Fluorescent sensor for Cu2+ with a tunable emission wavelength

A concept of fluorescent metal ion sensing with an easily tunable emission wavelength is presented and its principle demonstrated by detection of Cu(2+). A fluorescein dye was chemically modified with a metal chelating group and then attached to the terminus of ss-DNA. This was combined with a complementary ss-DNA modified with another fluorescent dye (ATTO 590), emitting at a longer wavelength. In the assembled duplex, fluorescence resonance energy transfer (FRET) between the fluorescein donor (excited at 470 nm) and the ATTO 590 acceptor (emitting at 624 nm) is observed. Proper positioning within the rigid DNA double helix prevents intramolecular contact quenching of the two dyes. Coordination of paramagnetic Cu(2+) ions by the chelating unit of the sensor results in direct fluorescence quenching of the fluorescein dye and indirect (by loss of FRET) quenching of the ATTO 590 emission at 624 nm. As a result, emission of the acceptor dye can be used for monitoring of the concentration of Cu(2+), with a 20 nM detection limit. The emission wavelength is readily tuned by replacement of ATTO-DNA by other commercially available DNA-acceptor dye conjugates. Fluorescent metal ion sensors emitting at >600 nm are very rare. The possibility of tuning the emission wavelength is important with respect to the optimization of this sensor type for application to biological samples, which usually show broad autofluorescence at <550 nm.     

Environment-sensitive fluorophores with benzothiadiazole and benzoselenadiazole structures as candidate components of a fluorescent polymeric thermometer

An environment-sensitive fluorophore can change its maximum emission wavelength (λ(em)), fluorescence quantum yield (Φ(f)), and fluorescence lifetime in response to the surrounding environment. We have developed two new intramolecular charge-transfer-type environment-sensitive fluorophores, DBThD-IA and DBSeD-IA, in which the oxygen atom of a well-established 2,1,3-benzoxadiazole environment-sensitive fluorophore, DBD-IA, has been replaced by a sulfur and selenium atom, respectively. DBThD-IA is highly fluorescent in n-hexane (Φ(f) =0.81, λ(em) =537?nm) with excitation at 449?nm, but is almost nonfluorescent in water (Φ(f) =0.037, λ(em) =616?nm), similarly to DBD-IA (Φ(f) =0.91, λ(em) =520?nm in n-hexane; Φ(f) =0.027, λ(em) =616?nm in water). A similar variation in fluorescence properties was also observed for DBSeD-IA (Φ(f) =0.24, λ(em) =591?nm in n-hexane; Φ(f) =0.0046, λ(em) =672?nm in water). An intensive study of the solvent effects on the fluorescence properties of these fluorophores revealed that both the polarity of the environment and hydrogen bonding with solvent molecules accelerate the nonradiative relaxation of the excited fluorophores. Time-resolved optoacoustic and phosphorescence measurements clarified that both intersystem crossing and internal conversion are involved in the nonradiative relaxation processes of DBThD-IA and DBSeD-IA. In addition, DBThD-IA exhibits a 10-fold higher photostability in aqueous solution than the original fluorophore DBD-IA, which allowed us to create a new robust molecular nanogel thermometer for intracellular thermometry.     

Development of Photoactivated Fluorescent N‐Hydroxyoxindoles and Their Application for Cell‐Selective Imaging

Photoactivatable fluorophores are essential tools for studying the dynamic molecular interactions within important biological systems with high spatiotemporal resolution. However, currently developed photoactivatable fluorophores based on conventional dyes have several limitations including reduced photoactivation efficiency, cytotoxicity, large molecular size, and complicated organic synthesis. To overcome these challenges, we herein report a class of photoactivatable fluorescent N‐hydroxyoxindoles formed through the intramolecular photocyclization of substituted o‐nitrophenyl ethanol (ONPE). These oxindole fluorophores afford excellent photoactivation efficiency with ultra‐high fluorescence enhancement (up to 800‐fold) and are small in size. Furthermore, the oxindole derivatives show exceptional biocompatibility by generating water as the only photolytic side product. Moreover, structure–activity relationship analysis clearly revealed the strong correlation between the fluorescent properties and the substituent groups, which can serve as a guideline for the further development of ONPE‐based fluorescent probes with desired photophysical and biological properties. As a proof‐of‐concept, we demonstrated the capability of a new substituted ONPE that has an uncaging wavelength of 365–405 nm and an excitation/emission at 515 and 620 nm, for the selective imaging of a cancer cell line (Hela cells) and a human neural stem cell line (hNSCs).     

