A reduction-triggered fluorescence probe for sensing nucleic acids

Mutual leveraging of proximity effects and click chemistry in chemical biology

Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.

Riboflavin-catalyzed templated reaction to translate nucleic acid cues into signals of rhodamine derivatives

We report a templated reaction for the facile translation of nucleic acid cues into signals of universal rhodamine derivatives based on the riboflavin-catalyzed oxidation of dihydrorhodamine compounds. The rhodamine-signaling operation enabled us to design a highly sequence-selective fluorescent sensor that can detect as little as 500 pM of the target nucleic acid in 90 min or to present a rhodamine antibody that can be further applied to immunoassays.

Development of Transition-Metal-Free Lewis Acid-Initiated Double Arylation of Aldehyde: A Facile Approach Towards the Total Synthesis of Anti-Breast-Cancer Agent

This work describes a mild and robust double hydroarylation strategy for the synthesis of symmetrical /unsymmetrical diaryl- and triarylmethanes in excellent yields using Lambert salt (0.2-1.0 mol%). Despite the anticipated challenges associated with controlling selective product formation, unsymmetrical diaryl- and triarylmethanes products are obtained unprecedentedly. A highly efficient gram scale reaction has also been reported (TON for symmetrical product=475 and for unsymmetrical product=390). The synthetic utility of the methodology is demonstrated by the preparation of several unexplored diaryl- and triarylmethane-based biologically relevant molecules, such as arundine, vibrindole A, turbomycin B, and certain anti-inflammatory agents. A total synthesis of an anti-breast-cancer agent is also demonstrated. Control experiments, Hammett analysis, HRMS and GC-MS studies reveal the reaction intermediates and reaction mechanism.

Achieving AIE from ACQ in positional isomeric triarylmethanes

This report demonstrate that the usual ‘aggregation caused quenching’ (ACQ) can be overcome by a change in the substitution position in naphthalene derivatives, leading to the much desired ‘aggregation induced emission’ (AIE).

Expanding the scope of native chemical ligation - templated small molecule drug synthesis via benzanilide formation

We describe a reaction system that enables the synthesis of Bcr–Abl tyrosine kinase inhibitors (TKI) via benzanilide formation in water. The reaction is based on native chemical ligation (NCL). In contrast to previous applications, we used the NCL chemistry to establish aromatic rather than aliphatic amide bonds in coupling reactions between benzoyl and o-mercaptoaniline fragments. The method was applied for the synthesis of thiolated ponatinib and GZD824 derivatives. Acid treatment provided benzothiazole structures, which opens opportunities for diversification. Thiolation affected the affinity for Abl1 kinase only moderately. Of note, a ponatinib-derived benzothiazole also showed nanomolar affinity. NCL-enabled benzanilide formation may prove useful for fragment-based drug discovery. To show that benzanilide synthesis can be put under the control of a template, we connected the benzoyl and o-mercaptoaniline fragments to DNA and peptide nucleic acid (PNA) oligomers. Complementary RNA templates enabled adjacent binding of reactive conjugates triggering a rapid benzoyl transfer from a thioester-linked DNA conjugate to an o-mercaptoaniline-DNA or -PNA conjugate. We evaluated the influence of linker length and unpaired spacer nucleotides within the RNA template on the product yield. The data suggest that nucleic acid-templated benzanilide formation could find application in the establishment of DNA-encoded combinatorial libraries (DEL).

The templated native chemical ligation between benzoyl thioesters and o-mercaptoaniline fragments proceeds in water and provides benzanilides that have nanomolar affinity for Abl1 kinase.

Metal- and solvent-free synthesis of aniline- and phenol-based triarylmethanes via Brönsted acidic ionic liquid catalyzed Friedel-Crafts reaction

A beneficial, scalable and efficient methodology for the synthesis of aniline-based triarylmethanes has been established through the double Friedel-Crafts reaction of commercial aldehydes and primary, secondary or tertiary anilines using Brönsted acidic ionic liquid as a powerful catalyst, namely [bsmim][NTf₂]. This protocol was successfully performed under metal- and solvent-free conditions with a broad range of substrates, giving the corresponding aniline-based triarylmethane products in good to excellent yields (up to 99%). In addition, alternative aromatic nucleophiles such as phenols and electron-rich arenes were also studied using this useful approach to achieve a diversity of triarylmethane derivatives in high to excellent yields.

