Reversed Assembly of Dyes in an RNA Duplex Compared with Those in DNA

We prepared reversed dye clusters by hybridizing two RNA oligomers, each of which tethered dyes (Methyl Red, 4′‐methylthioazobenzene, and thiazole orange) on D ‐threoninols (threoninol nucleotides) at the center of their strands. NMR spectroscopic analyses revealed that two dyes from each strand were axially stacked in an antiparallel manner to each other in the duplex, and were located adjacent to the 3′‐side of a natural nucleobase. Interestingly, this positional relationship of the dyes was completely the opposite of that assembled in DNA that we reported previously: dyes in DNA were located adjacent to the 5′‐side of a natural nucleobase. This observation was also consistent with the circular dichroism of dimerized dyes in which the Cotton effect of the dyes (i.e., the winding properties of two dyes) was inverted in RNA relative to that in DNA. Further spectroscopic analyses revealed that clustering of the dyes on RNA duplexes induced distinct hypsochromicity and narrowing of the band, thus demonstrating that the dyes were axially stacked (i.e., H‐aggregates) even on an A‐type helix. On the basis of these results, we also prepared heterodimers of a fluorophore (thiazole orange) and quencher (Methyl Red) in an RNA duplex. Fluorescence from thiazole orange was found to be strongly quenched by Methyl Red due to the excitonic interaction, so that the ratio of fluorescent intensities of the RNA–thiazole orange conjugate with and without its complementary strand carrying a quencher became as high as 27. We believe that these RNA–dye conjugates are potentially useful probes for real‐time monitoring of RNA interference (RNAi) mechanisms.     

Mechanisms and advancement of antifading agents for fluorescence microscopy and single-molecule spectroscopy

Modern fluorescence microscopy applications go along with increasing demands for the employed fluorescent dyes. In this work, we compared antifading formulae utilizing a recently developed reducing and oxidizing system (ROXS) with commercial antifading agents. To systematically test fluorophore performance in fluorescence imaging of biological samples, we carried out photobleaching experiments using fixed cells labeled with various commonly used organic dyes, such as Alexa 488, Alexa 594, Alexa 647, Cy3B, ATTO 550, and ATTO 647N. Quantitative evaluation of (i) photostability, (ii) brightness, and (iii) storage stability of fluorophores in samples mounted in different antifades (AFs) reveal optimal combinations of dyes and AFs. Based on these results we provide guidance on which AF should preferably be used with a specific dye. Finally, we studied the antifading mechanisms of the commercial AFs using single-molecule spectroscopy and reveal that these empirically selected AFs exhibit similar properties to ROXS AFs.     

Keto‐benzo[h]‐Coumarin‐Based Near‐Infrared Dyes with Large Stokes Shifts for Bioimaging Applications

Fluorescence imaging is a promising tool for the visualization of biomolecules in living systems and there is great demand for new fluorescent dyes that absorb and emit in the near‐infrared (NIR) region. Herein, we constructed three new fluorescent dyes ( NBC dyes) based on keto‐benzo[h]coumarin ( k‐BC ) and benzopyrilium salts. These dyes showed large Stokes shifts (>100 nm) and NIR emission (>800 nm). The relationship between the structures and optical properties of these dyes was further investigated by using density functional theory calculations at the B3LYP/6‐3G level of theory. Fluorescence images indicated that the fabricated dyes exhibited good photostability and low cytotoxicity and, thus, have potential applications as imaging agents in living cells and animals.     

New 8-amino-BODIPY derivatives: surpassing laser dyes at blue-edge wavelengths

The development of highly efficient and stable blue‐emitting dyes to overcome some of the most important shortcomings of available chromophores is of great technological importance for modern optical, analytical, electronic, and biological applications. Here, we report the design, synthesis and characterization of new tailor‐made BODIPY dyes with efficient absorption and emission in the blue spectral region. The major challenge is the effective management of the electron‐donor strength of the substitution pattern, in order to modulate the emission of these novel dyes over a wide spectral range (430–500 nm). A direct relationship between the electron‐donor character of the substituent and the extension of the spectral hypsochromic shift is seen through the energy increase of the LUMO state. However, when the electron‐donor character of the substituent is high enough, an intramolecular charge‐transfer process appears to decrease the fluorescence ability of these dyes, especially in polar media. Some of the reported novel BODIPY dyes provide very high fluorescence quantum yields, close to unity, and large Stokes shifts, leading to highly efficient tunable dye lasers in the blue part of the spectrum; this so far remains an unexploited region with BODIPYs. In fact, under demanding transversal pumping conditions, the new dyes lase with unexpectedly high lasing efficiencies of up to 63 %, and also show high photostabilities, outperforming the laser action of other dyes considered as benchmarks in the same spectral region. Considering the easy synthetic protocol and the wide variety of possible substituents, we are confident that this strategy could be successfully extended for the development of efficient blue‐edge emitting materials and devices, impelling biophotonic and optoelectronic applications.     

