Development of Near-Infrared Nucleic Acid Mimics of Fluorescent Proteins for In Vivo Imaging of Viral RNA with Turn-On Fluorescence

Deep-Learning-Assisted Microfluidic Immunoassay via Smartphone-Based Imaging Transcoding System for On-Site and Multiplexed Biosensing

Point-of-care testing (POCT) with multiplexed capability, ultrahigh sensitivity, affordable smart devices, and user-friendly operation is critically needed for clinical diagnostics and food safety. This study presents a deep-learning-assisted microfluidic immunoassay platform that uses a smartphone-based imaging transcoding system, polystyrene microsphere-based encoding, and artificial-intelligence-assisted decoding. Microspheres of varying sizes act as multiprobes, with their quantities correlating to target concentrations after an immunoreaction and separation-filtration within the microfluidic chip. A smartphone with intelligent decoding software captures images of multiprobes from the chip and performs classification, counting, and concentration calculations. The "encoding-decoding" strategy and integrated microfluidic chip design allow these processes to be completed in simple steps, eliminating the need for additional immunomagnetic separation. As a proof of concept, this platform successfully detected multiple respiratory viruses and antibiotics in various real samples with high sensitivity within 30 min, demonstrating great potential as a smart, universal toolkit for next-generation POCT applications.

Understanding the Properties of Donor-Acceptor Substituted Boron Difluoride 3-Cyanoformazanate Dyes

π-Conjugated materials offer attractive traits including semiconductivity, low-energy light absorption/photoluminescence, and solution processability that render them ubiquitous within the organic electronics field. Among many strategies for property tuning, the creation of asymmetric electronic structures through the installation of donor and acceptor substituents commonly results in low-energy absorption/photoluminescence bands. Boron difluoride formazanate dyes are readily synthesized, can be asymmetrically substituted with donor and acceptor groups, and have unexpectedly low-energy absorption/photoluminescence bands that extend into the near-infrared. In this study, we prepared a series of donor-acceptor substituted boron difluoride 3-cyanoformazanate dyes and compared their properties to symmetric analogues. Our findings suggest that donor-acceptor derivatives are highly delocalized with properties intermediate of their symmetric counterparts. Furthermore, the data obtained suggest that the N-aryl substituents act as donors to the strongly accepting boron difluoride formazanate core, regardless of the functional groups appended to them. These properties were reproduced computationally, and while the frontier orbitals calculated for donor-acceptor dyes were modestly asymmetric, there was no evidence of charge-transfer character. This work provides significant insight into the unexpected properties of boron difluoride formazanates and reveals that their strongly accepting nature circumvents the predicted augmentation of electronic structure commonly observed for donor-accepter substituted dyes.

Optical Probes for Cellular Imaging of G-quadruplexes: Beyond Fluorescence Intensity Probes

The study of G-quadruplex (G4) structures that form in DNA and RNA is a rapidly growing field, which has evolved from in vitro studies of isolated G4 sequences to genome-wide detection of G4s in a cellular context. This work has revealed the tangible and significant effects that G4s may have on biological regulation. This minireview describes recent progress in the design of photoluminescent intensity-independent optical probes for G4s. We discuss the design and use of probes based on fluorescence or phosphorescence lifetime, rather than intensity-based detection; spectral ratiometric probes; and fluorescent probes for single-molecule G4-detection. We argue that each of these modalities improve unbiased G4 detection in cellular experiments, overcoming problems associated with unknown cellular uptake of probes or their organelle concentration. We discuss the improvements offered by these types of probes, as well as limitations and future research directions needed to facilitate more robust research into G4 biology.

Developing Orthogonal Fluorescent RNAs for Photoactive Dual-Color Imaging of RNAs in Live Cells

Fluorogenic RNA aptamers have revolutionized the visualization of RNAs within complex cellular processes. A representative category of them employs the derivatives of green fluorescent protein chromophore, 4-hydroxybenzlidene imidazolinone (HBI), as chromophores. However, the structural homogeneity of their chromophoric backbones causes severe cross-reactivity with other homologous chromophores. This limitation impairs their multiplexing capabilities, which are essential for the simultaneous visualization of multiple RNA species in live cells. Herein, we rationally designed a series of red-shifted chromophores and employed SELEX-independent engineering to develop a novel fluorogenic RNA aptamer, mSquash. mSquash displays specific and intense fluorescence upon binding with our red-shifted chromophore DFHBFPD (Ex/Em=501/624 nm). The mSquash/DFHBFPD allows orthogonal imaging of selected RNA targets alongside the established Broccoli/DFHBI-1T (Ex/Em=472/501 nm), facilitating multiplexed live cell imaging of various targets. Moreover, we expanded the application of fluorescent RNA to photoactive imaging by constructing two genetically encoded photoactivatable fluorescent RNAs for the first time. This innovative approach allows photoactivatable control of fluorescent RNAs via specific light wavelengths (365 nm and 450 nm), enabling spatiotemporal dual-color imaging of RNAs in live cells. Our findings represent a significant advancement in fluorescent RNA-based orthogonal imaging and spatiotemporal analysis of RNAs.

