Universal Dark Quencher Based on “Clicked” Spectrally Distinct Azo Dyes

Dark times: iminothioindoxyl-C-nucleoside fluorescence quenchers with defined location and minimal perturbation in DNA

Fluorescence quenchers for application in DNA - like the BHQ family - tend to be large molecules which need to be attached, often post-synthetically, via long linkers. In this study, we present two new iminothioindoxyl-C-nucleosidic quenchers which are very compact, feature a native backbone and can be introduced into DNA via regular solid-phase synthesis. Especially with dT as juxtaposed nucleobase, they have a defined location and orientation in a DNA duplex with minimal perturbation of the structure and hence interaction capabilities. Depending on the nature of the fluorophore, they can be used for orientation-(un)specific FRET studies. Their Förster radius is smaller than the one of BHQ-2. This makes these quenchers ideal for sophisticated studies using conditional quenching in the range between 470 and 670 nm in DNA.

Azobenzene-Based Conjugated Polymers: Synthesis, Properties, and Biological Applications

Conjugated polymers (CPs) have been developed quickly as an emerging functional material with applications in optical and electronic devices, owing to their highly electron-delocalized backbones and versatile side groups for facile processibility, high mechanical strength, and environmental stability. CPs exhibit multistimuli responsive behavior and fluorescence quenching properties by incorporating azobenzene functionality into their molecular structures. Over the past few decades, significant progress has been made in developing functional azobenzene-based conjugated polymers (azo-CPs), utilizing diverse molecular design strategies and synthetic pathways. This article comprehensively reviews the rapidly evolving research field of azo-CPs, focusing on the structural characteristics and synthesis methods of general azo-CPs, as well as the applications of charged azo-CPs, specifically azobenzene-based conjugated polyelectrolytes (azo-CPEs). Based on their molecular structures, azo-CPs can be broadly categorized into three primary types: linear CPs with azobenzene incorporated into the side chain, linear CPs with azobenzene integrated into the main chain, and branched CPs containing azobenzene moieties. These systems are promising for biomedical applications in biosensing, bioimaging, targeted protein degradation, and cellular apoptosis.

Turn-on Fluorescent Biosensors for Imaging Hypoxia-like Conditions in Living Cells

We present the synthesis, photophysical properties, and biological application of nontoxic 3-azo-conjugated BODIPY dyes as masked fluorescent biosensors of hypoxia-like conditions. The synthetic methodology is based on an operationally simple N=N bond-forming protocol, followed by a Suzuki coupling, that allows for a direct access to simple and underexplored 3-azo-substituted BODIPY. These dyes can turn on their emission properties under both chemical and biological reductive conditions, including bacterial and human azoreductases, which trigger the azo bond cleavage, leading to fluorescent 3-amino-BODIPY. We have also developed a practical enzymatic protocol, using an immobilized bacterial azoreductase that allows for the evaluation of these azo-based probes and can be used as a model for the less accessible and expensive human reductase NQO1. Quantum mechanical calculations uncover the restructuration of the topography of the S₁ potential energy surface following the reduction of the azo moiety and rationalize the fluorescent quenching event through the mapping of an unprecedented pathway. Fluorescent microscopy experiments show that these azos can be used to visualize hypoxia-like conditions within living cells.

Design, Synthesis, and Utility of Defined Molecular Scaffolds

A growing theme in chemistry is the joining of multiple organic molecular building blocks to create functional molecules. Diverse derivatizable structures—here termed “scaffolds” comprised of “hubs”—provide the foundation for systematic covalent organization of a rich variety of building blocks. This review encompasses 30 tri- or tetra-armed molecular hubs (e.g., triazine, lysine, arenes, dyes) that are used directly or in combination to give linear, cyclic, or branched scaffolds. Each scaffold is categorized by graph theory into one of 31 trees to express the molecular connectivity and overall architecture. Rational chemistry with exacting numbers of derivatizable sites is emphasized. The incorporation of water-solubilization motifs, robust or self-immolative linkers, enzymatically cleavable groups and functional appendages affords immense (and often late-stage) diversification of the scaffolds. Altogether, 107 target molecules are reviewed along with 19 syntheses to illustrate the distinctive chemistries for creating and derivatizing scaffolds. The review covers the history of the field up through 2020, briefly touching on statistically derivatized carriers employed in immunology as counterpoints to the rationally assembled and derivatized scaffolds here, although most citations are from the past two decades. The scaffolds are used widely in fields ranging from pure chemistry to artificial photosynthesis and biomedical sciences.