Design of a Near Infrared Fluorescent Ureter Imaging Agent for Prevention of Ureter Damage during Abdominal Surgeries

The inadvertent severing of a ureter during surgery occurs in as many as 4.5% of colorectal surgeries. To help prevent this issue, several near-infrared (NIR) dyes have been developed to assist surgeons with identifying ureter location. However, the majority of these dyes exhibit at least some issue that precludes their widespread usage such as high levels of uptake in other tissues, overlapping emission wavelengths with other NIR dyes used for other fluorescence-guided surgeries, and/or rapid excretion times through the ureters. To overcome these limitations, we have synthesized and characterized the spectral properties and biodistribution of a new series of PEGylated UreterGlow derivatives. The most promising dye, UreterGlow-11 was shown to almost exclusively excrete through the kidneys/ureters with detectable fluorescence observed for at least 12 h. Additionally, while the excitation wavelength is similar to that of other NIR dyes used for cancer resections, the emission is shifted by ~30 nm allowing for discrimination between the different fluorescence-guided surgery probes. In conclusion, these new UreterGlow dyes show promising optical and biodistribution characteristics and are good candidates for translation into the clinic.     

A structural remedy toward bright dipolar fluorophores in aqueous media

The donor–acceptor (D–A) type dipolar fluorophores, an important class of luminescent dyes with two-photon absorption behaviour, generally emit strongly in organic solvents but poorly in aqueous media. To understand and enhance the poor emission behaviour of dipolar dyes in aqueous media, we undertake a rational approach that includes a systematic structure variation of the donor, amino substituent of acedan, an important two-photon dye. We identify several factors that influence the emission behaviour of the dipolar dyes in aqueous media through computational and photophysical studies on new acedan derivatives. As a result, we can make acedan dyes emit bright fluorescence under one- and two-photon excitation in aqueous media by suppressing the liable factors for poor emission: 1,3-allylic strain, rotational freedom, and hydrogen bonding with water. We also validate that these findings can be generally extended to other dipolar fluorophores, as demonstrated for naphthalimide, coumarin and (4-nitro-2,1,3-benzoxadiazol-7-yl)amine (NBD) dyes. The new acedan and naphthalimide dyes thus allow us to obtain much brighter two-photon fluorescent images in cells and tissues than in their conventional forms. As an application of these findings, a thiol probe is synthesized based on a new naphthalimide dye, which shows greatly enhanced fluorescence from the widely used N,N-dimethyl analogue. The results disclosed here provide essential guidelines for the development of efficient dipolar dyes and fluorescence probes for studying biological systems, particularly by two-photon microscopy.     

Reduced graphene oxide as capturer of dyes and electrons during photocatalysis: surface wrapping and capture promoted efficiency

To elucidate the roles of graphene in photoelectric events and mass transfer during photocatalytic process is important for engineering graphene-semiconductor hybrid photocatalyst. Here, we demonstrated reduced graphene oxide (RGO) capturing dyes and photoinduced electrons during photocatalytic degradation of organic dyes in water. It captures dyes from water through adsorption and desorption irreversible hysteresis, and captures photoinduced electrons from semiconductor through surface junction. The RGO was attached to the surface of TiO(2) in the form of surface wrapping. After one-step photocatalytic reduction of graphene oxide (GO) and TiO(2) in ethanol-water solvent under UV irradiation, the RGO wrapped TiO(2) hybrid (graphene-w-TiO(2)) photocatalyst was obtained. Using visible absorption spectroscopy, we also demonstrated these captured dyes were degraded during photocatalysis. The photocatalytic test showed the RGO significantly improved the photocatalytic activity of this hybrid photocatalyst.     