Engineered CRISPR/Cas Ribonucleoproteins for Enhanced Biosensing and Bioimaging

CRISPR-Cas systems represent a highly programmable and precise nucleic acid-targeting platform, which has been strategically engineered as a versatile toolkit for biosensing and bioimaging applications. Nevertheless, their analytical performance is constrained by inherent functional and activity limitations of natural CRISPR/Cas systems, underscoring the critical role of molecular engineering in enhancing their capabilities. This review comprehensively examines recent advancements in engineering CRISPR/Cas ribonucleoproteins (RNPs) to enhance their functional capabilities for advanced molecular detection and cellular imaging. We explore innovative strategies for developing enhanced CRISPR/Cas RNPs, including Cas protein engineering through protein mutagenesis and fusion techniques, and guide RNA engineering via chemical and structural modifications. Furthermore, we evaluate these engineered RNPs' applications in sensitive biomarker detection and live-cell genomic DNA and RNA monitoring, while analyzing the current challenges and prospective developments in CRISPR-Cas RNP engineering for advanced biosensing and bioimaging.

Precise photorelease in living cells by high-viscosity activatable coumarin-based photocages

Intracellular viscosity is a critical microenvironmental factor in various biological systems, and its abnormal increase is closely linked to the progression of many diseases. Therefore, precisely controlling the release of bioactive molecules in high-viscosity regions is vital for understanding disease mechanisms and advancing their diagnosis and treatment. However, viscosity alone cannot directly trigger chemical reactions. Inspired by molecular rotor fluorophores, we have developed a series of high-viscosity activated photocages by modifying the C3 position of the coumarin scaffold with electron-withdrawing groups. In low-viscosity environments, both fluorescence and photocleavage of the photocages are inhibited by nonradiative decay caused by intramolecular free rotation. In contrast, in high-viscosity environments, the restriction of this intramolecular rotation restores fluorescence and photocleavage. These unique photolysis properties enable the selective photorelease of these photocages in high-viscosity conditions. As a proof of concept, we have developed a drug delivery system that targets abnormal mitochondria with high viscosity. This system demonstrates enhanced photolysis efficiency in abnormal mitochondria compared to normal ones, allowing for precise drug release in diseased mitochondria while ensuring excellent biological safety in healthy mitochondria. We anticipate that these photocages will serve as convenient and efficient tools for the precise release of active molecules in high-viscosity environments.

Engineering a Novel NIR RNA-Specific Probe for Tracking Stress Granule Dynamics in Living Cells

Real-time monitoring of the dynamics of cytosolic RNA-protein condensates, termed stress granules (SGs), is vital for understanding their biological roles in stress response and related disease treatment but is challenging due to the lack of simple and accurate methods. Compared with protein visualization that requires complex transfection procedures, direct RNA labeling offers an ideal alternative for tracking SG dynamics in living cells. Here, we propose a novel molecular design strategy to construct a near-infrared RNA-specific fluorescent probe (HQBT) for tracking SGs in living cells. The positively charged probe HQBT was designed to target the negative groove of RNA, and its binding affinity to RNA was significantly improved by adjusting the position of the nitrogen atom in the molecule. Furthermore, an additional hydroxyl group was introduced to achieve near-infrared emission and enhance the RNA-binding capability. HQBT can rapidly stain RNA within 5 s in living cells and showed performance superior to the commercial SYTO RNA-Select dye in terms of photostability and selectivity. Importantly, the reversible assembly and disassembly dynamics of SGs are successfully visualized in living cells using this simple and direct RNA-selective imaging probe.

