Synthesis and evaluation of cyanine-styryl dyes with enhanced photostability for fluorescent DNA staining

Nucleic Acid-Templated Synthesis of Cationic Styryl Dyes in Vitro and in Living Cells

A novel method for synthesizing cationic styryl dyes through a nucleic acid-templated reaction has been developed. This approach overcomes issues associated with traditional synthesis methods, such as harsh conditions, low throughput, and wasteful chemicals. The presence of a nucleic acid template accelerated the styryl dye formation from quaternized heteroaromatic and cationic aldehyde substrates. These styryl dyes show remarkable optical properties change when bound to nucleic acids, hence the success of the synthesis could be readily monitored in situ by UV-Vis and fluorescence spectroscopy and the optical properties data were also observable at the same time. This method provides the desired products from a broad range of coupling partners. By employing different substrates and templates, it is possible to identify new dyes that can bind to a specific type of nucleic acid such as a G-quadruplex. The templated dye synthesis is also successfully demonstrated in live HeLa cells. This approach is a powerful tool for the rapid synthesis and screening of dyes specific for diverse types of nucleic acids or cellular organelles, facilitating new biological discoveries.

Effective synthesis, development and application of a highly fluorescent cyanine dye for antibody conjugation and microscopy imaging

An asymmetric cyanine-type fluorescent dye was designed and synthesized via a versatile, multi-step process, aiming to conjugate with an Her2+ receptor specific antibody by an azide-alkyne click reaction. The aromaticity and the excitation and relaxation energetics of the fluorophore were characterized by computational methods. The synthesized dye exhibited excellent fluorescence properties for confocal microscopy, offering efficient applicability in in vitro imaging due to its merits such as a high molar absorption coefficient (36 816 M-1 cm-1), excellent brightness, optimal wavelength (627 nm), larger Stokes shift (26 nm) and appropriate photostability compared to cyanines. The conjugated cyanine-trastuzumab was constructed via an effective, metal-free, strain-promoted azide-alkyne click reaction leading to a regulated number of dyes being conjugated. This novel cyanine-labelled antibody was successfully applied for in vitro confocal imaging and flow cytometry of Her2+ tumor cells.

Bright NIR-Emitting Styryl Pyridinium Dyes with Large Stokes' Shift for Sensing Applications

Two NIR-emitting donor-π-acceptor (D-π-A) type regioisomeric styryl pyridinium dyes (1a-1b) were synthesized and studied for their photophysical performance and environment sensitivity. The two regioisomers, 1a and 1b, exhibited interesting photophysical properties including, longer wavelength excitation (λex ≈ 530-560 nm), bright near-infrared emission (λem ≈ 690-720 nm), high-fluorescence quantum yields (ϕfl ≈ 0.24-0.72) large Stokes' shift (∆λ ≈ 150-240 nm) and high-environmental sensitivity. Probe's photophysical properties were studied in different environmental conditions such as polarity, viscosity, temperature, and concentration. Probes (1a-1b) exhibited noticeable changes in absorbance, emission and Stokes' shift while responding to the changes in physical environment. Probe 1b exhibited a significant bathochromic shift in optical spectra (∆λ ≈ 20-40 nm) compared to its isomer 1a, due to the regio-effect. Probes (1a-1b) exhibited an excellent ability to visualize bacteria (Bacillus megaterium, Escherichia coli), and yeast (Saccharomyces cerevisiae) via fluorescence microscopy.

Two-Factor Fluorogenicity of Tetrazine-Modified Cyanine-Styryl Dyes for Bioorthogonal Labelling of DNA

Two green fluorescent tetrazine-modified cyanine-styryl dyes were synthesized for bioorthogonal labelling of DNA by means of the Diels-Alder reaction with inverse electron demand. With DNA as target biopolymer the fluorescence of these dyes is released by two factors: (i) sterically by their interaction with DNA, and (ii) structurally via the conjugated tetrazine as quencher moiety. As a result, the reaction with bicyclononyne-modified DNA is significantly accelerated up to ≥284,000 M^-1  s^-1 , and the fluorescence turn-on is enhanced up to 560 by the two-factor fluorogenicity. These dyes are cell permeable even in low concentrations and undergo fluorogenic reactions with BCN-modified DNA in living HeLa cells. The two-factor fluorescence release improves the signal-to-noise ratio such that washing procedures prior to cell imaging are not needed, which is a great advantage for live cell imaging of DNA and RNA in the future.

Cationic styryl dyes for DNA labelling and selectivity toward cancer cells and Gram-negative bacteria

Fluorescence-based methods are important tools for the analysis of nucleic acids in vitro and in cells. In this study, two cationic cyanine-styryl derivatives were produced using a two-step synthesis. Their optical properties were evaluated in different solvents, and frontier molecular orbital theory was utilized to interpret the findings. The DNA binding of these molecules was investigated to show fluorescence intensification. The molecular docking of both dyes in DNA illustrated the relevance of the electrostatic interaction between the quaternary ammonium of both dyes and the phosphate of the DNA backbone. Last but not least, applications of the synthesized styryl dyes were demonstrated to be selective towards cancer cells and particular kinds of bacteria.