Nano versus Molecular: Optical Imaging Approaches to Detect and Monitor Tumor Hypoxia

Hypoxia is a ubiquitous feature of solid tumors, which plays a key role in tumor angiogenesis and resistance development. Conventional hypoxia detection methods lack continuous functional detection and are generally less suitable for dynamic hypoxia measurement. Optical sensors hereby provide a unique opportunity to noninvasively image hypoxia with high spatiotemporal resolution and enable real-time detection. Therefore, these approaches can provide a valuable tool for personalized treatment planning against this hallmark of aggressive cancers. Many small optical molecular probes can enable analyte triggered response and their photophysical properties can also be fine-tuned through structural modification. On the other hand, optical nanoprobes can acquire unique intrinsic optical properties through nanoconfinement as well as enable simultaneous multimodal imaging and drug delivery. Furthermore, nanoprobes provide biological advantages such as improving bioavailability and systemic delivery of the sensor to enhance bioavailability. This review provides a comprehensive overview of the physical, chemical, and biological analytes for cancer hypoxia detection and focuses on discussing the latest nano- and molecular developments in various optical imaging approaches (fluorescence, phosphorescence, and photoacoustic) in vivo. Finally, this review concludes with a perspective toward the potentials of these optical imaging approaches in hypoxia detection and the challenges with molecular and nanotechnology design strategies.

Development of Azo-Based Turn-On Chemical Array System for Hydrazine Detection with Fluorescence Pattern Analysis

A facile turn-on chemical sensor array was developed for hydrazine detection by means of fluorescence pattern recognition. Taking advantage of the unique properties of the azo group, four different fluorogenic probes, Seoul-Fluor (SF)-Azo 01-04, were designed and prepared. SF-Azo 01-04 displayed fluorescence enhancement of up to 800-fold upon reaction with hydrazine, and all probes exhibited excellent selectivity in the presence of various anions and nucleophiles. By employing the probes in a cellulose paper-based array system, the hydrazine concentration was successfully determined by monitoring the change in fluorescent patterns.

A "Quenchergenic" Chemoselective Protein Labeling Strategy

Dynamic changes in protein structure can be monitored by using a fluorescent probe and a dark quencher. This approach is contingent upon the ability to precisely introduce a fluorophore/quencher pair into two specific sites of a protein of interest. Despite recent advances, there is continued demand for new and convenient approaches to site-selectively label proteins with such optical probes. We have recently developed a chemoselectively rapid azo-coupling reaction (CRACR) for site-specific protein labeling; it relies on rapid coupling between a genetically encoded 5-hydroxytryptophan residue and various aromatic diazonium ions. Herein, it is reported that the product of this conjugation reaction, a highly chromophoric biarylazo group, is a potent fluorescence quencher. The absorption properties of this azo product can be tuned by systematically altering the structure of the aryldiazonium species. A particular "quenchergenic" aryldiazonium has been identified that, upon conjugation, efficiently quenches the fluorescence of green fluorescent protein, which is a widely used genetically encoded fluorescent probe that can be terminally attached to target proteins. This fluorophore/quencher pair was used to evaluate the protein-labeling kinetics of CRACR, as well as to monitor the proteolysis of a fusion protein.

Covalent Modification of Biomolecules through Maleimide-Based Labeling Strategies

Since their first use in bioconjugation more than 50 years ago, maleimides have become privileged chemical partners for the site-selective modification of proteins via thio-Michael addition of biothiols and, to a lesser extent, via Diels-Alder (DA) reactions with biocompatible dienes. Prominent examples include immunotoxins and marketed maleimide-based antibody-drug conjugates (ADCs) such as Adcetris, which are used in cancer therapies. Among the key factors in the success of these groups is the availability of several maleimides that can be N-functionalized by fluorophores, affinity tags, spin labels, and pharmacophores, as well as their unique reactivities in terms of selectivity and kinetics. However, maleimide conjugate reactions have long been considered irreversible, and only recently have systematic studies regarding their reversibility and stability toward hydrolysis been reported. This review provides an overview of the diverse applications for maleimides in bioconjugation, highlighting their strengths and weaknesses, which are being overcome by recent strategies. Finally, the fluorescence quenching ability of maleimides was leveraged for the preparation of fluorogenic probes, which are mainly used for the specific detection of thiol analytes. A summary of the reported structures, their photophysical features, and their relative efficiencies is discussed in the last part of the review.

Efficient Synthesis of a Wide-Range Absorbing Azaphthalocyanine Dark Quencher and Its Application to Dual-Labeled Oligonucleotide Probes for Quantitative Real-Time Polymerase Chain Reactions

Unsymmetrical dialkylamino-substituted zinc azaphthalocyanine (AzaPc) exhibits unique spectral and photophysical properties for dark quenchers of fluorescence in DNA hybridization probes. The panchromatic light absorption of AzaPc from 300 nm up to at least 700 nm and its lack of fluorescence make it an ideal candidate for a universal dark quencher. To prove this experimentally, oligodeoxyribonucleotide probes were labeled at the 3'-end by this AzaPc and at the 5'-end by a fluorophore used in the polymerase chain reaction (PCR)-that is, fluorescein, CAL Fluor Red 610, and Cy5. AzaPc showed a significantly higher quenching efficiency compared to the commercially available dark quenchers (BHQ-1, BHQ-2, BBQ-650) in a developed model of TaqMan PCR assay. The AzaPc-labeled probe proved to also be useful in a practical PCR assay for the quantification of the SLCO2B1 transporter gene expression. The constructed calibration curves indicated linearity in the range from 10² to 10⁷ of target copies.

