Synthesis of squaraine dyes under mild conditions: applications for labelling and sensing of biomolecules

Oxocarbon Acids and their Derivatives in Biological and Medicinal Chemistry

The biological and medicinal chemistry of the oxocarbon acids 2,3- dihydroxycycloprop-2-en-1-one (deltic acid), 3,4-dihydroxycyclobut-3-ene-1,2-dione (squaric acid), 4,5-dihydroxy-4-cyclopentene-1,2,3-trione (croconic acid), 5,6-dihydroxycyclohex- 5-ene-1,2,3,4-tetrone (rhodizonic acid) and their derivatives is reviewed and their key chemical properties and reactions are discussed. Applications of these compounds as potential bioisosteres in biological and medicinal chemistry are examined. Reviewed areas include cell imaging, bioconjugation reactions, antiviral, antibacterial, anticancer, enzyme inhibition, and receptor pharmacology.

Squaraine Dyes Derived from Indolenine and Benzo[e]indole as Potential Fluorescent Probes for HSA Detection and Antifungal Agents

Four squaraine dyes derived from 2,3,3-trimethylindolenine and 1,1,2-trimethyl-1H-benzo[e]indole with different combinations of barbituric groups attach to the central ring, having ester groups and alkyl chains in the nitrogen atoms of heterocyclic rings were synthesized. These dyes were fully characterized and their photophysical behavior was studied in ethanol and phosphate-buffered saline solution. Absorption and emission bands between 631 and 712 nm were detected, with the formation of aggregates in aqueous media, which is typical of this class of dyes. Tests carried out with 1,3-diphenylisobenzofuran allowed us to verify the ability of the dyes to produce singlet oxygen. The interaction of synthesized dyes with human serum albumin (HSA) was also evaluated, being demonstrated a linear correlation between fluorescence intensity and protein concentration. The antifungal potential of the dyes against the yeast Saccharomyces cerevisiae was evaluated using a broth microdilution assay. In order to test the photosensitizing capacity of the synthesized dyes, tests were carried out in the dark and with irradiation, using a custom-built light-emitting diode that emits close to the absorption wavelength of the studied dyes. The results showed that the interaction of dyes with HSA and the antifungal activity depends on the different structural modifications of the dyes.

Small-molecule fluorescent probes based on covalent assembly strategy for chemoselective bioimaging

In this review, we comprehensively summarize the recent progress in the development of small molecular fluorescent probes based on the covalent assembly principle. The challenges and perspective in this field are also presented.

Solvent-free Reactions for the Synthesis of Indolenine-based Squaraines and Croconaines: Comparison of Thermal Heating, Mechanochemical Milling, and IR Irradiation

Squaraines and croconaines are organic dyes characterized by intense absorption in the visible or near-infrared spectral regions with applications ranging from biology to material sciences. They are commonly synthesized by condensation reactions of oxocarbonic acids (squaric or croconic acid, respectively) with electron-rich aromatic compounds in high-boiling organic solvents. Here, a simple, cost-effective, and environmentally benign process was developed for the synthesis of indolenine-based squaraines and croconaines under solvent-free conditions. Protocols based on conventional thermal heating, mechanochemical milling, and IR-light activation were compared.

Rapid and Targeted Photoactivation of Ca2+ Channels Mediated by Squaraine To Regulate Intracellular and Intercellular Signaling Processes

As an important cellular signal transduction messenger, Ca²⁺ has the capability to regulate cell function and control many biochemical processes, including metabolism, gene expression, and cell survival and death. Here, we introduce an accessible method for the photoactivation of Ca²⁺ channels mediated by squaraine (SQ) to rapidly induce cellular Ca²⁺ release and activate signal transduction. With a short preparation time, the maximum Ca²⁺ concentration increase could reach approximately 450% in 30 s, resulting from marked Ca²⁺ release channel opening in the endoplasmic reticulum (ER). This release was enhanced by another target location of SQ, that is, the outer mitochondrial-associated membrane where Ca²⁺ channels accumulate, and by the consequent large amounts of reactive oxygen species resulting from the respiratory chain activity stimulated by Ca²⁺ load. We used this method to investigate cellular signal transduction in different cancer cells and revealed rapid intracellular Ca²⁺ flow, unidirectional intercellular signaling processes, and neuronal signaling activity, which demonstrated the potential and convenience of the method for routine Ca²⁺ research.