Direct Visualization of Hepatitis C Virus RNA in Living Cells and Mice

RNA virus infection is a global health issue with a significant economic burden. Direct visualization of the viral RNA genome in living cells is crucial for virological research and early clinical diagnosis. Thus, the need to continue research to find imaging toolkits is urgent. The RNA G-quadruplex (G4), a noncanonical secondary structure with stacked planar G-quartets, has recently been demonstrated in the RNA genomes of various viruses, especially the hepatitis C virus (HCV). Recent advancements in small molecular fluorescent probes have paved the way for a novel method of visualizing RNA G4s. Herein, we describe a fluorogenic probe-based RNA G4s light-up system for visualizing the HCV genome in living host cells and HCV RNA-presenting mini-organ-bearing mice without complicated sample pretreatment. Using this approach, we achieved (i) the visualization of HCV RNA genome in living cells, (ii) the investigation of viral RNA subcellular distribution, (iii) the dynamic tracking of native HCV infection and propagation in the host cell, and (iv) the high-contrast HCV RNA imaging in living mice bearing the HCV RNA-presenting mini-organ.

Stimuli-responsive AIEgens with an ultra acidochromic scope for self-reporting soft actuators

This study develops a series of NBI-based acidochromic AIEgens engineered for ultra-wide acidochromic scope in self-reporting soft actuators, establishing the relationship between the photophysical properties and structural configurations of the AIEgens, further investigating their acidochromic behavior and fabricating acidity monitoring chips. The acidochromic behaviors were thoroughly investigated, and high-precision acidity monitoring chips were fabricated. We confirmed the protonation order of nitrogen atoms within the molecules and elucidated the acidochromic mechanisms through DFT and 1H NMR analyses. Utilizing these findings, we designed acid-driven hydrogel-based biomimetic actuators that can self-report and control the release of heavy loads under acidic conditions. These actuators hold significant potential for applications in targeted drug delivery within acidic biological environments, controlled release systems, and specialized transportation of heavy loads under acidic conditions.

Synthetic Peptides with Genetic-Codon-Tailored Affinity for Assembling Tetraspanin CD81 at Cell Interfaces and Inhibiting Cancer Metastasis

Probing biomolecular interactions at cellular interfaces is crucial for understanding and interfering with life processes. Although affinity binders with site specificity for membrane proteins are unparalleled molecular tools, a high demand remains for novel multi-functional ligands. In this study, a synthetic peptide (APQQ) with tight and specific binding to the untargeted extracellular loop of CD81 evolved from a genetically encoded peptide pool. With tailored affinity, APQQ flexibly accesses, site-specifically binds, and forms a complex with CD81, enabling in-situ tracking of the dynamics and activity of this protein in living cells, which has rarely been explored because of the lack of ligands. Furthermore, APQQ triggers the relocalization of CD81 from diffuse to densely clustered at cell junctions and modulates the interplay of membrane proteins at cellular interfaces. Motivated by these, efficient suppression of cancer cell migration, and inhibition of breast cancer metastasis were achieved in vivo.

Rational Design of NIR-II G-Quadruplex Fluorescent Probes for Accurate In Vivo Tumor Metastasis Imaging

Accurate in vivo imaging of G-quadruplexes (G4) is critical for understanding the emergence and progression of G4-associated diseases like cancer. However, existing in vivo G4 fluorescent probes primarily operate within the near-infrared region (NIR-I), which limits their application accuracy due to the short emission wavelength. The transition to second near-infrared (NIR-II) fluorescent imaging has been of significant interest, as it offers reduced autofluorescence and deeper tissue penetration, thereby facilitating more accurate in vivo imaging. Nonetheless, the advancement of NIR-II G4 probes has been impeded by the absence of effective probe design strategies. Herein, through a "step-by-step" rational design approach, we have successfully developed NIRG-2, the first small-molecule fluorescent probe with NIR-II emission tailored for in vivo G4 detection. Molecular docking calculations reveal that NIRG-2 forms stable hydrogen bonds and strong π-π interactions with G4 structures, which effectively inhibit twisted intramolecular charge transfer (TICT) and, thereby, selectively illuminate G4 structures. Due to its NIR-II emission (940 nm), large Stokes shift (90 nm), and high selectivity, NIRG-2 offers up to 47-fold fluorescence enhancement and a tissue imaging depth of 5 mm for in vivo G4 detection, significantly outperforming existing G4 probes. Utilizing NIRG-2, we have, for the first time, achieved high-contrast visualization of tumor metastasis through lymph nodes and precise tumor resection. Furthermore, NIRG-2 proves to be highly effective and reliable in evaluating surgical and drug treatment efficacy in cancer lymphatic metastasis models. We are optimistic that this study not only provides a crucial molecular tool for an in-depth understanding of G4-related diseases in vivo but also marks a promising strategy for the development of clinical NIR-II G4-activated probes.

