Efficient reverse click labeling of azide oligonucleotides with multiple alkynyl Cy-Dyes applied to the synthesis of HyBeacon probes for genetic analysis

AIE-based dual-ratiometric chemosensor for detection of sulfur dioxide derivatives and viscosity and its application in food samples and biological imaging

BACKGROUND

SO2 is an important gas molecular messenger that participates in many physiological activities and helps maintaining the redox homeostasis in biological system. Especially, SO2 can effectively regulate oxidative stress and improve mitochondrial morphology. Abnormal mitochondrial viscosity can lead to a variety of diseases. Therefore, it is of great importance to detect SO2 derivatives and cell viscosity in biological systems.

RESULTS

Here, two mitochondria-targeted and dual-ratiometric chemosensors (TPE-1 and TPE-2) based on tetraphenylethene were constructed, which could be used to simultaneously detect SO2 derivatives and cell viscosity. Notably, TPE-2 as the preferable due to its superior discernibility to HSO3- than that of TPE-1. Moreover, TPE-2 featured rapid response, high sensitivity, excellent selectivity, and low cytotoxicity under physiological conditions which means that TPE-2 is more suitable for practical application than TPE-1. The response mechanism of TPE-2 for HSO3- was confirmed by the theoretical calculation and mass spectral analysis. Meanwhile, TPE-2 showed enhanced fluorescence intensity the increased viscosity environment due to it was subjected to structural rotation. In addition, the practical application for detecting HSO3- in real water samples was successfully carried out with good recovery, the test strips loaded TPE-2 was prepared and the detection of HSO3- in food samples was realized by a convenient smartphone analysis. Importantly, TPE-2 had good mitochondrial targeting ability and had successfully imaged HSO3- and viscosity in HeLa cells and zebrafish.

SIGNIFICANCE

This study provides an effective and potential tool for detecting HSO3- and viscosity in mitochondria and in vivo, the rational design strategy in this work holds potential to inspire the development of more powerful dual-response chemosensor for other biological factors.

Atom-Efficient Synthesis of Trimethine Cyanines Using Formaldehyde as a Single-Carbon Source

Herein, we present an innovative and atom-efficient synthesis of trimethine cyanines (Cy3) using formaldehyde (FA) as a single-carbon reagent. The widespread application of Cy3 dyes in bioimaging and genomics/proteomics is often limited by synthetic routes plagued by low atom economy and substantial side-product formation. Through systematic investigation, we have developed a practical and efficient synthetic pathway for both symmetrical and unsymmetrical Cy3 derivatives, significantly minimizing resource utilization. Notably, this approach yields water as the by-product, in alignment with sustainable chemistry principles. Moreover, the efficient one-pot synthesis facilitates the detection of intracellular FA levels, utilizing the fluorescence signal of Cy3 in live cells. It is also possible to detect endogenous FA in the intestinal tissues. We observed a significant decrease in FA in the small intestine of inflammatory bowel disease (IBD) mice as compared to healthy mice. This methodological advancement not only enhances the scope of fluorescent dye synthesis but also contributes to sustainable practices within chemical manufacturing, offering a significant leap forward in the development of environmentally friendly synthetic strategies.

Rational Design of Cyanine-Based Fluorogenic Dimers to Reduce Nonspecific Interactions with Albumin and Lipid Bilayers: Application to Highly Sensitive Imaging of GPCRs in Living Cells

Fluorogenic dimers with polarity-sensitive folding are powerful probes for live-cell bioimaging. They switch on their fluorescence only after interacting with their targets, thus leading to a high signal-to-noise ratio in wash-free bioimaging. We previously reported the first near-infrared fluorogenic dimers derived from cyanine 5.5 dyes for the optical detection of G protein-coupled receptors. Owing to their hydrophobic character, these dimers are prone to form nonspecific interactions with proteins such as albumin and with the lipid bilayer of the cell membrane resulting in a residual background fluorescence in complex biological media. Herein, we report the rational design of new fluorogenic dimers derived from cyanine 5. By modulating the chemical structure of the cyanine units, we discovered that the two asymmetric cyanine 5.25 dyes were able to form intramolecular H-aggregates and self-quenched in aqueous media. Moreover, the resulting original dimeric probes enabled a significant reduction of the nonspecific interactions with bovine serum albumin and lipid bilayers compared with the first generation of cyanine 5.5 dimers. Finally, the optimized asymmetric fluorogenic dimer was grafted to carbetocin for the specific imaging of the oxytocin receptor under no-wash conditions directly in cell culture media, notably improving the signal-to-background ratio compared with the previous generation of cyanine 5.5 dimers.