Hybridization-Sensitive Fluorescent Probes for DNA and RNA by a Modular "Click" Approach

Fluorescent DNA probes were prepared in a modular approach using the “click” post-synthetic modification strategy. The new glycol-based module and DNA building block place just two carbons between the phosphodiester bridges and anchor the dye by an additional alkyne group. This creates a stereocenter in the middle of this artificial nucleoside substitute. Both enantiomers and a variety of photostable cyanine–styryl dyes as well as thiazole orange derivatives were screened as “clicked” conjugates in different surrounding DNA sequences. The combination of the (S)-configured DNA anchor and the cyanylated cyanine–styryl dye shows the highest fluorescence light-up effect of 9.2 and a brightness of approximately 11,000 M^–1 cm^–1. This hybridization sensitivity and fluorescence readout were further developed utilizing electron transfer and energy transfer processes. The combination of the hybridization-sensitive DNA building block with the nucleotide of 5-nitroindole as an electron acceptor and a quencher increases the light-up effect to 20 with the DNA target and to 15 with the RNA target. The fluorescence readout could significantly be enhanced to values between 50 and 360 by the use of energy transfer to a second DNA probe with commercially available dyes, like Cy3.5, Cy5, and Atto590, as energy acceptors at the 5′-end. The latter binary probes shift the fluorescent readout from the range of 500–550 nm to the range of 610–670 nm. The optical properties make these fluorescent DNA probes potentially useful for RNA imaging. Due to the strong light-up effect, they will not require washing procedures and will thus be suitable for live-cell imaging.

Dicationic styryl dyes for colorimetric and fluorescent detection of nucleic acids

Nucleic acid staining dyes are important tools for the analysis and visualizing of DNA/RNA in vitro and in the cells. Nevertheless, the range of commercially accessible dyes is still rather limited, and they are often very costly. As a result, finding nontoxic, easily accessible dyes, with desirable optical characteristics remains important. Styryl dyes have recently gained popularity as potential biological staining agents with many appealing properties, including a straightforward synthesis procedure, excellent photostability, tunable fluorescence, and high fluorescence quantum yield in the presence of nucleic acid targets with low background fluorescence signals. In addition to fluorescence, styryl dyes are strongly colored and exhibit solvatochromic properties which make them useful as colorimetric stains for low-cost and rapid testing of nucleic acids. In this work, novel dicationic styryl dyes bearing quaternary ammonium groups are designed to improve binding strength and optical response with target nucleic acids which contain a negatively charged phosphate backbone. Optical properties of the newly synthesized styryl dyes have been studied in the presence and absence of nucleic acid targets with the aim to find new dyes that can sensitively and specifically change fluorescence and/or color in the presence of nucleic acid targets. The binding interaction and optical response of the dicationic styryl dyes with nucleic acid were superior to the corresponding monocationic styryl dyes. Applications of the developed dyes for colorimetric detection of DNA in vitro and imaging of cellular nucleic acids are also demonstrated.

Recent advances in bioprobes and biolabels based on cyanine dyes

As a functional dye, cyanine dye promotes the widespread application of bioprobes in the fields of medicine, genetics and environment, owing to its advantages of good photophysical properties, excellent biocompatibility and low toxicity to biological systems. Nowadays, it is mainly used in the fields of life sciences such as fluorescent labeling of biological macromolecules, disease diagnosis, immunoassay and DNA detection, all of which lie at the core of this review. First, we briefly introduced the characteristics and principles of the cyanine dye bioprobe. Afterward, we paid attention to the recent progress of cyanine dye bioprobes widely used in the 10 years from 2010 to 2020. The application of cyanine dyes as bioprobes with different identification elements, including enzymes, organelles, immunity and DNAs, was mainly summarized. Finally, this review gave an outlook on the future development trend of cyanine dye bioprobes. This facilitates the construction of a new type of multifunctional fluorescent probe and promotes its clinical application.

Organosulfur/selenium-based Highly Fluorogenic Molecular Probes for Live-Cell Nucleolus Imaging

We present rationally designed cationic organochalcogens highly selective to RNA. We have demonstrated that the conformational dynamics and subsequently the optical properties of these dyes can be controlled to facilitate efficient bioimaging. We report organoselenium and organosulfur-based cell-permeable red-emissive probes bearing favorable cyclic sidearm with potential for selective and high contrast imaging of cell nucleoli. The probes exhibit high quantum yield upon interaction with RNA in an aqueous solution. An in-depth multiscale simulation study reveals that the prominent rotational freezing of the electron-donating sidearm of the probes in the microenvironment of RNA helps in attaining more planar conformation when compared to DNA. It exerts a greater extent of intramolecular charge transfer and hence leads to enhanced fluorescence emission. A systematic structure-interaction relationship study highlighted the impact of heavy-chalcogens toward the improved emissive properties of the probes.