Synthesis of Dye-Modified Oligonucleotides via Copper(I)-Catalyzed Alkyne Azide Cycloaddition Using On- and Off-Bead Approaches

Fluorescence molecular imaging is widely used to visualize and observe different biomolecules, in particular DNA and RNA, in vivo and in real time. Typically, DNA strands are tagged with only one fluorophore, and, in the case of molecular beacons, an additional quencher is conjugated, which bears the risk of false-positive or false-negative results because only fluorescence intensities at one fluorescence wavelength (color) are compared. To address this drawback, the concept of "DNA/RNA traffic lights," which is characterized by a fluorescence color change due to energy transfer between two dyes, was developed by our working group. For these DNA and RNA systems, the oligonucleotides are post-synthetically labeled, specifically after solid-phase synthesis by chemical means, with a fluorescent dye using copper(I)-catalyzed cycloaddition at the 2' position of single uridines. In order to functionalize oligonucleotides with several different labels, an on-resin method is required to ensure the necessary selectivity. This unit describes two different CuAAC ("click") approaches-in solution (post-synthetic) and on solid phase (during synthesis)-for the attachment of fluorophores to the 2' position of DNA. © 2018 by John Wiley & Sons, Inc.

Vancomycin Determination by Disrupting Electron-Transfer in a Fluorescence Turn-On Squaraine-Anthraquinone Triad

A highly sensitive and selective probe for Vancomycin (Van) in aqueous and serum samples is developed in this study. The probe is based on a triad consisting of a near-infrared squaraine dye (Seta-640) conjugated to two anthraquinone molecules via Lys-d-Ala-d-Ala peptides. In the absence of Van, the close proximity and efficient electron-transfer from the excited Seta-640 dye to anthraquinone result in significant fluorescence quenching of the dye ("off"-state). When Van is added, the antibiotic molecules bind with high affinity to the -d-Ala-d-Ala ligands in a 2:1 stoichiometry (Van:triad), resulting in fluorescence recovery that is as high as 30 times ("on"-state). Even though bound Van enhances the fluorescence by reducing the rate of (intrinsic) polarity-induced nonradiative decay process, this effect plays only a minor role. Instead, the main reason behind the observed fluorescence recovery after drug binding is the effective inhibition of electron-transfer; plausibly arising from a steric-induced lengthening of the spatial separation between electron donor and acceptor. The probe has detection limits of 7.0 and 96.9 nM in buffer and human serum, respectively, operates in the clinically relevant range, is insensitive to Van crystalline degradation product (CDP-1), and is easy to operate by using a commonly available fluorescence spectrometer.

Subnanomolar Detection of Oligonucleotides through Templated Fluorogenic Reaction in Hydrogels: Controlling Diffusion to Improve Sensitivity

Oligonucleotide-templated reactions are valuable tools for nucleic acid sensing both in vitro and in vivo. They are typically carried out under conditions that make any reaction in the absence of template highly unfavorable (most commonly by using a low concentration of reactants), which has a negative impact on the detection sensitivity. Herein, we report a novel platform for fluorogenic oligonucleotide-templated reactions between peptide nucleic acid probes embedded within permeable agarose and alginate hydrogels. We demonstrate that under conditions of restricted mobility (that is, limited diffusion), non-specific interactions between probes are prevented, thus leading to lower background signals. When applied to nucleic acid sensing, this accounts for a significant increase in sensitivity (that is, lower limit of detection). Optical nucleic acid sensors based on fluorogenic peptide nucleic acid probes embedded in permeable, physically crosslinked, alginate beads were also engineered and proved capable of detecting DNA concentrations as low as 100 pm.

Amplification-Free Detection of Circulating microRNA Biomarkers from Body Fluids Based on Fluorogenic Oligonucleotide-Templated Reaction between Engineered Peptide Nucleic Acid Probes: Application to Prostate Cancer Diagnosis

Highly abundant in cells, microRNAs (or miRs) play a key role as regulators of gene expression. A proportion of them are also detectable in biofluids making them ideal noninvasive biomarkers for pathologies in which miR levels are aberrantly expressed, such as cancer. Peptide nucleic acids (PNAs) are engineered uncharged oligonucleotide analogues capable of hybridizing to complementary nucleic acids with high affinity and high specificity. Herein, novel PNA-based fluorogenic biosensors have been designed and synthesized that target miR biomarkers for prostate cancer (PCa). The sensing strategy is based on oligonucleotide-templated reactions where the only miR of interest serves as a matrix to catalyze an otherwise highly unfavorable fluorogenic reaction. Validated in vitro using synthetic RNAs, these newly developed biosensors were then shown to detect endogenous concentrations of miR in human blood samples without the need for any amplification step and with minimal sample processing. This low-cost, quantitative, and versatile sensing technology has been technically validated using gold-standard RT-qPCR. Compared to RT-qPCR however, this enzyme-free, isothermal blood test is amenable to incorporation into low-cost portable devices and could therefore be suitable for widespread public screening.