Protein-enhanced photoreactivity--dye promoted polymerization of acrylates

The photoinduced polymerization of acrylic monomers using dyes in a protein-restricted medium is reported. We studied dyes of different families as potential polymerization catalysts, exploiting the observation that the photophysical properties of some dyes are altered when bound to biopolymers. The light induced polymerization of acrylic monomers in the presence of bovine serum albumin or gelatin using triphenylmethane and azo dyes proceeded smoothly. Using GE Miser 120 W spotlights as a convenient illumination source, we found polymerization could be achieved in some cases within 60 min of irradiation. The polymerization rates were found to be dependent on the concentrations of the dye and the protein. In the absence of protein or dye polymerization was virtually non-existent. When the reaction mixture was blanketed with nitrogen, polymerization was observed to be faster than that that in air equilibrated samples. We believe these photopolymerizations may proceed via a free-radical pathway. Our results suggest the possible role of some of these dyes as polymerization catalysts, though they had previously seemed inert in fluid solutions.     

Optimization of the preparation of glass-coated, dye-tagged metal nanoparticles as SERS substrates

Dye-tagged metal nanoparticles are of significant interest in SERS-based sensitive detection applications. Coating these particles in glass results in an inert spectral tag that can be used in applications such as flow cytometry with significant multiplexing potential. Maximizing the SERS signal obtainable from these particles requires care in partitioning available nanoparticle surface area (binding sites) between the SERS dyes and the functionalized silanes necessary for anchoring the glass coating. In this article, we use the metal-mediated fluorescence quenching of SERS dyes to measure surface areas occupied by both dyes and silanes and thus examine SERS intensities as a function of both dye and silane loading. Notably, we find that increased surface occupation by silane increases the aggregative power of added dye but that decreasing the silane coverage allows a greater surface concentration of dye. Both effects increase the SERS intensity, but obtaining the optimum SERS intensity will require balancing aggregation against surface dye concentration.     

Longitudinal diffusion behavior of hemicyanine dyes across phospholipid vesicle membranes as studied by second-harmonic generation and fluorescence spectroscopies

The adsorption and longitudinal diffusion behaviors of a series of hemicyanine dyes to phospholipid vesicle membranes were studied by second-harmonic generation (SHG) and fluorescence spectroscopies. It was observed that the longitudinal diffusion of cationic hemicyanine dyes takes place immediately after the initial adsorption of these dyes to the outer surface of the vesicle membrane. In contrast, hardly any amount of a zwitterionic hemicyanine dye with a sulfonate group diffused across the vesicle membrane within the measurement time (<2000 s). Based on the difference in the time-course responses of SHG and fluorescence spectroscopies for all of the hemicyanine dyes tested, we propose that hydration of the sulfonate group is mainly responsible for the low diffusivity of the zwitterionic hemicyanine dye.     

新型水溶性荧光标示剂吲哚方酸菁染料的合成及光谱性能

用方酸与不同的N烷基取代吲哚啉季铵盐缩合制备了一系列对称的水溶性方酸菁染料. 通过核磁共振氢谱和质谱对合成的染料结构进行了表征, 研究了它们在不同溶剂中的吸收和发射光谱. 结果表明, 随着溶剂极性的增大, 染料的吸收光谱发生蓝移, 表现为负向溶剂化效应, 在极性溶剂中的荧光量子产率比在水中的大. 考察了N位取代基对染料水溶液光稳定性的影响, 结果表明在吲哚环N原子上引入较大的苄基有助于提高光稳定性, 且随着苄基上取代基吸电子能力的增强, 染料的光稳定性增强.     

p-型和pn-型染料敏化太阳能电池

针对 (1) p-型染料敏化太阳能电池(DSCs)存在的科学问题, 即光阴极染料的吸附量偏低和电池内部的暗反应比较严重和(2) pn-型DSCs存在的光阳极和光阴极不匹配等问题, 从电极、染料和电解质三个方面系统综述了p-型和pn-型DSCs的研究进展并分析了问题可行的解决方案, 最后对p-型和pn-型DSCs的发展前景进行了展望.     

Change of Boron Substitution Improves the Lasing Performance of Bodipy Dyes: A Mechanistic Rationalisation

Bodipy laser dyes are highly efficient but degrade rapidly in solution by reacting with in situ generated singlet oxygen (¹O₂). To increase the lasing lifetimes of these dyes, we have designed and synthesised two different congeners of the widely studied Pyrromethene 567 (PM567) by substitution at the boron centre and/or at both the boron centre and the meso position. The two new dyes showed high lasing efficiencies with increased photostability. The results of theoretical and pulse radiolysis studies revealed that the substitution at the boron centre reduced the ¹O₂ generation capacity of these dyes as well as their rate of reaction with ¹O₂, thereby enhancing their lifetimes even under lasing conditions.     

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.     