On-Strand Knoevenagel Insertion of a Hemicyanine Molecular Rotor Loop Residue for Turn-On Fluorescence Detection of Pb-Induced G-Quadruplex Rigidity

We demonstrate the ability to distinguish Pb²⁺ from K⁺ within the central cavity of the antiparallel G-quadruplex (GQ) DNA produced by the thrombin binding aptamer (TBA) using an internal molecular rotor fluorescent probe. An indole-aldehyde containing an acyclic N-glycol group was first employed in the on-strand Knoevenagel condensation with five different heterocyclic quaternary cationic acceptors to assess the molecular rotor character of the resulting cyanine-styryl dyes within duplex DNA. An indole-pyridinium (4PI) nucleobase surrogate displayed the greatest turn-on emission response to duplex formation and was thus inserted into the loop residues of TBA to monitor GQ-folding in the presence of Pb²⁺ versus K⁺. TBA-4PI exhibits turn-on emission upon Pb²⁺-binding with a brightness (ε·Φ_fl) of 9000 cm^-1 M^-1 compared to K⁺-binding (ε·Φ_fl ∼ 2000 cm^-1 M^-1) due to Pb²⁺-induced GQ rigidity with 4PI-G-tetrad stacking interactions. The Pb²⁺-bound TBA-4PI GQ also provides energy-transfer (ET) fluorescence with a diagnostic excitation at 310 nm for distinguishing Pb²⁺ from K⁺ within the antiparallel GQ. The TBA-4PI GQ affords the desired turn-on fluorescence response for detecting Pb²⁺ ions with an apparent dissociation constant (K_d) of 63 nM and a limit of detection (LOD) of 19 nM in an aqueous buffer. It can also distinguish Pb²⁺ (230 nM) from K⁺ (1.5 mM, 6500-fold excess) in an antiparallel GQ recognition motif without topology twitching.

Spectroscopic Studies on the Interaction of Naphthyridines with DNA and Fluorescent Detection of DNA in Agarose Gel

Four new naphthyridine derivatives (R1-R4) possessing amino acid or boronic acid moieties have been synthesized and characterized using ¹H and ¹³C NMR, FT-IR, and mass spectral techniques. The mechanism of binding of these probes with calf thymus DNA (CT-DNA) has been delineated through UV-Vis, fluorescence, and circular dichroism (CD) spectral techniques along with thermodynamic and molecular docking studies. Small hypochromicity in absorption maximum of the probes without any shift in wavelength of absorption suggests groove binding mode of interaction of these probes with CT-DNA, confirmed by CD and 1H NMR spectral data competitive binding assay with ethidium bromide (EB). CT-DNA quenches the fluorescence of these probes via a static quenching mechanism. In the case of R1 and R4, the observed ΔH^o < 0 and ΔS^o > 0suggest that these probes interact with CT-DNA through H-bonding and hydrophobic interactions, while in the interaction of R2 and R3, van der Walls and H-boding forces are found to be dominant (ΔH^o < 0 and ΔS^o < 0). Results of molecular docking investigations corroborate well with that of spectral studies, and these probes bind in the minor groove of DNA. These probes are found to be effective fluorescent staining agents for DNA in agarose gel in gel electrophoresis experiment with sensitivity comparable to that of EB, and DNA amounts as low as 37.5 ng are visually detectable in the gel.

Assembly and functionalization of supramolecular polymers from DNA-conjugated squaraine oligomers

DNA conjugated oligomers of organic molecules are candidates for applications in the materials and medical sciences, in diagnostics, in optical devices, for delivery or for the design of complex molecular architectures. Herein, we describe the synthesis and properties of DNA-conjugated squaraine (Sq) oligomers. The oligomers self-assemble into supramolecular polymers that are amenable to further functionalization via DNA hybridization, as shown by the attachment of gold nanoparticles (AuNPs).

The assembly of supramolecular polymers of DNA-linked squaraine oligomers and their subsequent derivatization is described.

Complexation-association-extraction spectrophotometric determination of Pt cations based on a multi-reagent analytical system with I- anions and 2-[2-[4-[(2-cyanoethyl)methylamino]phenyl]vinyl]-1,3,3-trimethyl-3H-indolium cations

A new multi-reagent analytical system with 2-[2-[4-[(2-cyanoethyl)methylamino]phenyl]vinyl]-1,3,3-trimethyl-3H-indolium chloride (CPVTI), which is a styryl hemicyanine cationic dye with good photostability and a high molar absorption coefficient, as its core is first established and utilized successfully to determine the content of Pt ions via a spectrophotometric method. The process involves two treatment steps: adding CPVTI and I solutions to the Pt solution to be detected, and then using butyl acetate for vortex liquid-liquid extraction. A Pt cation can be incorporated into the CPVTI cation with the help of an I^- anion, initially converting the Pt cation into a [PtI₆]^2- complex anion. After forming a [PtI₆^2-·2CPVTI⁺]_(aq) ion associate in the aqueous phase, the Pt cation can be extracted selectively by butyl acetate with maximum extraction efficiency, and exists as [PtI₆^2-·2CPVTI⁺]_(org) in the extract phase. Via the formation of the iodo-complex of Pt and its ion associate with CPVTI, and the extraction with butyl acetate, Pt is selectively partitioned into the butyl acetate extractant in a step-by-step manner with good interference resistance. In the CPVTI-Pt-I analytical system, the charge state of CPVTI is retained by adjustment with H₂SO₄; the monovalent CPVTI⁺ presents a strong spectrophotometric absorbance signal at 530 nm with long-term stability, which allows determination of the Pt content. The system shows a high molar absorption coefficient of 6.52 × 10⁴ L mol^-1 cm^-1 at 530 nm, a lower limit of detection of 0.07 mg L^-1, and a good Sandell's sensitivity of 0.0030 μg cm^-2. Mechanistic analysis of the establishment of the system, concentration optimization, standard working curve, system sensitivity and stability, resistance against interference from diverse metal ions, and practical applications are investigated and discussed.