A turn-on fluorescence probe for imaging tyrosinase at the wound site in broken tail of zebrafish

Tyrosinase (TYR) is a copper-containing oxidase that affects the synthesis of melanin in the human body, which is regulate to the pigmentation of the skin. Nevertheless, abnormal expression of TYR can lead to albinism, vitiligo and other skin diseases. Excessive accumulation of TYR is a marker of melanoma cancer and an important factor leading to pigmentation during wound healing, freckles and browning of fruits and vegetables. Efficient tracking of TYR is of significance for studying its pathophysiological mechanism. Herein, we synthesized a benzindole-based fluorescent probe Pro-OH to detect TYR in living cells and zebrafish. The probe displayed a high selectivity and sensitivity in distinguishing TYR from other analytes with the low detection limit of 1.024 U/mL. Importantly, Pro-OH was successfully used to imagine TYR at the wound site of broken tail of zebrafish.

4-Isocyanoindole-2'-deoxyribonucleoside (4ICIN): An Isomorphic Indole Nucleoside Suitable for Inverse Electron Demand Diels-Alder Reactions

Isomorphic nucleosides are powerful tool compounds for interrogating a variety of biological processes involving nucleosides and nucleic acids. We previously reported a fluorescent isomorphic indole nucleoside called 4CIN. A distinguishing molecular feature of 4CIN is the presence of a 4-cyano moiety on the indole that functions as the nucleobase. Given the known chemical reactivity of isonitriles with tetrazines through [4+1]-cycloaddition chemistry, we investigated whether conversion of 4CIN to the corresponding isonitrile would confer a useful chemical probe. Here we report the synthesis of 4-isocyanoindole-2'-deoxyribonucleoside (4ICIN) and the propensity of 4ICIN to undergo inverse electron demand Diels-Alder cycloaddition with a model tetrazine.

Multistate Switching of Some Ruthenium Alkynyl and Vinyl Spiropyran Complexes

To study the switching properties of photochromes, we undertook the synthesis and characterization of several ruthenium organometallic complexes of the type [Ru(Cp*)(dppe)(C≡C-SP)] or [Ru(CO)(dppe)(PPh3)Cl(CH═CH-SP)], where SP = spiropyran. The spectroscopic and electrochemical properties of the complexes were determined by careful cyclic voltammetric and spectroelectrochemical experiments. Whereas the mononuclear alkynyl ruthenium complexes undergo one-electron oxidations localized over the metal alkynyl moiety, the oxidation of the mononuclear vinyl ruthenium complexes is centered on the indoline moiety of the spiropyran. Through these studies, we demonstrate access to several stable redox states, in addition to switching states attained via acidochromism and/or photoisomerization.

Synthesis of Cy5-Labelled C5-Alkynyl-modified cytidine triphosphates via Sonogashira coupling for DNA labelling

New applications of palladium-catalyzed Sonogashira-type cross-coupling reaction between C5-halogenated 2'-deoxycytidine-5'-monophosphate and novel cyanine dyes with a terminal alkyne group have been developed. The present methodology allows to synthesize of fluorescently labeled C5-nucleoside triphosphates with different acetylene linkers between the fluorophore and pyrimidine base in good to excellent yields under mild reaction conditions. Modified 2'-deoxycytidine-5'-triphosphates were shown to be good substrates for DNA polymerases and were incorporated into the DNA by polymerase chain reaction.