Rational design of novel near-infrared fluorescent DCM derivatives and their application in bioimaging

Tailoring the wavelength to NIR emission was realized by replacing the strong electron-withdrawing groups or extending the π-conjugated system based on the DCM chromophore, along with beneficial characteristics such as bright NIR fluorescence, large Stokes shift and low photo-bleaching.

PNA as a Biosupramolecular Tag for Programmable Assemblies and Reactions

The programmability of oligonucleotide hybridization offers an attractive platform for the design of assemblies with emergent properties or functions. Developments in DNA nanotechnologies have transformed our thinking about the applications of nucleic acids. Progress from designed assemblies to functional outputs will continue to benefit from functionalities added to the nucleic acids that can participate in reactions or interactions beyond hybridization. In that respect, peptide nucleic acids (PNAs) are interesting because they combine the hybridization properties of DNA with the modularity of peptides. In fact, PNAs form more stable duplexes with DNA or RNA than the corresponding natural homoduplexes. The high stability achieved with shorter oligomers (an 8-mer is sufficient for a stable duplex at room temperature) typically results in very high sequence fidelity in the hybridization with negligible impact of the ionic strength of the buffer due to the lack of electrostatic repulsion between the duplex strands. The simple peptidic backbone of PNA has been shown to be tolerant of modifications with substitutions that further enhance the duplex stability while providing opportunities for functionalization. Moreover, the metabolic stability of PNAs facilitates their integration into systems that interface with biology. Over the past decade, there has been a growing interest in using PNAs as biosupramolecular tags to program assemblies and reactions. A series of robust templated reactions have been developed with functionalized PNA. These reactions can be used to translate DNA templates into functional polymers of unprecedented complexity, fluorescent outputs, or bioactive small molecules. Furthermore, cellular nucleic acids (mRNA or miRNA) have been harnessed to promote assemblies and reactions in live cells. The tolerance of PNA synthesis also lends itself to the encoding of small molecules that can be further assembled on the basis of their nucleic acid sequences. It is now well-established that hybridization-based assemblies displaying two or more ligands can interact synergistically with a target biomolecule. These assemblies have now been shown to be functional in vivo. Similarly, PNA-tagged macromolecules have been used to prepare bioactive assemblies and three-dimensional nanostructures. Several technologies based on DNA-templated synthesis of sequence-defined polymers or DNA-templated display of ligands have been shown to be compatible with reiterative cycles of selection/amplification starting with large libraries of DNA templates, bringing the power of in vitro evolution to synthetic molecules and offering the possibility of exploring uncharted molecular diversity space with unprecedented scope and speed.

Oligonucleotide-templated reactions based on Peptide Nucleic Acid (PNA) probes: concept and biomedical applications

Sensing technologies based on Peptide Nucleic Acids (PNAs) and oligonucleotide-templated chemistry are perfectly suited for biomedical applications (e.g., diagnosis, prognosis and stratification of diseases) and could compete well with more traditional amplification technologies using expensive dual-labelled oligonucleotide probes. PNAs can be easily synthesised and functionalised, are more stable and are more responsive to point-mutations than their DNA counterpart. For these reasons, fluorogenic PNAs represent an interesting alternative to DNA-based molecular beacons for sensing applications in a cell-free environment, where cellular uptake is not required.

A sensitive colorimetric and fluorescent sensor based on imidazolium-functionalized squaraines for the detection of GTP and alkaline phosphatase in aqueous solution

Imidazolium-functionalized squaraine ImSQ8 is synthesized as a sensitive colorimetric and fluorescent chemosensor for GTP in aqueous solution. The detection limit of GTP reaches 5.4 ppb. Its applications in the live-cell imaging and enzyme activity assay have also been demonstrated.

Host–guest assembly of adamantyl tethered squaraine in β-cyclodextrin for monitoring pH in living cells

A host-guest assembly of adamantyl tethered squaraine in β-cyclodextrin has been designed as a sensitive near-infrared fluorescent probe for imaging intracellular pH in living cells.