Lighting Up the Thrombin-Binding Aptamer G-Quadruplex with an Internal Cyanine-Indole-Quinolinium Nucleobase Surrogate. Direct Fluorescent Intensity Readout for Thrombin Binding without Topology Switching

Fluorescent nucleobases represent an important class of molecular reporters of nucleic acid interactions. In this work, the advantages of utilizing a noncanonical fluorescent nucleobase surrogate for monitoring thrombin binding by the 15-mer thrombin binding aptamer (TBA) is presented. TBA folds into an antiparallel G-quadruplex (GQ) with loop thymidine (T) residues interacting directly with the protein in the thrombin-TBA complex. In the free GQ, T3 is solvent-exposed and does not form canonical base-pairs within the antiparallel GQ motif. Upon thrombin binding, T3 interacts directly with a hydrophobic protein binding pocket. Replacing T3 with a cyanine-indole-quinolinium (4QI) hemicyanine dye tethered to an acyclic 1,2-propanediol linker is shown to have minimal impact on GQ stability and structure with the internal 4QI displaying a 40-fold increase in emission intensity at 586 nm (excitation 508 nm) compared to the free dye in solution. Molecular dynamics (MD) simulations demonstrate that the 4QI label π-stacks with T4 and T13 within the antiparallel GQ fold, which is supported by strong energy transfer (ET) fluorescence from the GQ (donor) to the 4QI label (acceptor). Thrombin binding to 4QI-TBA diminishes π-stacking interactions between 4QI and the GQ structure to cause a turn-off emission intensity response with an apparent dissociation constant (K_d) of 650 nM and a limit of detection (LoD) of 150 nM. These features highlight the utility of internal noncanonical fluorescent surrogates for monitoring protein binding by GQ-folding aptamers in the absence of DNA topology switching.

Photobleaching of organic fluorophores: quantitative characterization, mechanisms, protection

Photochemical stability is one of the most important parameters that determine the usefulness of organic dyes in different applications. This Review addresses key factors that determine the dye photostability. It is shown that photodegradation can follow different oxygen-dependent and oxygen-independent mechanisms and may involve both ¹S₁-³T₁ and higher-energy ¹S_n-³T_n excited states. Their involvement and contribution depends on dye structure, medium conditions, irradiation power. Fluorescein, rhodamine, BODIPY and cyanine dyes, as well as conjugated polymers are discussed as selected examples illustrating photobleaching mechanisms. The strategies for modulating and improving the photostability are overviewed. They include the improvement of fluorophore design, particularly by attaching protective and anti-fading groups, creating proper medium conditions in liquid, solid and nanoscale environments. The special conditions for biological labeling, sensing and imaging are outlined.

Clickable styryl dyes for fluorescence labeling of pyrrolidinyl PNA probes for the detection of base mutations in DNA

Fluorescent hybridization probes are important tools for rapid, specific and sensitive analysis of genetic mutations. In this work, we synthesized novel alkyne-modified styryl dyes for conjugation with pyrrolidinyl peptide nucleic acid (acpcPNA) by click chemistry for the development of hybridization responsive fluorescent PNA probes. The free styryl dyes generally exhibited weak fluorescence in aqueous media, and the fluorescence was significantly enhanced (up to 125-fold) upon binding with DNA duplexes. Selected styryl dyes that showed good responses with DNA were conjugated with PNA via sequential reductive alkylation-click chemistry. Although these probes showed little fluorescence change when hybridized to complementary DNA, significant fluorescence enhancements were observed in the presence of structural defects including mismatched, abasic and base-inserted DNA targets. The largest increase in fluorescence quantum yield (up to 14.5-fold) was achieved with DNA carrying base insertion. Although a number of probes were designed to give fluorescence response to complementary DNA targets, probes that are responsive to mutations such as single nucleotide polymorphism (SNP), base insertion/deletion and abasic site are less common. Therefore, styryl-dye-labeled acpcPNA is a unique probe that is responsive to structural defects in the duplexes that may be further applied for diagnostic purposes.

Ligand-Induced G-Quadruplex Polymorphism: A DNA Nanodevice for Label-Free Aptasensor Platforms

