene (DNT) and 2,4,6-trinitrotoluene (TNT), by using polyaromatic hydrocarbon (PAH, PAH = 1-pyrenyl or 9-anthracenyl) – based bola-type chemosensors. The PAH components of these chemical bolas are able to form stable, bright emissive in a visual wavelength region excimers, which allows their use as extended matrices of the RGB colors after imaging and digital processing. In non-polar solvents, the excimers have poor chemosensing properties, while in aqueous solutions, due to the possible micellar formation, these excimers provide “turn-off” fluorescence detection of DNT and TNT in the sub-nanomolar concentrations. A combination of these PAH-based fluorescent chemosensors with the proposed CV-assisted algorithm offers a fast and convenient approach for on-site, real-time, multi-thread analyte detection without the use of fluorometers. Although we focus on the analysis of nitro-explosives, the presented method is a conceptual work describing a general use of CV for quantitative fluorescence detection of various analytes as a simpler alternative to spectrofluorometer-assisted methods.

Simplified computer vision-assisted algorithm for the excimer fluorescence "turn-off" detection of nitro-analytes in aqueous media is described.

5'-Monopyrene and 5'-Bispyrene 2'-O-methyl RNA Probes for Detection of RNA Mismatches

Progress in synthesis of novel fluorescent oligonucleotides has provided effective instruments for nucleic acid detection. Pyrene conjugated oligonucleotides have demonstrated their effectiveness as fluorescent hybridization probes. Here we describe the synthesis, isolation, and analysis of 5'-monopyrene and 5'-bispyrene conjugates of oligo(2'-O-methylribonucleotides) and their application as probes for fluorescent detection of mismatches in RNA targets.

Organic Thermometers Based on Aggregation of Difluoroboron β-Diketonate Chromophores

We report several novel thermometers resulting from the temperature-induced aggregation of difluoroboron β-diketonate chromophores. These thermometers exhibit a much wider temperature-dependent fluorescence emission from 445 to 592 nm along with the color change from blue to red in a dilute chloroform solution. Spectroscopy measurements and theoretical calculations confirm that the thermochromic luminescence originates from the reversible change in the noncovalent intermolecular interactions and the abrupt volume shrinkage of the solvent at its melting point. The present work provides a new strategy for rationally designing high-performance thermometers having a wide emission property.

Electrosynthesis and Electrochromism of a New Crosslinked Polydithienylpyrrole with Diphenylpyrenylamine Subunits

A new electroactive monomer with two 2,5-di(2-thienyl)pyrrole (SNS) units and one diphenylpyrenylamine (DPPA) subunit, namely N,N-bis(4-(2,5-di(2-thienyl)-1H-pyrrol-1-yl)-phenyl)-1-aminopyrene (DPPA-2SNS), was synthesized from 1,4-di-(2-thienyl)butane-1,4-dione with N,N-di(4-aminophenyl)-1-aminopyrene through the Paal–Knorr condensation reaction. Visible and near-infrared (NIR) electrochromic polymer films could be facilely generated on the ITO-glass surface by the electrochemical polymerization of DPPA-2SNS in an electrolyte solution. The electro-synthesized polymer films exhibit multi-staged redox processes and multi-colored anodic electrochromic behavior. A multi-colored electrochromism, with yellowish orange, greyish blue, and purplish black colors, was observed in the polymer film by applying a positive potential. The polymer films exhibit reasonable coloration efficiency, fast response time, and good cycling stability, especially when switched between neutral and the first oxidation states. For comparison, N-(1-pyrenyl)-2,5-di(2-thienyl)pyrrole (Py-SNS) was also prepared and characterized with electrochemical and electro-optical properties.