Two-Photon-Responsive "TICT + AIE" Active Naphthyridine-BF2 Photoremovable Protecting Group: Application for Specific Staining and Killing of Cancer Cells

The combined effects of twisted intramolecular charge transfer (TICT) and aggregation-induced emission (AIE) phenomena have demonstrated a significant influence on excited-state chemistry. These combined TICT and AIE features have been extensively utilized to enhance photodynamic and photothermal therapy. Herein, we demonstrated the synergistic capabilities of TICT and AIE phenomena in the design of the photoremovable protecting group (PRPG), namely, NMe2-Napy-BF2. This innovative PRPG incorporates TICT and AIE characteristics, resulting in four remarkable properties: (i) red-shifted absorption wavelength, (ii) strong near-infrared (NIR) emission, (iii) viscosity-sensitive emission property, and (iv) accelerated photorelease rate. Inspired by these intriguing attributes, we developed a nanodrug delivery system (nano-DDS) using our PRPG for cancer treatment. In vitro studies showed that our nano-DDS manifested effective cellular internalization, specific staining of cancer cells, high-resolution confocal imaging of cancerous cells in the NIR region, and controlled release of the anticancer drug chlorambucil upon exposure to light, leading to cancer cell eradication. Most notably, our nano-DDS exhibited a substantially increased two-photon (TP) absorption cross section (435 GM), exhibiting its potential for in vivo applications. This development holds promise for significant advancements in cancer treatment strategies.

Fluorophore Label-Free Light-up Near Infrared Deoxyribonucleic Acid Nanosensor for Monitoring Extracellular Potassium Levels

Fluorescent DNA nanosensors have been widely used due to their unique advantages, among which the near-infrared (NIR) imaging mode can provide deeper penetration depth and lower biological background for the nanosensors. However, efficient NIR quenchers require ingenious design, complex synthesis, and modification, which severely limit the development of NIR DNA nanosensors. Label-free strategies based on G-quadruplex (G4) and NIR G4 dyes were first introduced into in situ extracellular imaging, and a novel NIR sensing strategy for the specific detection of extracellular targets is proposed. The strategy avoids complex synthesis and site-specific modification by controlling the change of the NIR signal through the formation of a G4 nanostructure. A light-up NIR DNA nanosensor based on potassium ion (K+)-sensitive G4 chain PS2.M was constructed to verify the strategy. PS2.M forms a stable G4 nanostructure in the presence of K+ and activates the NIR G4 dye CSTS, thus outputting NIR signals. The nanosensor can rapidly respond to K+ with a linear range of 5-50 mM and has good resistance to interference. The nanosensor with cholesterol can provide feedback on the changes in extracellular K+ concentration in many kinds of cells, serving as a potential tool for the study of diseases such as epilepsy and cancer, as well as the development of related drugs. The strategy can be potentially applied to the NIR detection of a variety of extracellular targets with the help of functional DNAs such as aptamer and DNAzyme.

Recent advancements of fluorescent biosensors using semisynthetic probes

Fluorescent biosensors are crucial experimental tools for live-cell imaging and the quantification of different biological analytes. Fluorescent protein (FP)-based biosensors are widely used for imaging applications in living systems. However, the use of FP-based biosensors is hindered by their large size, poor photostability, and laborious genetic manipulations required to improve their properties. Recently, semisynthetic fluorescent biosensors have been developed to address the limitations of FP-based biosensors using chemically modified fluorescent probes and self-labeling protein tag/peptide tags or DNA/RNA-based hybrid systems. Semisynthetic biosensors have unique advantages, as they can be easily modified using different probes. Moreover, the self-labeling protein tag, which labels synthetically developed ligands via covalent bonds, has immense potential for biosensor development. This review discusses the recent progress in different types of fluorescent biosensors for metabolites, protein aggregation and degradation, DNA methylation, endocytosis and exocytosis, membrane tension, and cellular viscosity. Here, we explain in detail the design strategy and working principle of these biosensors. The information presented will help the reader to create new biosensors using self-labeling protein tags for various applications.