G-Quadruplexes (GQs) serve as popular recognition elements for DNA aptasensors and are incorporated into a DNA nanodevice capable of controlled conformational changes to activate a sensing mechanism. Herein we highlight the utility of a GQ-GQ nanodevice fueled by GQ-specific ligands as a label-free aptasensor detection strategy. The concept was first illustrated utilizing the prototypical polymorphic human telomeric repeat sequence (H-Telo22, d[AG3(T2AG3)3]) that can undergo ligand-induced topology changes between antiparallel, parallel, or hybrid GQ structures. The H-Telo22-ligand interactions served as a model of the GQ-GQ nanodevice. The utility of the device in a real aptasensor platform was then highlighted utilizing the ochratoxin A (OTA) binding aptamer (OTABA) that folds into an antiparallel GQ in the absence and presence of target OTA. Three cationic fluorogenic ligands served as GQ-specific light-up probes and as potential fuel for the GQ-GQ nanodevice by producing an inactive GQ topology (parallel or hybrid) of OTABA. Our findings demonstrate efficient OTA-mediated dye displacement with excellent emission sensitivity for OTA detection when the fluorogenic dyes induce a topology change in OTABA (parallel or hybrid). However, when the fluorogenic dye fails to induce a conformational change in the antiparallel fold of OTABA, subsequent additions of OTA to the aptamer-dye complex results in poor dye displacement with weak emission response for OTA detection. These results are the first to exemplify a ligand-induced GQ-GQ nanodevice as an aptasensor mechanism and demonstrate diagnostic applications for topology-specific GQ binders.

Spectroscopic investigations on DNA binding profile of two new naphthyridine carboxamides and their application as turn-on fluorescent DNA staining probes

Two new 10-methoxydibenzo[b,h][1,6]naphthyridine-2-carboxamide derivatives (R1 and R2) have been synthesized and characterized using different spectral techniques. The binding of these probes with DNA was investigated using spectral (Electronic, fluorescence, ¹H NMR and circular dichroism) and molecular docking studies. These probes exhibited a strong fluorescence around 440 nm upon excitation around 380 nm. Electronic and competitive fluorescence titration studies, in HEPES [(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)] buffer/dimethyl sulfoxide (pH 7.4) medium, suggest that these probes bind strongly to DNA, which is substantiated by ¹H NMR study. The binding constants are calculated to be 5.3 × 10⁷ and 6.8 × 10⁶ M^-1 for R1 and R2, respectively. From the results of spectral studies, it is proposed that the mechanism of binding of these probes with DNA is through minor groove binding mode, which is further confirmed by circular dichroism and molecular docking studies. Initial cell viability screening using MTT (3-[4,5-methylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide) assay shows that normal Vero cells are viable towards these probes at nano molar concentration, which is the concentration range employed in the present study for DNA staining (IC₅₀ in the order of 0.023 mM). The enhancement in fluorescence intensity of these probes upon binding with DNA enables the staining of DNA in agarose gel in gel electrophoresis experiment. The sensitivity of these probes is comparable with that of ethidium bromide and DNA amounts as low as 4 nano gram are detectable.Communicated by Ramaswamy H. Sarma.

Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries

A library of 52 distyryl and 9 mono-styryl cationic dyes was synthesized and investigated with respect to their optical properties, propensity to aggregation in aqueous medium, and capacity to serve as fluorescence “light-up” probes for G-quadruplex (G4) DNA and RNA structures. Among the 61 compounds, 57 dyes showed preferential enhancement of fluorescence intensity in the presence of one or another G4-DNA or RNA structure, while no dye displayed preferential response to double-stranded DNA or single-stranded RNA analytes employed at equivalent nucleotide concentration. Thus, preferential fluorimetric response towards G4 structures appears to be a common feature of mono- and distyryl dyes, including long-known mono-styryl dyes used as mitochondrial probes or protein stains. However, the magnitude of the G4-induced “light-up” effect varies drastically, as a function of both the molecular structure of the dyes and the nature or topology of G4 analytes. Although our results do not allow to formulate comprehensive structure–properties relationships, we identified several structural motifs, such as indole- or pyrrole-substituted distyryl dyes, as well as simple mono-stryryl dyes such as DASPMI [2-(4-(dimethylamino)styryl)-1-methylpyridinium iodide] or its 4-isomer, as optimal fluorescent light-up probes characterized by high fluorimetric response (I/I₀ of up to 550-fold), excellent selectivity with respect to double-stranded DNA or single-stranded RNA controls, high quantum yield in the presence of G4 analytes (up to 0.32), large Stokes shift (up to 150 nm) and, in certain cases, structural selectivity with respect to one or another G4 folding topology. These dyes can be considered as promising G4-responsive sensors for in vitro or imaging applications. As a possible application, we implemented a simple two-dye fluorimetric assay allowing rapid topological classification of G4-DNA structures.

Bright red-emitting highly reliable styryl probe with large Stokes shift for visualizing mitochondria in live cells under wash-free conditions

Bright red-emitting pyridinium cyanine based styryl probe 2 is synthesized in good yields. Probe 2 demonstrated a large Stokes' shift (Δλ ≈ 128 nm, 4227 cm^-1 in DCM) and excellent fluorescent quantum yield (ϕ_fl ≈ 0.2 - 0.7) due to strong Intra-molecular charge transfer (ICT). Probe 2 found to exhibit exceptional selectivity for cellular mitochondria in both normal (COS-7) and cancer (A549) cell lines. Probe 2 is readily applicable as a "wash-free" dye to visualize mitochondria as it does not require post-staining washing prior to imaging. Styryl probe 2 also showed an excellent biocompatibility as the calculated LC₅₀ (lethal concentration, 50%) value was > 20 μM. Probe 2 emission did not show any interferences from anionic species or other biological molecules. Probe 2 is readily excitable (λ_ex ∼460 and λ_em ∼618 nm) with the available laser (454 nm) in commercial microscopes and thus it can be a useful probe for mitochondrial tracking in live cells.