Absorption and fluorescence spectral characteristics of norepinephrine,epinephrine, isoprenaline,methyl dopa,terbutaline and orciprenaline drugs

The absorption and fluorescence spectral characteristics of norepinephrine, epinephrine, isoprenaline, methyl dopa, orciprenaline and terbutaline have been investigated for levels of different pH and β-cyclodextrin (β-CD). The inclusion processes are discussed based on absorption, emission and semiempirical quantum mechanical calculations (CAChe – DFT). The pH study reveals that, deprotonation takes place in the CHOH group and the longer wavelength emission at 450?nm is due to intramolecular proton transfer. The β-CD study shows that the above-mentioned drugs form 1:1 inclusion complexes. Single-emission maximum in water (～316?nm) and dual emission (316?nm, 450?nm) in β-CD is noticed for drugs. In the β-CD solutions, the shorter wavelength fluorescence intensity is regularly decreased and longer wavelength fluorescence intensity is increased. The alkyl chain and the hydroxyl group are present in the interior and hydrophilic parts of the β-CD cavity, respectively.     

Ensemble and single-molecule fluorescence spectroscopy of a calcium-ion indicator dye

The spectroscopic properties of Calcium Green 2 (CG-2), a dual-fluorophore Ca(2+) indicator dye, were characterized by a combination of steady state and time-resolved ensemble spectroscopic measurements, molecular mechanics calculations and single-molecule fluorescence spectroscopy. It was found that in Ca(2+) free solutions, CG-2 exists primarily as a highly quenched intramolecular dimer, but when bound to Ca(2+), the molecule adopts an extended, fluorescent conformation. The difference in emission properties of these two CG-2 conformations is explained in terms of simple exciton theory. Through single-molecule fluorescence measurements, we have shown that the bulk increase in ensemble fluorescence intensity correlates with a simple statistical increase in the number of fluorescent molecules in solution. In addition, we have also observed that the majority of CG-2 molecules photobleach in a single step, despite the molecule possessing two distinct fluorophores. A small fraction of molecules photobleach in multiple steps or show a series of transitions between emissive and nonemissive fluorescent states ("blinking"). We rationalize these photophysical phenomena using a simple model based on dipole-dipole F?rster coupling between fluorophores in conjunction with irreversible photodamage to one of the constituent chromophores.     

Study of the fluorescent properties of partially hydrogenated 1,1'-bi-2-naphthol-amine molecules and their use for enantioselective fluorescent recognition

The fluorescent properties of a series of H(8)BINOL-amine compounds are investigated. It is revealed that the intramolecular hydrogen bonds of these compounds contribute to the shift of the emission of their H(8)BINOL unit to a much longer wavelength. That is, the emission of H(8)BINOL is at λ = 323 nm, but that of the H(8)BINOL-amino alcohol (S)-5 is at λ = 390 nm. Binding of (S)-5 with mandelic acid suppresses its intramolecular hydrogen bonding and restores the short wavelength emission of the H(8)BINOL unit. When (S)-5 (1.0 × 10(-4) in CH(2)Cl(2)) was treated with (R)-mandelic acid (4.0 × 10(-3)), a large fluorescence enhancement at the short wavelength (λ(emi) = 330 nm) was observed with I(R)/I(0) = 11.7. When (S)-MA was used under the same conditions, the enhancement at the short wavelength emission was much smaller. Thus, a good enantioselective fluorescent response was observed with ef =3.5 [ef: enantioselective fluorescence enhancement ratio = (I(R) - I(0))/(I(S) - I(0))]. This study demonstrates that the H(8)BINOL-based molecules are promising as a new class of enantioselective fluorescent sensors.     