De Novo Green Fluorescent Protein Chromophore-Based Probes for Capturing Latent Fingerprints Using a Portable System

Rapid visualization of latent fingerprints, preferably at their point of origin, is essential for effective crime scene evaluation. Here, we present a new class of green fluorescent protein chromophore-based fluorescent dyes (LFP-Yellow and LFP-Red) that can be used for real-time visualization of LFPs within 10 s. Compared with traditional chemical reagents for LFPs, these fluorescent dyes are completely water-soluble, exhibit low cytotoxicity, and are harmless to users. Level 1-3 details of the LFPs could be clearly revealed through "off-on" fluorescence signal readout. Additionally, the fluorescent dyes were constructed based on an imidazolinone core and so do not contain pyridine groups or metal ions, which ensures that the DNA is not contaminated during extraction and identification after the LFPs are treated with the dyes. Combined with our as-developed portable system for capturing LFPs, LFP-Yellow and LFP-Red enabled the rapid capture of LFPs. Therefore, these green fluorescent protein chromophore-based probes provide an approach for the rapid identification of individuals who were present at a crime scene.

Living virus-based nanohybrids for biomedical applications

Living viruses characterized by distinctive biological functions including specific targeting, gene invasion, immune modulation, and so forth have been receiving intensive attention from researchers worldwide owing to their promising potential for producing numerous theranostic modalities against diverse pathological conditions. Nevertheless, concerns during applications, such as rapid immune clearance, altering immune activation modes, insufficient gene transduction efficiency, and so forth, highlight the crucial issues of excessive therapeutic doses and the associated biosafety risks. To address these concerns, synthetic nanomaterials featuring unique physical/chemical properties are frequently exploited as efficient drug delivery vehicles or treatments in biomedical domains. By constant endeavor, researchers nowadays can create adaptable living virus-based nanohybrids (LVN) that not only overcome the limitations of virotherapy, but also combine the benefits of natural substances and nanotechnology to produce novel and promising therapeutic and diagnostic agents. In this review, we discuss the fundamental physiochemical properties of the viruses, and briefly outline the basic construction methodologies of LVN. We then emphasize their distinct diagnostic and therapeutic performances for various diseases. Furthermore, we survey the foreseeable challenges and future perspectives in this interdisciplinary area to offer insights. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.

Near-Infrared Fluorescent Switch-On Probe for Guanine-Quadruplex Imaging with Extremely Large Stokes Shift

To visualize the guanine-quadruplex (G4) nucleic acids in cells or in biological tissues, near-infrared (NIR) fluorescent probes that can respond specifically to G4 nucleic acids are required. Herein, an NIR fluorescence switch-on probe for G4 imaging having higher selectivity and extremely large Stokes shift (ca. 220 nm) was successfully developed by the modification of our original tripodal quinone-cyanine fluorescent dye. The target binding-induced intramolecular stacking interaction of the probe might cause red shifting of the fluorescence emission. The NIR fluorescence switch-on probe developed here might contribute largely to revealing the behaviors of G4 nucleic acids not only in cells but also in biological tissues.

Small molecules and conjugates as theranostic agents

Theranostics, the integration of therapy and diagnostics into a single entity for the purpose of monitoring disease progression and treatment response. Diagnostics involves identifying specific characteristics of a disease, while therapeutics refers to the treatment of the disease based on this identification. Advancements in medicinal chemistry and technology have led to the development of drug modalities that provide targeted therapeutic effects while also providing real-time updates on disease progression and treatment. The inclusion of imaging in therapy has significantly improved the prognosis of devastating diseases such as cancer and neurodegeneration. Currently, theranostic treatment approaches are based on nuclear medicine, while nanomedicine and a wide diversity of macromolecular systems such as gels, polymers, aptamers, and dendrimer-based agents are being developed for the purpose. Theranostic agents have significant roles to play in both early-stage drug development and clinical-stage therapeutic-containing drug candidates. This review will briefly outline the pros and cons of existing and evolving theranostic approaches before comprehensively discussing the role of small molecules and their conjugates.