Tuning the selectivity of N-alkylated styrylquinolinium dyes for sensing of G-quadruplex DNA

Selective and sensitive detection of G-quadruplex DNA structures is an important issue and attracts extensive interest. To this end, numerous small molecular fluorescent probes have been designed. Here, we present a series of N-alkylated styrylquinolinium dyes named Ls-1, Ls-2 and Ls-3 with varying side groups at the chain end. We found that these dyes exhibited different binding behaviors to DNAs, and Ls-2 with a sulfonato group at the chain end displayed sensitivity and selectivity to G-quadruplex DNA structures in vitro. The characteristics of this dye and its interaction with G-quadruplex DNA were comprehensively investigated by means of UV-vis spectrophotometry, fluorescence, circular dichroism and molecular docking. Furthermore, confocal fluorescence images and MTT assays indicated dye Ls-2 could pass through membrane and enter the living HepG2 cells with low cytotoxicity.

A new structure-activity relationship for cyanine dyes to improve photostability and fluorescence properties for live cell imaging

A new set of cyanine-indole dyes was synthesized, characterized by optical and cytotoxic properties and subsequently applied for live cell imaging. Furthermore, these dyes were postsynthetically linked covalently to the 2'-position of uridine anchors in presynthesized oligonucleotides using the copper(i)-catalyzed azide-alkyne cycloaddition in order to evaluate their photostability and imaging properties in living cells. The nucleophilicity at position C-2 of the indole part of the dyes was elucidated as key for a new structure-activity relationship that served as a rational guide to improve the photostability and optical properties of these green-emitting dyes for live cell imaging of nucleic acids. While the photostability rises exponentially with decreasing nucleophilicity, thermal bleaching experiments confirmed an opposite trend supposing that the superoxide radical anion is mainly responsible for the photobleaching of the dyes. Furthermore, the cytotoxicities of the dyes were tested in HeLa cells and moderate to low LD₅₀ values were obtained. This interdisciplinary strategy allowed us to identify one dye with excellent optical properties and even better photostability and decreased cytotoxicity compared to a cyanine-indole dye that bears an additional cyclooctatetraene group as a triplet state quencher.

Synthesis of Wavelength-Shifting Fluorescent DNA and RNA with Two Photostable Cyanine-Styryl Dyes as the Base Surrogate Pair

Two nucleic acid building blocks were synthesized, consisting of two photostable green‐ and red‐emitting cyanine–styryl dyes and (S)‐3‐amino‐1,2‐propanediol as a substitute for the ribofuranoside, and incorporated as base‐pair surrogates by using automated phosphoramidte chemistry in the solid phase. The optical properties and, in particular, the energy‐transfer properties were screened in a range of DNA duplexes, in which the “counter bases” of the two dyes were varied and the distance between the two dyes was enlarged to up to three intervening adenosine–thymidine pairs. The DNA duplex with the best optical properties and the best red/green emission ratio as the readout bore adenosine and thymidine opposite to the dyes, and the two dyes directly adjacent to each other as the base surrogate pair. This structural arrangement can be transferred to RNA to obtain similarly fluorescent RNA probes. Representatively, the positively evaluated DNA duplex was applied to verify the fluorescence readout in living HeLa cells by using fluorescence confocal microscopy.

A postsynthetically 2'-"clickable" uridine with arabino configuration and its application for fluorescent labeling and imaging of DNA

The arabino-configured analog of uridine with a propargyl group at the 2’-position was synthesized and incorporated into DNA by solid-phase chemistry. The fluorescence quantum yields of DNA strands that were postsynthetically modified by blue and green emitting cyanine-styryl dyes were improved due to the arabino-configured anchor. These oligonucleotides were used as energy transfer donors in hybrids with oligonucleotides modified with acceptor dyes that emit in the yellow-red range. These combinations give energy transfer pairs with blue–yellow, blue–red and green–red emission color changes. All combinations of arabino- and ribo-configured donor strands with arabino- and ribo-configured acceptor strands were evaluated. This array of doubly modified hybrids was screened by their emission color contrast and fluorescence quantum yield. Especially mixed combinations, that means donor dyes with arabino-configured anchor with acceptor dyes with ribo-configured anchor, and vice versa, showed significantly improved fluorescence properties. Those were successfully applied for fluorescent imaging of DNA after transport into living cells.

Emergence through delicate balance between the steric factor and molecular orientation: a highly bright and photostable DNA marker for real-time monitoring of cell growth dynamics

A bright and biostable molecular fluorogenic material for real-time monitoring of in vitro cellular growth dynamics.