Component analysis of the fluorescence spectra of a lignin model compound

In order to test whether lignin fluorescence originates from discrete fluorophores, fluorescence emission spectra of the lignin model dehydrogenative polymer (DHP) were analyzed by the band deconvolution method and time-resolved analysis of both the excitation and emission spectra. Two series of 22 fluorescence emission spectra of DHP in chloroform/methanol (3:1, v/v) solution, and as a solid suspension in water, were deconvoluted into three fluorescence and one Raman Gaussian components. Emission spectra were obtained by stepwise variation of the excitation wavelength from 360 to 465 nm. Deconvolution was performed by nonlinear fitting of all three Gaussian parameters: area, width and position. Position of all components in a series was treated as a random variable and its approximate probability distribution (APD) calculated from a series of histograms with increasing number of abscissa intervals. A five peak multimodal APD profile was obtained for both series of DHP emission spectra. The mean fluorescence lifetime varied with wavelength both in the emission and the excitation decay-associated spectra (DAS), where four kinetic components were resolved. The shapes of the excitation spectra of the four components were quite different and gradually shifted bathochromically. The multicomponent nature of the DHP emission spectra along with the changes in the mean fluorescence lifetime and the form of the excitation DAS of the four components give evidence of the heterogeneous origin of fluorescent species emitting in the visible.     

Genetically encoded fluorescent reporters of histone methylation in living cells

We report the design and characterization of two genetically encoded fluorescent reporters of histone protein methylation. The reporters are four-part chimeric proteins consisting of a substrate peptide from the N-terminus of histone H3 fused to a chromodomain (a natural methyllysine-specific recognition domain), sandwiched between a fluorescence resonance energy transfer (FRET)-capable pair of fluorophores, cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP). Enzymatic methylation by a methyltransferase induces complexation of the methylated substrate peptide to the chromodomain, changing the FRET level between the flanking CFP and YFP domains. Reporters developed using the chromodomains from HP1 and Polycomb respond to enzymatic methylation at the lysine 9 and lysine 27 positions of histone H3, respectively, giving 60% and 28% YFP/CFP emission ratio increases in vitro or in single living cells. These reporters should be useful for studying gene silencing and X-chromosome inactivation with high spatial and temporal resolution in intact cells and may also aid in the search for conjectured histone demethylase activity.     

Synthesis and Photophysical Properties of a Series of Cyclopenta[b]naphthalene Solvatochromic Fluorophores

The synthesis and photophysical properties of a series of naphthalene-containing solvatochromic fluorophores are described within. These novel fluorophores are prepared using a microwave-assisted dehydrogenative Diels-Alder reaction of styrene, followed by a palladium-catalyzed cross coupling reaction to install an electron donating amine group. The new fluorophores are structurally related to Prodan. Photophysical properties of the new fluorophores were studied and intriguing solvatochromic behavior was observed. For most of these fluorophores, high quantum yields (60-99%) were observed in methylene chloride in addition to large Stokes shifts (95-226 nm) in this same solvent. As the solvent polarity increased, so did the observed Stokes shift with one derivative displaying a Stokes shift of ～300 nm in ethanol. All fluorophore emission maxima, and nearly all absorption maxima were significantly red-shifted when compared to Prodan. Shifting the absorption and emission maxima of a fluorophore into the visible region increases its utility in biological applications. Moreover, the cyclopentane portion of the fluorophore structure provides an attachment point for biomolecules that will minimize disruptions of the photophysical properties.     