Oxidized Low-Density Lipoprotein (Ox-LDL)-Triggered Double-Lock Probe for Spatiotemporal Lipoprotein Oxidation and Atherosclerotic Plaque Imaging

Low-density lipoprotein (LDL), especially oxidative modified LDL (Ox-LDL), is the key risk factor for plaque accumulation and the development of cardiovascular disease. Herein, a highly specific Ox-LDL-triggered fluorogenic-colorimetric probe Pro-P1 is developed for visualizing the oxidation and aggregation progress of lipoproteins and plaque. A series of green fluorescent protein chromophores with modified donor-acceptor structures, containing carbazole as an electron donor and various substituents including pyridine-vinyl (P1), phenol-vinyl (P2), N, N-dimethylaniline-vinyl (P3), and thiophene-vinyl (P4), have been synthesized and evaluated. Emission spectroscopy and theoretical calculations of P1-P4 indicate that P1 shows enhanced green fluorescence (λem = 560 nm) by inhibiting its twisted intramolecular charge transfer in the presence of Ox-LDL. This feature allows the selection of P1 as a sensitive probe to directly visualize ferroptosis and Cu2+ -mediated LDL oxidative aggregation via in situ formation of fluorophore-bound Ox-LDL in living cells. The red-emissive probe Pro-P1 (λem = 660 nm) is prepared via borate protection of P1, which can be cleaved into P1 under high expression of HOCl and Ox-LDL condition at the lesion site, resulting in enhanced green emission. The plaque area and size with clear boundaries can be delineated by colorimetric fluorescence imaging and fluorescence lifetime imaging with precise differentiation.

An epoxide-based covalent sensor to detect cardiac proteome aggregation in a cardio-oncology model

Covalent sensors to detect and capture aggregated proteome in stressed cells are rare. Herein, we construct a series of covalent fluorogenic sensors for aggregated proteins by structurally modulating GFP chromophore and arming it with an epoxide warhead. Among them, P2 probe selectively modifies aggregated proteins over folded ones and turns on fluorescence as evidenced by biochemical and mass spectrometry results. The coverage of this epoxide-based covalent chemistry is demonstrated using different types of aggregated proteins. Finally, the covalent fluorescent sensor P2 allows for direct visualization and capture of aggregated proteome in stressed cardiomyocytes and cardiac tissue samples from a cardio-oncology mouse model. The epoxide-based covalent sensor developed herein may become useful for future chemical proteomics analysis of aggregated proteins to dissect the mechanism underlying cardio-oncology.

Sunlight-directed fluorophore-switch in photosynthesis of cyanine subcellular organelle markers for bio-imaging

The photoconvertible fluorophore synthesis enables the light controlled imaging channels switch for accurate tracking the quantity and localization of intracellular biomolecules in chemical biology. Herein, we repurposed the photochemistry of Fischer's base and developed a sunlight-directed fluorophore-switch strategy for high-efficiency trimethine cyanine (Cy3.5/Cy3) synthesis. The unexpected sunlight-directed photoconversion of Fischer's base proceeds in conventional solvents and accelerates in chloroform via photo-oxidation and hydrogen atom transfer without using extra additives, and the heterogenous dimerization mechanism was proposed and confirmed by isolation of the reactive intermediates. The reliable strategy is employed in the photosynthesis of commercially available cytomembrane marker (DiI) and other cyanine based organelle markers with appreciable yields. Sunlight-controlled fluorophore-switch of subcellular organelle markers in living cells validated the feasibility of our strategy with cell-tolerant character. Moreover, remote control synthesis of Cy3.5 in vivo directed via sunlight further demonstrated the extended application of our strategy. Therefore, this sunlight-directed strategy will facilitate exploitation of cyanine-based probes with switched fluorescence imaging channels and further enable precise description of the dynamic variations in living cells with minimal autofluorescence and cellular disturbance.

Engineering a Red Fluorescent Protein Chromophore for Visualization of RNA G-Quadruplexes

Synthetic red fluorescent protein (RFP) chromophores have emerged as valuable tools for biological imaging and therapeutic applications, but their application in the visualization of endogenous RNA G-quadruplexes (G4s) in living cells has been rarely reported so far. Here, by integrating the group of the excellent G4 dye ThT, we modulate RFP chromophores to create a novel fluorescent probe DEBIT with red emission. DEBIT selectively recognizes the G4 structure with the advantage of strong binding affinity, high selectivity, and excellent photostability. Using DEBIT as a fluorescent indicator, the real-time monitoring of RNA G4 in biological systems can be achieved. In summary, our work expands the application of synthetic RFP chromophores and provides an essential dye category to the classical G4 probes.