Key Structural Elements of Unsymmetrical Cyanine Dyes for Highly Sensitive Fluorescence Turn-On DNA Probes

Unsymmetrical cyanine dyes, such as thiazole orange, are useful for the detection of nucleic acids with fluorescence because they dramatically enhance the fluorescence upon binding to nucleic acids. Herein, we synthesized a series of unsymmetrical cyanine dyes and evaluated their fluorescence properties. A systematic structure-property relationship study has revealed that the dialkylamino group at the 2-position of quinoline in a series of unsymmetrical cyanine dyes plays a critical role in the fluorescence enhancement. Four newly designed unsymmetrical cyanine dyes showed negligible intrinsic fluorescence in the free state and strong fluorescence upon binding to double-stranded DNA (dsDNA) with a quantum yield of 0.53 to 0.90, which is 2 to 3 times higher than previous unsymmetrical cyanine dyes. A detailed analysis of the fluorescence lifetime revealed that the dialkylamino group at the 2-position of quinoline suppressed nonradiative decay in favor of increased fluorescence quantum yield. Moreover, these newly developed dyes were able to stain the nucleus specifically in fixed HeLa cells examined by using a confocal laser-scanning microscope.

A large stokes-shifted fluorescent dye synthesized as a new probe for the determination of protein

A novel fluorescent dye, 1-(2-hydroxyethyl)-4-((E)-2-(3-benzothiazol-2yl-9-ethyl-carbazole-3yl)vinyl) pyridinium bromide, was synthesized for determination of protein and its structure was characterized by (1)H NMR. Photophysics of the new probe in different solvents has been delineated in this paper, the new fluorescent molecular dye exhibited a large stokes-shifted and fluorescence quantum yields in organic solvent. The photostability and thermostability of the new dye were also studied and the results suggested the stable was excellent. The interactions of the dye with bovine serum albumin (BSA) , Human serumal bumin (HSA) and calf thymus deoxyribonucleic acid (ctDNA) were studied by fluorescence and absorption spectroscopy. The binding constant for BSA, HSA and DNA were calculated to be 8.91 × 10(7), 1.86 × 10(6) and 2.9 × 10(4), respectively. The experimental results indicated a potential value of the new dye for biomarker.

Selenium Incorporated Cationic Organochalcogen: Live Cell Compatible and Highly Photostable Molecular Stain for Imaging and Localization of Intracellular DNA

Successful integration of selenium unit into a newly designed cationic chemical architecture led to the development of a highly photostable molecular maker PA5 to be used in fluorescence microscopy as cellular nucleus staining agent for longer duration imaging under continuous laser illumination. Adaptation of a targeted single-atom modification strategy led to the development of a series of proficient DNA light-up probes (PA1-PA5). Further, their comparative photophysical studies in the presence of DNA revealed the potential of electron rich heteroatoms of chalcogen family in improving binding efficiency and specificity of molecular probes toward DNA. The findings of cell studies confirmed the outstanding cell compatibility of probe PA5 in terms of cell permeability, biostability, and extremely low cytotoxicity. Moreover, the photostability experiment employing continuous laser illumination in solution phase as well as in cell assay (both fixed and live cells) revealed the admirable photobleaching resistance of PA5. Finally, while investigating the phototoxicity of PA5, the probe was found not to exhibit light-induced toxicity even when irradiated for longer duration. All these experimental results demonstrated the promising standing of PA5 as a futuristic cell compatible potential stain for bioimaging and temporal profiling of DNA.

Two wavelength-shifting molecular beacons for simultaneous and selective imaging of vesicular miRNA-21 and miRNA-31 in living cancer cells

Two molecular beacons were designed as complementary fluorescent imaging probes for miRNA-21 and miRNA-31. Both beacons were prepared by a combination of solid-phase protocol and Cu(i)-catalyzed cycloaddition chemistry. The four photostable and bright fluorophores were attached to 2'-positions in the stem part of the two beacons. One beacon was labeled by a green-to-red emitting and the other by a blue-to-yellow emitting energy transfer pair. This two by two combination yields the four color emission readout. In vitro experiments demonstrate rapid and highly selective opening of both molecular beacons upon addition of the complementary target RNA and excellent green : red and blue : yellow emission color contrasts. Confocal microscopy of selected cancer cell lines provides evidence that a four color imaging of versicular miRNA-21 and miRNA-31 can be achieved both selectively and simultaneously upon transfection by the beacons, and that the fluorescent readouts track well with miRNA levels determined by PCR.

Biomolecular recognition at the cellular level: geometrical and chemical functionality dependence of a low phototoxic cationic probe for DNA imaging

Potential application of a biocompatible and low phototoxic cationic stain with semilunar geometry for longer duration visualization of cellular DNA is reported.

Bright and photostable cyanine-styryl chromophores with green and red fluorescence colour for DNA staining

The synthesis and optical characterisation of a series of green- and red-emitting cyanine and cyanine-styryl dyes is presented that were developed based on the cyanine-indole-quinolinium and based on the thiazole red type structure. For the green emitting fluorophores the quinolinium part was replaced by a pyridinium group. The bridge to the indole group was attached either to the 2-position or to the 4-position of the pyridinium moiety. For the red-emitting dyes the connection to the indole moiety is at the 4-position of the quinolinium part. In each set of dyes a methyl group at the indole-NH and/or a phenyl group at the 2-position of the indole part were introduced to tune the optical properties and photostability. Additionally, two dyes were modified with a cyano group to tune the photophysical properties and to enhance the photostabilities. The developed dyes show good photostabilities and bright green or red fluorescence intensities in the presence of DNA. Thus, these dyes represent important and promising candidates for fluorescent molecular imaging of nucleic acids inside living cells.