A miniaturized peptidyl-prolyl isomerase enzyme assay

Prolyl-peptidyl isomerases (PPIases) are enzymes that are found in all living organisms. They form an essential part of the cellular protein folding homeostasis machinery. PPIases are associated with many important human diseases, e.g. cardiovascular disease, cancer and Alzheimer's. The development of novel PPIase inhibitors has been limited by the lack of a rapid, laboratory-based assay for these enzymes, as their substrates and products are challenging to distinguish. A well described continuous assay, coupled with the hydrolysis of a peptide by chymotrypsin is highly effective, but comparatively slow. To address this, we developed an improved version of the traditional assay using a temperature controlled plate reader. This assay allows semi-automated medium throughput assays in an academic laboratory for 84 samples per day. The assay shows lower errors, with an average Z' of 0.72. We further developed the assay using a fluorogenic peptide-based FRET probe. This provides an extremely sensitive PPIase assay using substrate at 200 nM, which approaches single turnover conditions. The fluorescent probe achieves an excellent quenching efficiency of 98.6%, and initial experiments showed acceptable Z' of 0.31 and 0.30 for cyclophilin A and hFKBP12 respectively. The assays provide an improved toolset for the quantitative, biochemical analysis of PPIases.

Versatile Platform for the Synthesis of Orthogonally Cleavable Heteromultifunctional Cross-Linkers

Cleavable and heteromultifunctional cross-linkers have proven critical in a wide range of biological applications. Traditional approaches for synthesizing these linkers suffer from various synthetic and functional limitations. In this work, an efficient sequence-defined synthetic methodology, developed for the assembly of oligothioetheramides, was used to address many of these limitations. Four heterotrifunctional cross-linkers with up to two orthogonal internal cleavage sites were synthesized. These linkers were conjugated to a pair of fluorophores that undergo Förster resonance energy transfer (FRET) and a model protein-human transferrin. Orthogonal bond cleavage was validated by mass spectrometry, fluorescent gel electrophoresis, and confocal microscopy. These studies demonstrate the versatility and biological utility of oligothioetheramides as a new class of multifunctional chemical cross-linkers and biologically relevant fluorescent probes.

High-Throughput Genotyping with TaqMan Allelic Discrimination and Allele-Specific Genotyping Assays

Real-time PCR-based genotyping methods, such as TaqMan allelic discrimination assays and allele-specific genotyping, are particularly useful when screening a handful of single nucleotide polymorphisms in hundreds of samples; either derived from different individuals, tissues, or pre-amplified DNA. Although real-time PCR-based methods such as TaqMan are well-established, alternative methods, like allele-specific genotyping, are powerful alternatives, especially for genotyping short tandem repeat (STR) length polymorphisms. Here, we describe all relevant aspects when developing an assay for a new SNP or STR using either TaqMan or allele-specific genotyping, respectively, such as primer and probe design, optimization of reaction conditions, the experimental procedure for typing hundreds of samples, and finally the data evaluation. Our goal is to provide a guideline for developing genotyping assays using these two approaches that render reliable and reproducible genotype calls involving minimal optimization.

A biotin-conjugated glutathione-responsive FRET-based fluorescent probe with a ferrocenyl BODIPY as the dark quencher

A ferrocenyl BODIPY quencher has been developed and employed to construct the captioned probe, of which its behaviour in phosphate buffered saline and inside cancer cells has been examined.

Azobenzene-caged sulforhodamine dyes: a novel class of 'turn-on' reactive probes for hypoxic tumor cell imaging

New sulforhodamine-based fluorescent 'turn-on' probes have been developed for the direct imaging of cellular hypoxia. Rapid access to this novel class of water-soluble 'azobenzene-caged' fluorophores was made possible through an easily-implementable azo-coupling reaction between a fluorescent primary arylamine derived from a sulforhodamine 101 scaffold (named SR101-NaphtNH ₂ ) and a tertiary aniline whose N-substituents are neutral, cationic, or zwitterionic. The detection mechanism is based on the bioreductive cleavage of the azo bond that restores strong far-red fluorescence (emission maximum at 625 nm) by regenerating the original sulforhodamine SR101-NaphtNH ₂ . This valuable fluorogenic response was obtained for the three 'smart' probes studied in this work, as shown by an in vitro assay using rat liver microsomes placed under aerobic and then under hypoxic conditions. Most importantly, the probe namely SR101-NaphtNH ₂ -Hyp-diMe was successfully applied for imaging the hypoxic status of tumor cells (A549 cells).