Brönsted acidic ionic liquid catalyzed the synthesis of aniline- and phenol-based triarylmethanes via Friedel-Crafts reaction under metal- and solvent-free conditions.

A Simple Reaction for DNA Sensing and Chemical Delivery

Reactions templated by nucleic acids are currently at the heart of applications in biosensing and drug release. The number of chemical reactions selectively occurring only in the presence of the template, in aqueous solutions, and at room temperature and able to release a chemical moiety is still very limited. Here, we report the use of the p-nitrophenyl carbonate (NPC) as a new reactive moiety for DNA templated reactions releasing a colored reporter by reaction with a simple amine. The easily synthesized p-nitrophenyl carbonate was integrated in an oligonucleotide and showed a very good stability as well as a high reactivity toward amines, without the need for any supplementary reagent, quantitatively releasing the red p-nitrophenolate with a half-life of about 1 h.

Bioorthogonal Ligations and Cleavages in Chemical Biology

Bioorthogonal reactions including the bioorthogonal ligations and cleavages have become an active field of research in chemical biology, and they play important roles in chemical modification and functional regulation of biomolecules. This review summarizes the developments and applications of the representative bioorthogonal reactions including the Staudinger reactions, the metal-mediated bioorthogonal reactions, the strain-promoted cycloadditions, the inverse electron demand Diels-Alder reactions, the light-triggered bioorthogonal reactions, and the reactions of chloroquinoxalines and ortho-dithiophenols.

Quantification of native mRNA dynamics in living neurons using fluorescence correlation spectroscopy and reduction-triggered fluorescent probes

RNA localization in subcellular compartments is essential for spatial and temporal regulation of protein expression in neurons. Several techniques have been developed to visualize mRNAs inside cells, but the study of the behavior of endogenous and nonengineered mRNAs in living neurons has just started. In this study, we combined reduction-triggered fluorescent (RETF) probes and fluorescence correlation spectroscopy (FCS) to investigate the diffusion properties of activity-regulated cytoskeleton-associated protein (Arc) and inositol 1,4,5-trisphosphate receptor type 1 (Ip3r1) mRNAs. This approach enabled us to discriminate between RNA-bound and unbound fluorescent probes and to quantify mRNA diffusion parameters and concentrations in living rat primary hippocampal neurons. Specifically, we detected the induction of Arc mRNA production after neuronal activation in real time. Results from computer simulations with mRNA diffusion coefficients obtained in these analyses supported the idea that free diffusion is incapable of transporting mRNA of sizes close to those of Arc or Ip3r1 to distal dendrites. In conclusion, the combined RETF-FCS approach reported here enables analyses of the dynamics of endogenous, unmodified mRNAs in living neurons, affording a glimpse into the intracellular dynamics of RNA in live cells.

Thiol-responsive pro-fluorophore labeling: Synthesis of a pro-fluorescent labeled oligonucleotide for monitoring cellular uptake

Pro-fluorescent labeled oligonucleotides are potential alternative tools to classical fluorescently labeled oligonucleotides for monitoring cellular uptake. Here, we report the design and synthesis of a thiol-responsive pro-fluorophore labeled oligonucleotide, and its fluorescence responsivity to glutathione in the test tube and live cells.

Light-induced metal-free transformations of unactivated pyridotriazoles

A highly efficient and practical method for incorporation of the arylmethylpyridyl moiety into diverse molecules has been developed. This method features the transition metal-free light-induced room temperature transformation of pyridotriazoles into pyridyl carbenes, which are capable of smooth arylation, X-H insertion, and cyclopropanation reactions. The synthetic usefulness of the developed method was illustrated in a facile synthesis of biologically active molecules.