Pyrene Excimer-Based Fluorescent Labeling of Cysteines Brought into Close Proximity by Protein Dynamics: ASEM-Induced Thiol-Ene Click Reaction for High Spatial Resolution CLEM

Fluorescence microscopy (FM) has revealed vital molecular mechanisms of life. Mainly, molecules labeled by fluorescent probes are imaged. However, the diversity of labeling probes and their functions remain limited. We synthesized a pyrene-based fluorescent probe targeting SH groups, which are important for protein folding and oxidative stress sensing in cells. The labeling achieved employs thiol-ene click reactions between the probes and SH groups and is triggered by irradiation by UV light or an electron beam. When two tagged pyrene groups were close enough to be excited as a dimer (excimer), they showed red-shifted fluorescence; theoretically, the proximity of two SH residues within ~30 Å can thus be monitored. Moreover, correlative light/electron microscopy (CLEM) was achieved using our atmospheric scanning electron microscope (ASEM); radicals formed in liquid by the electron beam caused the thiol-ene click reactions, and excimer fluorescence of the labeled proteins in cells and tissues was visualized by FM. Since the fluorescent labeling is induced by a narrow electron beam, high spatial resolution labeling is expected. The method can be widely applied to biological fields, for example, to study protein dynamics with or without cysteine mutagenesis, and to beam-induced micro-fabrication and the precise post-modification of materials.

Interaction of Cucurbit[7]uril With Protease Substrates: Application to Nanosecond Time-Resolved Fluorescence Assays

We report the use of the macrocyclic host cucurbit[7]uril (CB7) as a supramolecular additive in nanosecond time-resolved fluorescence (Nano-TRF) assays for proteases to enhance the discrimination of substrates and products and, thereby, the sensitivity. A peptide substrate was labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a long-lived (>300 ns) fluorescent probe and 3-nitrotyrosine was established as a non-fluorescent fluorescence resonance energy transfer (FRET) acceptor that acts as a “dark quencher.” The substrate was cleaved by the model proteases trypsin and chymotrypsin and the effects of the addition of CB7 to the enzyme assay mixture were investigated in detail using UV/VIS absorption as well as steady-state and time-resolved fluorescence spectroscopy. This also allowed us to identify the DBO and nitrotyrosine residues as preferential binding sites for CB7 and suggested a hairpin conformation of the peptide, in which the guanidinium side chain of an arginine residue is additionally bound to a vacant ureido rim of one of the CB7 hosts.

Donor-Pyrene-Acceptor Distance-Dependent Intramolecular Charge-Transfer Process: A State-Specific Solvation Preferred to the Linear-Response Approach

Photoinduced intramolecular charge-transfer (ICT) molecules are important in various applications such as a probe for single-molecule spectroscopy, cell imaging, laser dyes, biomarkers, solar cells, in photosynthesis, etc. Here, we report a new set of substituted pyrene dye molecules, N,N-dimethylamino nitrilo pyrene and its higher analogues, containing pull-push donor (D)-chromophore (π)-acceptor (A) functional groups with enhanced photophysical characteristics like oscillator strength, light-harvesting, and ICT properties. The excited-state ICT process has been established by quantum chemical calculations using the density functional theory method in vacuo and in solvents of different polarity and hydrogen-bonding ability using linear-response (LR) and state-specific (SS) solvation approaches with gradually increasing the D-A distance. The studied molecules show solvent polarity-dependent larger Stokes' shifts (3609-9016 cm^-1, in acetonitrile), higher excited-state dipole moments (11.7-16.8 Debye, in acetonitrile), higher possibilities of highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) electronic transitions, etc., which support the occurrence of the excited-state ICT process. Here, we demonstrate how to increase the efficiency of the ICT process and also tune the ICT fluorescence maximum. We find that with a variation of the D-A distance, studied molecules show a noticeable effect on the spectroscopic and molecular properties such as the position of absorption and fluorescence band maxima, Stokes' shift, dipole moment, light-harvesting, and ICT properties. We also show that the SS solvation approach is more supportive than the LR method to the ICT process.

Ab initio study on the excited states of pyrene and its derivatives using multi-reference perturbation theory methods

The excited states of phenyl-substituted pyrene derivatives were calculated using multi-reference perturbation theory methods.