Strand displacement and duplex invasion into double-stranded DNA by pyrrolidinyl peptide nucleic acids

The so-called acpcPNA system bears a peptide backbone consisting of 4'-substituted proline units with (2'R,4'R) configuration in an alternating combination with (2S)-amino-cyclopentane-(1S)-carboxylic acids. acpcPNA forms exceptionally stable hybrids with complementary DNA. We demonstrate herein (i) strand displacements by single-stranded DNA from acpcPNA-DNA hybrids, and by acpcPNA strands from DNA duplexes, and (ii) strand invasions by acpcPNA into double-stranded DNA. These processes were studied in vitro using synthetic oligonucleotides and by means of our concept of wavelength-shifting fluorescent nucleic acid probes, including fluorescence lifetime measurements that allow quantifying energy transfer efficiencies. The strand displacements of preannealed 14mer acpcPNA-7mer DNA hybrids consecutively by 10mer and 14mer DNA strands occur with rather slow kinetics but yield high fluorescence color ratios (blue : yellow or blue : red), fluorescence intensity enhancements, and energy transfer efficiencies. Furthermore, 14mer acpcPNA strands are able to invade into 30mer double-stranded DNA, remarkably with quantitative efficiency in all studied cases. These processes can also be quantified by means of fluorescence. This remarkable behavior corroborates the extraordinary versatile properties of acpcPNA. In contrast to conventional PNA systems which require 3 or more equivalents PNA, only 1.5 equivalents acpcPNA are sufficient to get efficient double duplex invasion. Invasions also take place even in the presence of 250 mM NaCl which represents an ionic strength nearly twice as high as the physiological ion concentration. These remarkable results corroborate the extraordinary properties of acpcPNA, and thus acpcPNA represents an eligible tool for biological analytics and antigene applications.

The effect of LNA nucleobases as enhancers for the binding of amiloride to an abasic site in DNA/DNA and DNA/RNA duplexes

We report on a significant effect of locked nucleic acid (LNA) nucleobases on the binding of amiloride for abasic site (AP)-containing DNA duplexes. Fluorescence titration experiments showed that the binding affinity of amiloride for the target thymine (T) opposite an AP site significantly improves for the DNA duplexes possessing LNA nucleobases that flank the AP site, compared to the corresponding normal DNA duplexes. In particular, LNA flanking nucleobases on both 5'- and 3'-sides of the AP site are found to be effective for the enhancement of the binding affinity. From thermodynamic characterization of the amiloride binding, the loss in the binding entropy is remarkably reduced for the LNA-containing DNA duplexes, which is indeed responsible for the enhanced affinity of amiloride. Moreover, such an effect of LNA nucleobases was also observed for amiloride binding to DNA/RNA hybrid duplexes.

Development of a wavelength-shifting fluorescent module for the adenosine aptamer using photostable cyanine dyes

DNA-based aptamers are commonly used recognition elements in biosensors for a range of target molecules. Here, the development of a wavelength-shifting optical module for a DNA-based adenosine-binding aptamer is described. It applies the combination of two photostable cyanine-styryl dyes as covalent modifications. This energy-transfer pair is postsynthetically attached to oligonucleotides via a copper(I)-catalyzed azide-alkyne cycloaddition by two structurally different approaches: 1) as nucleotide modifications at the 2'-position of uridines and 2) as nucleotide substitutions using (S)-amino-1,2-propanediol as acyclic linker between the phosphodiester bridges. Both dyes exhibit a remarkable photostability. A library of DNA aptamers consisting of different combinations of the two dyes in diagonal orientations were evaluated by their emission color contrast as readout. Further optimization led to aptasensors with improved fluorescent readout as compared with previously reported aptasensors. This approach described is synthetically facile using simple propargylated phosphoramidites as DNA building blocks. As such, this approach could be applied for other dyes and other chemical/biological applications.

Stability enhancement of fluorophores for lighting up practical application in bioimaging

In this Highlight, we emphasize some representative strategies including nanoparticle-encapsulating dyes, dye-doped nanoparticles and molecular engineering for stabilizing fluorophores.

Acridine orange coated magnetic nanoparticles for nucleus labeling and DNA adsorption

The magnetic-fluorescent nanoparticles are the integration of fluorophores and magnetic nanoparticles (MNP), which are superior to traditional single-modal nanoparticles. Here, we develop magnetic nanoparticles functionalized by acridine orange (ACO) for labeling nucleus and separating DNA. The ACO, a cell-permeant nucleic acid binding dye, is conjugated with amine on magnetic nanoparticles by glutaraldehyde-mediated coupling and characterized by TEM and FT-IR. Fluorescence spectroscopy, INCell analyzer, and confocal microscopy analyses confirmed the fluorescent property of ACO modified MNP. Furthermore, the modified magnetic nanoparticles showed strong intracellular fluorescence when incubated with 293T cells for a short period of time. The adsorption capacities measured at various concentrations showed enhanced adsorption capacities for double or single stranded DNA when compared to amine MNP conjugated with glutaraldehyde. The cell viability tests of the composite nanoparticles on 293T cells showed low cytotoxicity indicating the safeness of the nanoparticles. The modified magnetic nanoparticles pave a versatile platform for biological applications such as cell labeling and DNA adsorption.