RNA imaging by chemical probes

Sequence-specific detection of intracellular RNA is one of the most important approaches to understand life phenomena. However, it is difficult to detect RNA in living cells because of its variety and scarcity. In the last three decades, several chemical probes have been developed for RNA detection in living cells. These probes are composed of DNA or artificial nucleic acid and hybridize with the target RNA in a sequence-specific manner. This hybridization triggers a change of fluorescence or a chemical reaction. In this review, we classify the probes according to the associated fluorogenic mechanism, that is, interaction between fluorophore and quencher, environmental change of fluorophore, and template reaction with/without ligation. In addition, we introduce examples of RNA imaging in living cells.

Dissociative Bioorthogonal Reactions

Bioorthogonal reactions that proceed readily under physiological conditions without interference from biomolecules have found widespread application in the life sciences. Complementary to the bioorthogonal reactions that ligate two molecules, reactions that release a molecule or cleave a linker are increasingly attracting interest. Such dissociative bioorthogonal reactions have a broad spectrum of uses, for example, in controlling bio-macromolecule activity, in drug delivery, and in diagnostic assays. This review article summarizes the developed bioorthogonal reactions linked to a release step, outlines representative areas of the applications of such reactions, and discusses aspects that require further improvement.

A highly efficient nucleophilic substitution reaction between R2P(O)H and triarylmethanols to synthesize phosphorus-substituted triarylmethanes

A highly efficient nucleophilic substitution reaction between R₂P(O)H and triarylmethanols was reported, which provides phosphorus-substituted triarylmethanes in rich diversity with 40–96% yields.

Use of a small molecule as an initiator for interchain staudinger reaction: A new ATP sensing platform using product fluorescence

We demonstrated that a small molecule induced interchain Staudinger reaction can be employed for highly selective detection of adenosine triphosphate (ATP), an important energy-storage biomolecule. A designed ATP split aptamer (A1) was first functionalized with a weakly fluorescent coumarin derivative due to an azide group (azido-coumarin). The second DNA strand (A2) was covalently linked with triphenylphosphine, which could selectively and efficiently reduce azido to amino group through the Staudinger reaction. The A2 was then hybridized with a half of another designed longer DNA strand (T1). The second half of T1 was a split aptamer and selectively recognized ATP with A1 to form a sandwich structure. The specific interaction between ATP and the aptamers drew the two functionalized DNA strands (A1 and A2) together to initiate the interchain Staudinger reduction at fmol-nmol concentration level, hence produced fluorescent 7-aminocoumarin which could be used as an indicator for the presence of trace ATP. The reaction process had a concentration dependent manner with ATP in a large concentration range. Such a strategy of interchain Staudinger reaction can be extended to construct biosensors for other small functional molecules on the basis of judiciously designed aptamers.

Maximizing Output in RNA-Programmed Peptidyl-Transfer Reactions

A chemical reaction that is triggered by a specific RNA molecule might provide opportunities for the design of artificial feedback loops. We envision a peptidyl transfer reaction in which mRNA encoding an antiapoptotic protein would instruct the synthesis of apoptosis-inducing peptides. In this study, we used the RNA-programmed synthesis of a 16-mer peptide derived from the BH3 domain of the protein Bak, which inhibits the antiapoptotic protein Bcl-x_L . The reaction involves the transfer of a thioester-linked donor peptide fragment from one PNA conjugate to an acceptor peptide-PNA conjugate. We asked two key questions. What are the chemical requirements that allow RNA-templated synthesis of a 16-mer peptide to proceed at lower (nanomolar) concentrations of RNA, that is, the concentration range found in cancer cells? Will such reactions provide sufficient amounts of peptide product and sufficient affinity to interfere with the targeted protein-protein interaction? Perhaps surprisingly, the lengths of the peptides involved in peptidyl transfer chemistry have little effect on the achievable rate enhancements. However, the nature of the thioester C terminus, the distance between the targeted template annealing sites, and template affinity play important roles. The investigation revealed guidelines for the reaction design for peptidyl transfer with low amounts (1-10 nm) of RNA, yet still provide sufficient product to antagonize a protein-protein interaction.