Synthesis of Substituted Cy5 Phosphoramidite Derivatives and Their Incorporation into Oligonucleotides Using Automated DNA Synthesis

Cyanine dyes represent a family of organic fluorophores with widespread utility in biological-based applications ranging from real-time PCR probes to protein labeling. One burgeoning use currently being explored with indodicarbocyanine (Cy5) in particular is that of accessing exciton delocalization in designer DNA dye aggregate structures for potential development of light-harvesting devices and room-temperature quantum computers. Tuning the hydrophilicity/hydrophobicity of Cy5 dyes in such DNA structures should influence the strength of their excitonic coupling; however, the requisite commercial Cy5 derivatives available for direct incorporation into DNA are nonexistent. Here, we prepare a series of Cy5 derivatives that possess different 5,5'-substituents and detail their incorporation into a set of DNA sequences. In addition to varying dye hydrophobicity/hydrophilicity, the 5,5'-substituents, including hexyloxy, triethyleneglycol monomethyl ether, tert-butyl, and chloro groups were chosen so as to vary the inherent electron-donating/withdrawing character while also tuning their resulting absorption and emission properties. Following the synthesis of parent dyes, one of their pendant alkyl chains was functionalized with a monomethoxytrityl protective group with the remaining hydroxyl-terminated N-propyl linker permitting rapid, same-day phosphoramidite conversion and direct internal DNA incorporation into nascent oligonucleotides with moderate to good yields using a 1 μmole scale automated DNA synthesis. Labeled sequences were cleaved from the controlled pore glass matrix, purified by HPLC, and their photophysical properties were characterized. The DNA-labeled Cy5 derivatives displayed spectroscopic properties that paralleled the parent dyes, with either no change or an increase in fluorescence quantum yield depending upon sequence.

"Click-switch" - one-step conversion of organic azides into photochromic diarylethenes for the generation of light-controlled systems

Diarylethenes (DAEs) are an established class of photochromic molecules, but their effective incorporation into pre-existing targets is synthetically difficult. Here we describe a new class of DAEs in which one of the aryl rings is a 1,2,3-triazole that is formed by “click” chemistry between an azide on the target and a matching alkyne–cyclopentene–thiophene component. This late-stage zero-length linking allows for tight integration of the DAE with the target, thereby increasing the chances for photomodulation of target functions. Nineteen different DAEs were synthesized and their properties investigated. All showed photochromism. Electron-withdrawing groups, and in particular −M-substituents at the triazole and/or thiophene moiety resulted in DAEs with high photo- and thermostability. Further, the chemical nature of the cyclopentene bridge had a strong influence on the behaviour upon UV light irradiation. Incorporation of perfluorinated cyclopentene led to compounds with high photo- and thermostability, but the reversible photochromic reaction was restricted to halogenated solvents. Compounds containing the perhydrogenated cyclopentene bridge, on the other hand, allowed the reversible photochromic reaction in a wide range of solvents, but had on average lower photo- and thermostabilities. The combination of the perhydrocyclopentene bridge and electron-withdrawing groups resulted in a DAE with improved photostability and no solvent restriction. Quantum chemical calculations helped to identify the photoproducts formed in halogenated as well as non-halogenated solvents. For two optimized DAE photoswitches, photostationary state composition and reaction quantum yields were determined. These data revealed efficient photochemical ring closure and opening. We envision applications of these new photochromic diarylethenes in photonics, nanotechnology, photobiology, photopharmacology and materials science.

New photochromic diarylethenes are reported in which one aryl ring is a 1,2,3-triazole that is formed by “click” chemistry between an azide on the target and a matching alkyne–cyclopentene–thiophene component.

Förster Resonance Energy Transfer Nanoplatform Based on Recognition-Induced Fusion/Fission of DNA Mixed Micelles for Nucleic Acid Sensing

The dynamic nature of micellar nanostructures is employed to form a self-assembled Förster resonance energy transfer (FRET) nanoplatform for enhanced sensing of DNA. The platform consists of lipid oligonucleotide FRET probes incorporated into micellar scaffolds, where single recognition events result in fusion and fission of DNA mixed micelles, triggering the fluorescence response of multiple rather than a single FRET pair. In comparison to conventional FRET substrates where a single donor interacts with a single acceptor, the micellar multiplex FRET system showed ∼20- and ∼3-fold enhancements in the limit of detection and FRET efficiency, respectively. This supramolecular signal amplification approach could potentially be used to improve FRET-based diagnostic assays of nucleic acid and non-DNA based targets.