A Switchable Near-Infrared-Absorbing Dye Based on Redox-Bistable Benzitetraazaporphyrin

Activatable near-infrared (NIR) dyes responsive to external stimuli are used in medical and other applications. Here, we describe the design and synthesis of bench-stable 18π- and 20π-electron benzitetraazaporphyrins (BzTAPs) possessing redox-switchable NIR properties. X-Ray, NMR, and UV/Visible-NIR analyses revealed that 20π-electron BzTAP 1 exhibits NIR absorption and antiaromaticity with a paratropic ring-current, while 18π-electron BzTAP 2 shows weakly aromatic character with NIR inertness. Notably, the NIR-silent BzTAP 2 was readily converted to the NIR-active BzTAP 1 in the presence of mild reducing agents such as amine. The intense NIR absorption band of BzTAP 1 is in sharp contrast to the very weak absorption bands of previously reported antiaromatic porphyrinoids. Molecular orbital analysis revealed that symmetry-lowering perturbation of the 20π-electron porphyrinoid skeleton enables the HOMO-LUMO transition of 1 to be electric-dipole-allowed. BzTAPs are expected to be useful for constructing activatable NIR probes working in reductive environments.

Configuration-Induced Multichromism of Phenanthridine Derivatives: A Type of Versatile Fluorescent Probe for Microenvironmental Monitoring

Fluorescent probes are attractive in diagnosis and sensing. However, most reported fluorophores can only detect one or few analytes/parameters, notably limiting their applications. Here we have designed three phenanthridine-based fluorophores (i.e., B1, F1, and T1 with 1D, 2D, and 3D molecular configuration, respectively) capable of monitoring various microenvironments. In rigidifying media, all fluorophores show bathochromic emissions but with different wavelength and intensity changes. Under compression, F1 shows a bathochromic emission of over 163 nm, which results in organic fluorophore-based full-color piezochromism. Moreover, both B1 and F1 exhibit an aggregation-caused quenching (ACQ) behavior, while T1 is an aggregation-induced emission (AIE) fluorophore. Further, F1 and T1 selectively concentrate in cell nucleus, whereas B1 mainly stains the cytoplasm in live cell imaging. This work provides a general design strategy of versatile fluorophores for microenvironmental monitoring.

Live-cell RNA imaging using the CRISPR-dCas13 system with modified sgRNAs appended with fluorescent RNA aptamers

The development of RNA imaging strategies in live cells is essential to improve our understanding of their role in various cellular functions. We report an efficient RNA imaging method based on the CRISPR-dPspCas13b system with fluorescent RNA aptamers in sgRNA (CasFAS) in live cells. Using modified sgRNA attached to fluorescent RNA aptamers that showed reduced background fluorescence, this approach provides a simple, sensitive way to image and track endogenous RNA with high accuracy and efficiency. In addition, color switching can be easily achieved by changing the fluorogenic dye analogues in living cells through user-friendly washing and restaining operations. CasFAS is compatible with orthogonal fluorescent aptamers, such as Broccoli and Pepper, enabling multiple colors RNA labeling or intracellular RNA-RNA interaction imaging. Finally, the visualization of severe fever with thrombocytopenia syndrome virus (SFTSV) was achieved by CasFAS, which may facilitate further studies on this virus.

Recent Developments in G-Quadruplex Binding Ligands and Specific Beacons on Smart Fluorescent Sensor for Targeting Metal Ions and Biological Analytes

The G-quadruplex structure is crucial in several biological processes, including DNA replication, transcription, and genomic maintenance. G-quadruplex-based fluorescent probes have recently gained popularity because of their ease of use, low cost, excellent selectivity, and sensitivity. This review summarizes the latest applications of G-quadruplex structures as detectors of genome-wide, enantioselective catalysts, disease therapeutics, promising drug targets, and smart fluorescence probes. In every section, sensing of G-quadruplex and employing G4 for the detection of other analytes were introduced, respectively. Since the discovery of the G-quadruplex structure, several studies have been conducted to investigate its conformations, biological potential, stability, reactivity, selectivity for chemical modification, and optical properties. The formation mechanism and advancements for detecting different metal ions (Na⁺, K⁺, Ag⁺, Tl⁺, Cu⁺/Cu²⁺, Hg²⁺, and Pb²⁺) and biomolecules (AMP, ATP, DNA/RNA, microRNA, thrombin, T4 PNK, RNase H, ALP, CEA, lipocalin 1, and UDG) using fluorescent sensors based on G-quadruplex modification, such as dye labels, artificial nucleobase moieties, dye complexes, intercalating dyes, and bioconjugated nanomaterials (AgNCs, GO, QDs, CDs, and MOF) is described herein. To investigate these extremely efficient responsive agents for diagnostic and therapeutic applications in medicine, fluorescence sensors based on G-quadruplexes have also been employed as a quantitative visualization technique.