Copper-mediated arylation with arylboronic acids: Facile and modular synthesis of triarylmethanes

A facile and modular synthesis of triarylmethanes was achieved in good yield via a two-step sequence in which the final step is the copper(II)-catalyzed arylation of diarylmethanols with arylboronic acids. By using this protocol a variety of symmetrical and unsymmetrical triarylmethanes were synthesized. As an application of the newly developed methodology, we demonstrate a high-yielding synthesis of the triarylmethane intermediate towards an anti-breast-cancer drug candidate.

Nickel-Catalyzed Arylation of Heteroaryl-containing Diarylmethanes: Exceptional Reactivity of the Ni(NIXANTPHOS)-based Catalyst

Nickel(0)-catalyzed cross-coupling of heteroaryl-containing diarylmethanes with both aryl bromides and chlorides has been achieved. The success of this reaction relies on the introduction of a unique nickel/NIXANTPHOS-based catalyst system, which provides a direct route to triarylmethanes from heteroaryl-containing diarylmethanes. Reactivity studies indicate the Ni(NIXANTPHOS)-based catalyst exhibits enhanced reactivity over XANTPHOS derivatives and other Ni(phosphine)-based catalysts in the reactions examined.

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.

Isothermal amplified detection of DNA and RNA

This review highlights various methods that can be used for a sensitive detection of nucleic acids without using thermal cycling procedures, as is done in PCR or LCR. Topics included are nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), loop-mediated amplification (LAMP), Invader assay, rolling circle amplification (RCA), signal mediated amplification of RNA technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), nicking endonuclease signal amplification (NESA) and nicking endonuclease assisted nanoparticle activation (NENNA), exonuclease-aided target recycling, Junction or Y-probes, split DNAZyme and deoxyribozyme amplification strategies, template-directed chemical reactions that lead to amplified signals, non-covalent DNA catalytic reactions, hybridization chain reactions (HCR) and detection via the self-assembly of DNA probes to give supramolecular structures. The majority of these isothermal amplification methods can detect DNA or RNA in complex biological matrices and have great potential for use at point-of-care.

Brightness through local constraint--LNA-enhanced FIT hybridization probes for in vivo ribonucleotide particle tracking

Imaging the dynamics of RNA in living cells is usually performed by means of transgenic approaches that require modification of RNA targets and cells. Fluorogenic hybridization probes would also allow the analysis of wild-type organisms. We developed nuclease-resistant DNA forced intercalation (FIT) probes that combine the high enhancement of fluorescence upon hybridization with the high brightness required to allow tracking of individual ribonucleotide particles (RNPs). In our design, a single thiazole orange (TO) intercalator dye is linked as a nucleobase surrogate and an adjacent locked nucleic acid (LNA) unit serves to introduce a local constraint. This closes fluorescence decay channels and thereby increases the brightness of the probe-target duplexes. As few as two probes were sufficient to enable the tracking of oskar mRNPs in wild-type living Drosophila melanogaster oocytes.

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.

Templated native chemical ligation: peptide chemistry beyond protein synthesis

Native chemical ligation (NCL) is a powerful method for the convergent synthesis of proteins and peptides. In its original format, NCL between a peptide containing a C-terminal thioester and another peptide offering an N-terminal cysteine has been used to enable protein synthesis of unprotected peptide fragments. However, the applications of NCL extend beyond the scope of protein synthesis. For instance, NCL can be put under the control of template molecules. In such a scenario, NCL enables the design of conditional reaction systems in which, peptide bond formation occurs only when a specific third party molecule is present. In this review, we will show how templates can be used to control the reactivity and chemoselectivity of NCL reactions. We highlight peptide and nucleic-acid-templated NCL reactions and discuss potential applications in nucleic acid diagnosis, origin-of-life studies and gene-expression-specific therapies.