A Hitchhiker's Guide to Click-Chemistry with Nucleic Acids

Click chemistry is an immensely powerful technique for the fast and efficient covalent conjugation of molecular entities. Its broad scope has positively impacted on multiple scientific disciplines, and its implementation within the nucleic acid field has enabled researchers to generate a wide variety of tools with application in biology, biochemistry, and biotechnology. Azide-alkyne cycloadditions (AAC) are still the leading technology among click reactions due to the facile modification and incorporation of azide and alkyne groups within biological scaffolds. Application of AAC chemistry to nucleic acids allows labeling, ligation, and cyclization of oligonucleotides efficiently and cost-effectively relative to previously used chemical and enzymatic techniques. In this review, we provide a guide to inexperienced and knowledgeable researchers approaching the field of click chemistry with nucleic acids. We discuss in detail the chemistry, the available modified-nucleosides, and applications of AAC reactions in nucleic acid chemistry and provide a critical view of the advantages, limitations, and open-questions within the field.

MemBright: A Family of Fluorescent Membrane Probes for Advanced Cellular Imaging and Neuroscience

The proper staining of the plasma membrane (PM) is critical in bioimaging as it delimits the cell. Herein, we developed MemBright, a family of six cyanine-based fluorescent turn-on PM probes that emit from orange to near infrared when reaching the PM, and enable homogeneous and selective PM staining with excellent contrast in mono- and two-photon microscopy. These probes are compatible with long-term live-cell imaging and immunostaining. Moreover, MemBright label neurons in a brighter manner than surrounding cells, allowing identification of neurons in acute brain tissue sections and neuromuscular junctions without any use of transfection or transgenic animals. In addition, MemBright probes were used in super-resolution imaging to unravel the neck of dendritic spines. 3D multicolor dSTORM in combination with immunostaining revealed en-passant synapse displaying endogenous glutamate receptors clustered at the axonal-dendritic contact site. MemBright probes thus constitute a universal toolkit for cell biology and neuroscience biomembrane imaging with a variety of microscopy techniques. VIDEO ABSTRACT.

Synthesis of stable azide and alkyne functionalized phosphoramidite nucleosides

The use of CuAAC chemistry to crosslink and stabilize oligonucleotides has been limited by the incompatibility of azides with the phosphoramidites used in automated oligonucleotide synthesis. Herein we report optimized reaction conditions to synthesize azide derivatives of thymidine and cytidine phosphoramidites. Investigation of the stability of the novel phosphoramidites using ³¹P NMR at room temperature showed less than 10% degradation after 6 hours. The azide modified thymidine was successfully utilized as an internal modifier in the standard phosphoramidite synthesis of a DNA sequence. The synthesized azide and alkyne derivatives of pyrimidines will allow efficient incorporation of azide and alkyne click pairs into nucleic acids, thus widening the applicability of click chemistry in investigating the chemistry of nucleic acids.

Modulation of Mitochondriotropic Properties of Cyanine Dyes by in Organello Copper-Free Click Reaction

Cyanine (Cy) dyes show a general propensity to localize in polarized mitochondria. This mitochondriotropism was used to perform a copper-free click reaction in the mitochondria of living cells. The in organello reaction of dyes Cy3 and Cy5 led to a product that was easily traceable by Förster resonance energy transfer (FRET). As determined by confocal laser scanning microscopy, the Cy3-Cy5 conjugate showed enhanced retention in mitochondria, relative to that of the starting compounds. This enhancement of a favorable property can be achieved by synthesis in organello, but not outside mitochondria.

Real-Time Imaging of the Azole Class of Antifungal Drugs in Live Candida Cells

Azoles are the most commonly used class of antifungal drugs, yet where they localize within fungal cells and how they are imported remain poorly understood. Azole antifungals target lanosterol 14α-demethylase, a cytochrome P450, encoded by ERG11 in Candida albicans, the most prevalent fungal pathogen. We report the synthesis of fluorescent probes that permit visualization of antifungal azoles within live cells. Probe 1 is a dansyl dye-conjugated azole, and probe 2 is a Cy5-conjugated azole. Docking computations indicated that each of the probes can occupy the active site of the target cytochrome P450. Like the azole drug fluconazole, probe 1 is not effective against a mutant that lacks the target cytochrome P450. In contrast, the azole drug ketoconazole and probe 2 retained some antifungal activity against mutants lacking the target cytochrome P450, implying that both act against more than one target. Both fluorescent azole probes colocalized with the mitochondria, as determined by fluorescence microscopy with MitoTracker dye. Thus, these fluorescent probes are useful molecular tools that can lead to detailed information about the activity and localization of the important azole class of antifungal drugs.