Color-Tunable Indolizine-Based Fluorophores and Fluorescent pH Sensor

A new fluorescent indolizine-based scaffold was developed using a straightforward synthetic scheme starting from a pyrrole ring. In this fluorescent system, an N,N-dimethylamino group in the aryl ring at the C-3 position of indolizine acted as an electron donor and played a crucial role in inducing a red shift in the emission wavelength based on the ICT process. Moreover, various electron-withdrawing groups, such as acetyl and aldehyde, were introduced at the C-7 position of indolizine, to tune and promote the red shift of the emission wavelength, resulting in a color range from blue to orange (462–580 nm). Furthermore, the ICT effect in indolizine fluorophores allowed the design and development of new fluorescent pH sensors of great potential in the field of fluorescence bioimaging and sensors.     

Review: fluorescent cyclodextrins for molecule sensing

Cyclodextrins (CDs), which are spectroscopically inert, were converted into fluorescent CDs by modification with one or two fluorophores. Many fluorescent CDs changed the fluorescent intensities upon addition of guest compounds, causing the locational change of the fluorophore mostly from inside to outside of the CD cavities. On this basis, the fluorescent CDs were used as fluorescent chemosensors for molecule recognition. Modified CDs bearing two naphthalene or pyrene moieties exhibit intramolecular excimer emission and their guest-responsive excimer intensity variations were used for molecule sensing. Fluorescent CDs bearing a dansyl moiety decreased the fluorescence intensity upon guest addition, reflecting the environmental change around the fluorophore from the hydrophobic interior of the CD cavities to bulk water solution. Modified CDs bearing a p-N,N-dimethylaminobenzoyl (DMAB) moiety exhibit dual emissions from nonpolar planar (NP) and twisted intramolecular charge transfer (TICT) excited states, and the TICT emission intensity was useful for sensing molecules. A biotin-bound DMAB system was also constructed, and the presence of the protein (avidin) was found to enhance the NP fluorescence. This avidin-bound DMAB system showed higher sensitivities and stronger binding ability for guest species than the system without avidin.     

聚对苯二甲酸乙二酯荧光光谱的激发波长依赖性研究

聚对苯二甲酸乙二酯（PET）的荧光光谱已经得到了相当广泛和深入的研究,当激发光波长位于310～360nm时,可以观察到位于360～390nm范围的荧光发光,这部分荧光的来源有很多争议,至今未取得一致的看法,有作者认为,此处的荧光发光是PET链段上苯环之间的相互作用形成的基态二聚体（ground-state dimer）引起的发光;还有人认为这是苯环基团之间相互作用形成的激基缔合物的发光（excimeric emission）。     

Optimization of pairings and detection conditions for measurement of FRET between cyan and yellow fluorescent proteins.

Detection of F?rster resonance energy transfer (FRET) between cyan and yellow fluorescent proteins is a key method for quantifying dynamic processes inside living cells. To compare the different cyan and yellow fluorescent proteins, FRET efficiencies were measured for a set of the possible donor:acceptor pairs. FRET between monomeric Cerulean and Venus is more efficient than the ECFP:EYFP pair and has a 10% greater F?rster distance. We also compared several live cell microscopy methods for measuring FRET. The greatest contrast for changes in intramolecular FRET is obtained using a combination of ratiometric and spectral imaging. However, this method is not appropriate for establishing the presence of FRET without extra controls. Accurate FRET efficiencies are obtained by fluorescence lifetime imaging microscopy, but these measurements are difficult to collect and analyze. Acceptor photobleaching is a common and simple method for measuring FRET efficiencies. However, when applied to cyan to yellow fluorescent protein FRET, this method becomes prone to an artifact that leads to overestimation of FRET efficiency and false positive signals. FRET was also detected by measuring the acceptor fluorescence anisotropy. Although difficult to quantify, this method is exceptional for screening purposes, because it provides high contrast for discriminating FRET.     