Tuning uracil derivatives for the AIE-based detection of pyrene at a nano-molar level: single-crystal X-ray structure and DFT support

Single crystal X-ray structurally characterized azo-uracil derivative (L) is explored for the selective detection of pyrene via aggregation-induced emission (AIE) with 99-fold fluorescence enhancement.

"Dial-In" Emission from a Unique Flexible Material with Polarization Tuneable Spectral Intensity

The development of organic photoluminescent materials, which show promising roles as catalysts, sensors, organic light-emitting diodes, logic gates, etc., is a major demand and challenge for the global scientific community. In this context, a photoclick polymerization method is adopted for the growth of a unique photoluminescent three-dimensional (3D) polymer film, E, as a model system that shows emission tunability over the range 350-650 nm against the excitation range 295-425 nm. The DFT analysis of energy calculations and π-stacking supports the spectroscopic observations for the material exhibiting a broad range of emission owing to newly formed chromophoric units within the film. Full polarization spectroscopic Mueller matrix studies were employed to extract and quantify the molecular orientational order of both the ground (excitation) and excited (emission) state anisotropies through a set of newly defined parameters, namely the fluorescence diattenuation and fluorescence polarizance. The information contained in the recorded fluorescence Mueller matrix of the organic polymer material provided a useful way to control the spectral intensity of emission by using pre- and post-selection of polarization states. The observation was based on the assumption that the longer lifetime of the excited dipolar orientation is attributed to the compactness of the film.

Positive Identification of DNA Cleavage by CRISPR-Cas9 Using Pyrene Excimer Fluorescence to Detect a Subnanometer Structural Change

The Cas9 nuclease binds and cleaves DNA through its large-scale structural rearrangements. However, its unique property of not releasing the cleaved DNA has forbidden spectroscopic detection of the cleavage event. Here, we employ a novel fluorescence probe based on pyrene excimer emission to detect a minute structural change not detectable by other methods and demonstrate its applicability to spectroscopic tracking of the Cas9 nuclease activity in time. We show that the intensity of excimer emission depends sensitively on a subtle change in the structural environment of the target nucleic acid, which enables discrimination between cleaved and uncleaved nucleic acids within the DNA/Cas9/gRNA ternary complex. Kinetic parameters were obtained from the temporal evolution of the excimer emission, which revealed that DNA binding is hardly affected by PAM-distal mismatches, whereas the rate of cleavage by Cas9 decreases dramatically even with a 1-bp mismatch. Spectroscopic studies using the pyrene-based probe should be promising for biomolecular systems affected by subnm structural changes.

Hydrophilic, Red-Emitting, and Thermally Activated Delayed Fluorescence Emitter for Time-Resolved Luminescence Imaging by Mitochondrion-Induced Aggregation in Living Cells

Thermally activated delayed fluorescence (TADF) materials have provided new strategies for time-resolved luminescence imaging (TRLI); however, the development of hydrophilic TADF luminophores for specific imaging in cells remains a substantial challenge. In this study, a mitochondria-induced aggregation strategy for TRLI is proposed with the design and utilization of the hydrophilic TADF luminophore ((10-(1,3-dioxo-2-phenyl-2,3-dihydro-1H-benzo[de]isoquinolin-6-yl)-9,9-dimethyl-9,10-dihydroacridin-2-yl)methyl)triphenylphosphonium bromide (NID-TPP). Using a nonconjugated linker to introduce a triphenylphosphonium (TPP+) group into the 6-(9,9-dimethylacridin-10(9H)-yl)-2-phenyl-1H-benzo[de]isoquinoline-1,3(2H)-dione (NID) TADF luminophore preserves the TADF emission of NID-TPP. NID-TPP shows clear aggregation-induced delayed fluorescence enhancement behavior, which provides a practical strategy for long-lived delayed fluorescence emission in an oxygen-containing environment. Finally, the designed mitochondrion-targeting TPP+ group in NID-TPP induces the adequate accumulation of NID-TPP and results in the first reported TADF-based time-resolved luminescence imaging and two-photon imaging of mitochondria in living cells.