Tuning the Cellular Uptake and Retention of Rhodamine Dyes by Molecular Engineering for High-Contrast Imaging of Cancer Cells

Probes allowing high-contrast discrimination of cancer cells and effective retention are powerful tools for the early diagnosis and treatment of cancer. However, conventional small-molecule probes often show limited performance in both aspects. Herein, we report an ingenious molecular engineering strategy for tuning the cellular uptake and retention of rhodamine dyes. Introduction of polar aminoethyl leads to the increased brightness and reduced cellular uptake of dyes, and this change can be reversed by amino acetylation. Moreover, these modifications allow cancer cells to take up more dyes than normal cells (16-fold) through active transport. Specifically, we further improve the signal contrast (56-fold) between cancer and normal cells by constructing activatable probes and confirm that the released fluorophore can remain in cancer cells with extended time, enabling long-term and specific tumor imaging.     

Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series**

The use of fluorescence techniques has an enormous impact on various research fields including imaging, biochemical assays, DNA-sequencing and medical technologies. This has been facilitated by the development of numerous commercial dyes with optimized photophysical and chemical properties. Often, however, information about the chemical structures of dyes and the attached linkers used for bioconjugation remain a well-kept secret. This can lead to problems for research applications where knowledge of the dye structure is necessary to predict or understand (unwanted) dye-target interactions, or to establish structural models of the dye-target complex. Using a combination of optical spectroscopy, mass spectrometry, NMR spectroscopy and molecular dynamics simulations, we here investigate the molecular structures and spectroscopic properties of dyes from the Alexa Fluor (Alexa Fluor 555 and 647) and AF series (AF555, AF647, AFD647). Based on available data and published structures of the AF and Cy dyes, we propose a structure for Alexa Fluor 555 and refine that of AF555. We also resolve conflicting reports on the linker composition of Alexa Fluor 647 maleimide. We also conducted a comprehensive comparison between Alexa Fluor and AF dyes by continuous-wave absorption and emission spectroscopy, quantum yield determination, fluorescence lifetime and anisotropy spectroscopy of free and protein-attached dyes. All these data support the idea that Alexa Fluor and AF dyes have a cyanine core and are a derivative of Cy3 and Cy5. In addition, we compared Alexa Fluor 555 and Alexa Fluor 647 to their structural homologs AF555 and AF(D)647 in single-molecule FRET applications. Both pairs showed excellent performance in solution-based smFRET experiments using alternating laser excitation. Minor differences in apparent dye-protein interactions were investigated by molecular dynamics simulations. Our findings clearly demonstrate that the AF-fluorophores are an attractive alternative to Alexa- and Cy-dyes in smFRET studies or other fluorescence applications.     

Cyanide sensing with organic dyes: studies in solution and on nanostructured Al2O3 surfaces

The synthesis of two new azo phenyl thiourea compounds and their optical response to different anions is reported herein. Solution studies in methanol indicate that cyanide induces a colour change in these dyes (whereas no changes are observed in the presence of other anions, such as F(-), Cl(-), Br(-), CH(3)COO(-), H(2)PO(4) (-), HSO(4) (-)). Interestingly, in DMSO these dyes are responsive not only to cyanide, but also to fluoride, acetate and dihydrogen phosphate. Each of these anions induces a different colour change. In the second part of the paper, we report the attachment of one of these dyes onto nanostructured TiO(2) and Al(2)O(3) films. The stability of these sensitised films to pH was studied and we concluded that the sensitised Al(2)O(3) films are more robust, and hence, better than the TiO(2) for anion sensing. The dye-sensitised Al(2)O(3) films were immersed in solutions of different anions and their response studied. The films can detect cyanide down to 3 ppm in aqueous solution with relatively good selectivity over other anions.     

A comparative study of assembly and disassembly process of dimeric and monomeric cyanine dyes with DNA templates

H-aggregates of dimeric cyanine dyes (TC-P4) formed in PBS could be disassembled by G-quadruplex into dimer and/or monomer, resulting in higher fluorescent selectivity than its corresponding monomer (TC).     

Coumarin-based two-photon AIE fluorophores: Photophysical properties and biological application

Based on the coumarin skeleton, we deliberately designed two groups of fluorophores, termed as Coum-R and Naph-Coum-R, using the diphenylamino group as the electron donor, which displayed long-wavelength emissions (red spectral region), large Stokes shift (up to 204 nm), superior AIE performance, and large two-photon absorbance cross-sections (as high as 365 GM). The electron-withdrawing substituents at the 3-position of these dyes could induce a significant red-shift in their emission spectra. Preliminary imaging experiments demonstrated the capability of these dyes as two-photon fluorophores for specifically staining lipid droplets in living cells.