Single molecule studies of quantum dot conjugates in a submicrometer fluidic channel

A microfluidic and optical system was created for the detection and analysis of single molecules in solution. Fluidic channels with submicrometer dimensions were used to isolate, detect and identify individual quantum dots conjugated with organic fluorophores. The channels were fabricated in fused silica with a 500 nm square cross section. The resulting focal volume of approximately 500 aL reduced fluorescent background and increased the signal to noise ratio of single molecule detection. The channels also enabled the rapid detection of 99% of quantum dots and organic fluorophores traversing the focal volume. Conjugates were driven through the channels electrokinetically at 2.3 kV cm(-1), excited with a single 476 nm wavelength laser and detected with a confocal microscope. Fluorescence emission was collected simultaneously from green (500-590 nm) and red (610-680 nm) regions of the spectrum. Signal rejection was minimized by the narrow and symmetric emission spectra of the quantum dots. To demonstrate efficient multicolor detection and characterization of single molecule binding, Qdot 655 Streptavidin Conjugates were bound to Alexa Fluor 488 molecules and individually detected. Photon counting histogram analysis was used to quantify coincident detection and degree of binding. Fluorescence correlation spectroscopy was used to measure the mobility of bound and unbound species. The union of fluidic channels with submicrometer dimensions and quantum dots as fluorescent labels resulted in efficient and rapid multiplexed single molecule detection and analysis.     

Fluorescence of size-expanded DNA bases: reporting on DNA sequence and structure with an unnatural genetic set

We recently described the synthesis and helix assembly properties of expanded DNA (xDNA), which contains base pairs 2.4 A larger than natural DNA pairs. This designed genetic set is under study with the goals of mimicking the functions of the natural DNA-based genetic system and of developing useful research tools. Here, we study the fluorescence properties of the four expanded bases of xDNA (xA, xC, xG, xT) and evaluate how their emission varies with changes in oligomer length, composition, and hybridization. Experiments were carried out with short oligomers of xDNA nucleosides conjugated to a DNA oligonucleotide, and we investigated the effects of hybridizing these fluorescent oligomers to short complementary DNAs with varied bases opposite the xDNA bases. As monomer nucleosides, the xDNA bases absorb light in two bands: one at approximately 260 nm (similar to DNA) and one at longer wavelength ( approximately 330 nm). All are efficient violet-blue fluorophores with emission maxima at approximately 380-410 nm and quantum yields (Phifl) of 0.30-0.52. Short homo-oligomers of the xDNA bases (length 1-4 monomers) showed moderate self-quenching except xC, which showed enhancement of Phifl with increasing length. Interestingly, multimers of xA emitted at longer wavelengths (520 nm) as an apparent excimer. Hybridization of an oligonucleotide to the DNA adjacent to the xDNA bases (with the xDNA portion overhanging) resulted in no change in fluorescence. However, addition of one, two, or more DNA bases in these duplexes opposite the xDNA portion resulted in a number of significant fluorescence responses, including wavelength shifts, enhancements, or quenching. The strongest responses were the enhancement of (xG)n emission by hybridization of one or more adenines opposite them, and the quenching of (xT)n and (xC)n emission by guanines opposite. The data suggest multiple ways in which the xDNA bases, both alone and in oligomers, may be useful as tools in biophysical analysis and biotechnological applications.     