In vitro labeling strategies for in cellulo fluorescence microscopy of single ribonucleoprotein machines

RNA plays a fundamental, ubiquitous role as either substrate or functional component of many large cellular complexes-"molecular machines"-used to maintain and control the readout of genetic information, a functional landscape that we are only beginning to understand. The cellular mechanisms for the spatiotemporal organization of the plethora of RNAs involved in gene expression are particularly poorly understood. Intracellular single-molecule fluorescence microscopy provides a powerful emerging tool for probing the pertinent mechanistic parameters that govern cellular RNA functions, including those of protein coding messenger RNAs (mRNAs). Progress has been hampered, however, by the scarcity of efficient high-yield methods to fluorescently label RNA molecules without the need to drastically increase their molecular weight through artificial appendages that may result in altered behavior. Herein, we employ T7 RNA polymerase to body label an RNA with a cyanine dye, as well as yeast poly(A) polymerase to strategically place multiple 2'-azido-modifications for subsequent fluorophore labeling either between the body and tail or randomly throughout the tail. Using a combination of biochemical and single-molecule fluorescence microscopy approaches, we demonstrate that both yeast poly(A) polymerase labeling strategies result in fully functional mRNA, whereas protein coding is severely diminished in the case of body labeling.

Nuclease stability of boron-modified nucleic acids: application to label-free mismatch detection

5'-End boronic acid-modified oligonucleotides were evaluated against various nucleases at single and double stranded levels. The results show that these modifications induce a high resistance to degradation by calf-spleen and snake venom phosphodiesterases. More importantly, this eventually led to the development of a new label-free enzyme-assisted fluorescence-based method for single mismatch detection.

Site-Specific Difunctionalization of Structured RNAs Yields Probes for microRNA Maturation

Modified oligonucleotides bearing multiple functional labels are valuable tools in RNA biology. Efficient synthetic access to singly modified short DNAs and RNAs has been developed in the past years and paved the way to a first generation of oligonucleotide tools. Here, we describe an efficient procedure for the site-specific hetero bis-labeling of long RNAs. We exemplified the method with the preparation of Cy3/Cy5 pre-microRNAs labeled at selected internal sites as probes for microRNA maturation.

Pulsed EPR spectroscopy distance measurements of DNA internally labelled with Gd(3+)-DOTA

Gd(3+) is increasingly used in EPR spectroscopy due to its increased intracellular stability and signal-to-noise ratios. Here we present the incorporation of Gd(3+)-DOTA into internal positions in DNA. Distance measurements via pulsed Electron Paramagnetic Resonance (EPR) spectroscopy in vitro and in cellula proved enhanced stability and efficiency compared to nitroxide labels.

Azide phosphoramidite in direct synthesis of azide-modified oligonucleotides

Azide and phosphoramidite functions were found to be compatible within one molecule and stable for months in solution kept frozen at -20 °C. An azide-carrying phosphoramidite was used for direct introduction of multiple azide modifications into synthetic oligonucleotides. A series of azide-containing oligonucleotides were modified further using click reactions with alkynes.

Symmetrical and asymmetrical cyanine dyes. Synthesis, spectral properties, and BSA association study

New cyanines were prepared by an efficient and practical route with satisfactory overall yield from low-cost starting materials. The photophysical behavior of the cyanines was investigated using UV-vis and steady-state fluorescence in solution, as well as their association with bovine serum albumin (BSA) in phosphate buffer solution (PBS). No cyanine aggregation was observed in organic solvents or in phosphate buffer solution. The alkyl chain length in the quaternized nitrogen was shown to be fundamental for BSA detection in PBS in these dyes.

Efficient access to 3'-terminal azide-modified RNA for inverse click-labeling patterns

Labeled RNA becomes increasingly important for molecular diagnostics and biophysical studies on RNA with its diverse interaction partners, which range from small metabolites to large macromolecular assemblies, such as the ribosome. Here, we introduce a fast synthesis path to 3'-terminal 2'-O-(2-azidoethyl) modified oligoribonucleotides for subsequent bioconjugation, as exemplified by fluorescent labeling via Click chemistry for an siRNA targeting the brain acid-soluble protein 1 gene (BASP1). Importantly, the functional group pattern is inverse to commonly encountered alkyne-functionalized "click"-able RNA and offers increased flexibility with respect to multiple and stepwise labeling of the same RNA molecule. Additionally, our route opens up a minimal step synthesis of 2'-O-(2-aminoethyl) modified pyrimidine nucleoside phosphoramidites which are of widespread use to generate amino-modified RNA for N-hydroxysuccinimide (NHS) ester-based conjugations.