Visualization of Deep Tissue G-quadruplexes with a Novel Large Stokes-Shifted Red Fluorescent Benzothiazole Derivative

G-quadruplex (G4) is a noncanonical nucleic acid secondary structure that has implications for various physiological and pathological processes and is thus essential to exploring new approaches to G4 detection in live cells. However, the deficiency of molecular imaging tools makes it challenging to visualize the G4 in ex vivo tissue samples. In this study, we established a G4 probe design strategy and presented a red fluorescent benzothiazole derivative, ThT-NA, to detect and image G4 structures in living cells and tissue samples. By enhancing the electron-donating group of thioflavin T (ThT) and optimizing molecular structure, ThT-NA shows excellent photophysical properties, including red emission (610 nm), a large Stokes shift (>100 nm), high sensitivity selectivity toward G4s (1600-fold fluorescence turn-on ratio) and robust two-photon fluorescence emission. Therefore, these features enable ThT-NA to reveal the endogenous RNA G4 distribution in living cells and differentiate the cell cycle by monitoring the changes of RNA G4 folding. Significantly, to the best of our knowledge, ThT-NA is the first benzothiazole-derived G4 probe that has been developed for imaging G4s in ex vivo cancer tissue samples by two-photon microscopy techniques.

Fluorescent probes for the detection of disease-associated biomarkers

Fluorescent probes have emerged as indispensable chemical tools to the field of chemical biology and medicine. The ability to detect intracellular species and monitor physiological processes has not only advanced our knowledge in biology but has provided new approaches towards disease diagnosis. In this review, we detail the design criteria and strategies for some recently reported fluorescent probes that can detect a wide range of biologically important species in cells and in vivo. In doing so, we highlight the importance of each biological species and their role in biological systems and for disease progression. We then discuss the current problems and challenges of existing technologies and provide our perspective on the future directions of the research area. Overall, we hope this review will provide inspiration for researchers and prove as useful guide for the development of the next generation of fluorescent probes.

Characterization of G-Quadruplexes in Enterovirus A71 Genome and Their Interaction with G-Quadruplex Ligands

Human enteroviruses cause many diseases; however, there is no specific therapeutic drug. G-quadruplex is an atypical secondary structure formed in the guanine rich region of DNA or RNA, which can exist in the viral genome. The different positions of G-quadruplex play an important role in the regulation of virus replication and infection. Whether G-quadruplexes are present in human enteroviruses is unknown. In current study, we analyzed the potential quadruplex forming sequences of human enteroviruses, especially EV-A71 virus, which causes hand, foot, and mouth disease. The results showed that there were a certain number of potential quadruplex-forming sequences in human enteroviruses. Through a variety of experimental methods, we evaluated the formation potential of EV-A71 encoded G-quadruplex and analyzed the binding ability of G-quadruplex ligands, including BRACO-19, pyridostatin and TMPyP4 to virus encoded G-quadruplexes. G-quadruplex ligands BRACO-19, PDS and TMPyP4 could inhibit the transcription of constructs containing EV-A71 G-quadruplex sequences. Moreover, we found that BRACO-19 was able to inhibit the replication of EV-A71, suggesting that targeting G-quadruplexes in EV-A71 genome by G-quadruplex ligands could be a novel antiviral way against EV-A71. Our finding not only uncovered the G-quadruplexes in human enteroviruses, but also would provide a new strategy for human enteroviruses therapy. IMPORTANCE G-quadruplex is a stable nucleic acid secondary structure formed by the folding of guanine rich nucleic acid. The important regulatory function of G-quadruplex makes it an attractive target of antiviral effect. Human enteroviruses cause a variety of human diseases, including common cold, nervous system diseases, cardiovascular damage, and diabetes. Enterovirus A71 (EV-A71) is one of pathogens causing hand, foot, and mouth disease; however, whether G-quadruplexes are present in the genomes of human enteroviruses is unknown. The function of G-quadruplexes in the EV-A71 genomes is not clear. We predicted and characterized G-quadruplex sequences in EV-A71. G-quadruplex ligands were identified to stabilize EV-A71 G-quadruplexes with high affinities. We also demonstrated G-quadruplex ligand BRACO-19 inhibited EV-A71 replication. Our studies provide a framework for targeting G-quadruplexes in the enteroviruses genome, which will be a new way to develop antiviral agents against human enteroviruses.