Rapid miRNA imaging in cells using fluorogenic templated Staudinger reaction between PNA-based probes

Reactions templated by a specific nucleic acid sequence have emerged as an attractive strategy for nucleic acid sensing. The Staudinger reaction using an azide-quenched fluorophore and a phosphine is particularly well suited by virtue of its bioorthogonality and biocompatibility. The reaction is promoted by a complementary nucleic acid that aligns the phosphine with the azide-quenched fluorophore. Cellular RNAs can catalyze the Staudinger reaction and signal amplification can be achieved through multiple turnover of the template. Peptide nucleic acids (PNA) provide a convenient platform for the preparation of specific probes as they combine desirable hybridization properties, robust synthesis, ease of fluorophore conjugation, and high biochemical stability. Herein, we describe protocols for fast fluorescent detection of miRNAs in human cells with PNA-based probes via reductive unquenching of bis-azidorhodamine by trialkylphosphine.

Reducing product inhibition in nucleic acid-templated ligation reactions: DNA-templated cycligation

Programmable interactions allow nucleic acid molecules to template chemical reactions by increasing the effective molarities of appended reactive groups. DNA/RNA-triggered reactions can proceed, in principle, with turnover in the template. The amplification provided by the formation of many product molecules per template is a valuable asset when the availability of the DNA or RNA target is limited. However, turnover is usually impeded by reaction products that block access to the template. Product inhibition is most severe in ligation reactions, where products after ligation have dramatically increased template affinities. We introduce a potentially generic approach to reduce product inhibition in nucleic acid-programmed ligation reactions. A DNA-triggered ligation-cyclization sequence ("cycligation") of bifunctional peptide nucleic acid (PNA) conjugates affords cyclic ligation products. Melting experiments revealed that product cyclization is accompanied by a pronounced decrease in template affinity compared to linear ligation products. The reaction system relies upon haloacetylated PNA-thioesters and isocysteinyl-PNA-cysteine conjugates, which were ligated on a DNA template according to a native chemical ligation mechanism. Dissociation of the resulting linear product-template duplex (induced by, for example, thermal cycling) enabled product cyclization through sulfur-halide substitution. Both ligation and cyclization are fast reactions (ligation: 86 % yield after 20 min, cyclization: quantitative after 5 min). Under thermocycling conditions, the DNA template was able to trigger the formation of new product molecules when fresh reactants were added. Furthermore, cycligation produced 2-3 times more product than a conventional ligation reaction with substoichiometric template loads (0.25-0.01 equiv). We believe that cyclization of products from DNA-templated reactions could ultimately afford systems that completely overcome product inhibition.

Very rapid DNA-templated reaction for efficient signal amplification and its steady-state kinetic analysis of the turnover cycle

Oligonucleotide-templated reactions are powerful tools for the detection of nucleic acid sequences. One of the major scientific challenges associated with this technique is the rational design of non-enzyme-mediated catalytic templated reactions capable of multiple turnovers that provide high levels of signal amplification. Herein, we report the development of a nucleophilic aromatic substitution reaction-triggered fluorescent probe. The probe underwent a rapid templated reaction without any of the undesired background reactions. The fluorogenic reaction conducted in the presence of a template provided a 223-fold increase in fluorescence after 30 s compared with the nontemplated reaction. The probe provided an efficient level of signal amplification that ultimately enabled particularly sensitive levels of detection. Assuming a simple model for the templated reactions, it was possible to estimate the rate constants of the chemical reaction in the presence and in the absence of the template. From these kinetic analyses, it was possible to confirm that an efficient turnover cycle had been achieved, on the basis of the dramatic enhancement in the rate of the chemical reaction considered to be the rate-determining step. With maximized turnover efficiency, it was demonstrated that the probe could offer a high turnover number of 1500 times to enable sensitive levels of detection with a detection limit of 0.5 pM in the catalytic templated reactions.