Synthesis of quaternary heterocyclic salts

The microwave synthesis of twenty quaternary ammonium salts is described. The syntheses feature comparable yields to conventional synthetic methods reported in the current literature with reduced reaction times and the absence of solvent or minimal solvent.

A retrievable and highly selective fluorescent probe for monitoring dihydrogen phosphate ions based on a naphthalimide framework

A novel selective fluorescent chemosensor based on naphthalimide derivatives (AN-SB) was synthesized and characterized. Once combined with Cu(2+), compound AN-SB could give rise to a visible yellow to orange color change and fluorescence quenching, while other metal ions showed subtle disturbance. The complex (AN-SB-Cu(2+)) formed by Cu(2+) and AN-SB displayed high specificity for H2PO4(-). Among the various anions, only H2PO4(-) induced the revival of color and fluorescence of AN-SB, resulting in "off-on" type sensing of H2PO4(-) anion. The signal transduction occured via reversible formation-separation of complex AN-SB-Cu(2+), however, slight changes were observed in the presence of other anions.

5'-deoxy-5'-hydrazinylguanosine as an initiator of T7 Rna polymerase-catalyzed transcriptions for the preparation of labeling-ready RNAs

5'-deoxy-5'-hydrazinylguanosine was incorporated into the 5'-termini of RNA transcripts using T7 RNA polymerase. Transcriptions provided 5'-hydrazinyl-RNA that was readily labeled and purified. The use of fluorophore-labeled material was validated in an endoribonuclease activity assay.

Click Chemistry – a Versatile Method for Nucleic Acid Labelling, Cyclisation and Ligation

The copper-catalysed [3+2] alkyne azide cycloaddition reaction (the CuAAC reaction) is the classic example of ‘click’ chemistry, a relatively new concept that has been influential in many areas of science. It is used in the nucleic acid field for DNA cross-linking, oligonucleotide ligation and cyclisation, DNA and RNA labelling, attaching DNA to surfaces, producing modified nucleobases and backbones, synthesising ribozymes and monitoring nucleic acid biosynthesis. More recently a related click reaction, the ring strain-promoted azide–alkyne [3+2] cycloaddition (SPAAC) reaction has been used successfully in DNA strand ligation and labelling. This does not require copper catalysis, and therefore has many potential uses in vivo. In this review we discuss recent developments in nucleic acid click chemistry and their applications in biology, biotechnology and nanotechnology.

A highly fluorescent DNA toolkit: synthesis and properties of oligonucleotides containing new Cy3, Cy5 and Cy3B monomers

Cy3B is an extremely bright and stable fluorescent dye, which is only available for coupling to nucleic acids post-synthetically. This severely limits its use in the fields of genomics, biology and nanotechnology. We have optimized the synthesis of Cy3B, and for the first time produced a diverse range of Cy3B monomers for use in solid-phase oligonucleotide synthesis. This molecular toolkit includes phosphoramidite monomers with Cy3B linked to deoxyribose, to the 5-position of thymine, and to a hexynyl linker, in addition to an oligonucleotide synthesis resin in which Cy3B is linked to deoxyribose. These monomers have been used to incorporate single and multiple Cy3B units into oligonucleotides internally and at both termini. Cy3B Taqman probes, Scorpions and HyBeacons have been synthesized and used successfully in mutation detection, and a dual Cy3B Molecular Beacon was synthesized and found to be superior to the corresponding Cy3B/DABCYL Beacon. Attachment of Cy3, Cy3B and Cy5 to the 5-position of thymidine by an ethynyl linker enabled the synthesis of an oligonucleotide FRET system. The rigid linker between the dye and nucleobase minimizes dye–dye and dye–DNA interactions and reduces fluorescence quenching. These reagents open up new future applications of Cy3B, including more sensitive single-molecule and cell-imaging studies.