PHOTOCHEMISTRY OF TYPE I ACID-SOLUBLE CALF SKIN COLLAGEN: DEPENDENCE ON EXCITATION WAVELENGTH

Although previous studies have demonstrated that the predominant photochemistry of type I collagen under 254 nm irradiation may be attributed either to direct absorption by tyrosine/phenylalanine or to peptide bonds, direct collagen photochemistry via solar UV wavelengths is much more likely to involve several age- and tissue-related photolabile collagen fluorophores that absorb in the latter region. In this study, we compare and contrast results obtained from irradiation of a commercial preparation of acid-soluble calf skin type I collagen in solution with UVC (primarily 254 nm), UVA (335–400nm) and broad-band solar-simulating radiation (SSR; 290^1–00nm). Excitation spectroscopy and analysis of photochemically induced disappearance of fluorescence (fluorescence fading) indicates that this preparation has at least four photolabile fluorescent chromophores. In addition to tyrosine and L-3,4-dihydroxyphenylalanine, our sample contains two other fluorophores. Chromophore I, with emission maximum at 360 nm, appears to be derived from interacting aromatic moieties in close mutual proximity. Chromophore II, with broad emission at430–435 nm, may be composed of one or more age-related molecules. Collagen fluorescence fading kinetics are sensitive to excitation wavelength and to conformation. Under UVC, chromophore I fluorescence disappears with second-order kinetics, indicating a reaction between two proximal like molecules. Adherence to second-order kinetics is abrogated by prior denaturation of the collagen sample. A new broad, weak fluorescence band at400–420 nm, attributable to dityrosine, forms under UVC, but not under solar radiation. This band is photolabile to UVA and UVB wavelengths. Amino acid analysis indicates significant destruction of aromatic amino acids under UVC, but not under UVA or SSR. When properly understood, collagen fluorescence fading phenomena may act as a sensitive molecular probe of structure, conformation and reactivity.     

Improvement of fluorescence characteristics of coumarins: syntheses and fluorescence properties of 6-methoxycoumarin and benzocoumarin derivatives as novel fluorophores emitting in the longer wavelength region and their application to analytical reagents

To improve the fluorescence characteristics, especially emission wavelength, of coumarins, various 3-substituted-6-methoxycoumarin derivatives were synthesized, and then benzocoumarin derivatives were also synthesized in expectation of the shift to the longer wavelength region by the extension of the conjugated system. Their fluorescence properties were investigated spectrophotometrically in acetonitrile and evaluated from the viewpoint of the intramolecular charge transfer (ICT) between push- and pull-substituents in the ground and the excited states. Among them, benzocoumarin derivatives especially fluoresced in the longer wavelength around 540 nm with remarkably large Stokes shifts beyond 10,000 cm(-1). Using such fluorophores, some novel fluorescence derivatization reagents for carboxylic acids, alcohols, phenols, and amines were preliminarily prepared as an example, and their derivatized products were also found to fluoresce in the longer wavelength region with large Stokes shifts.     

Two-photon excitation induced fluorescence of a trifluorophore-labeled DNA

Two-photon excitation of a trifluorophore (6-carboxyfluorescein, N,N,N',N'-tetramethyl-6-carboxyrhodamine and cyanine-5 monofunctional dye) labeled DNA, which has a scaffold of 26 nucleotides, was achieved using focused laser light of a Q-switched Nd-YAG laser (1064 nm). The observed fluorescence signature (emission ratio from the three fluorophores) of the labeled DNA after two-photon excitation is very different from the fluorescence signatures produced by one-photon excitation at different wavelength. The additional fluorescence signatures produced by two-photon excitation of the fluorescent oligonucleotides will facilitate their use as combinatorial fluorescence energy transfer tags for multiplex genetic analysis.     

Fluorescent Molecular Probes II. The Synthesis, Spectral Properties and Use of Fluorescent Solvatochromic Dapoxyl Dyes

Abstract— 2,5-Diphenyloxazoles that embody a dimethylamino group at position 4 of the 5-phenyl ring and a sulfonyl group at position 4 of the 2-phenyl ring were prepared as new fluorescent solvatochromic dyes. In these molecules, there is a "push-pull" electron transfer system from the 5-phenyl moiety to the 2-phenyl ring. These compounds show strong solvent-dependent fluorescence that is well correlated with the empirical solvent polarity parameter ET (30). The solvent polarity dependence suggests that the fluorescence arises from an intramolecular charge transfer. The fluorescence-environment dependence, long emission wavelength, large extinction coefficients, high fluorescence quantum yields and large Stokes shift of the fluorophores can be used to develop ultrasensitive fluorescent molecular probes to study a variety of biological events and processes.     

Time-resolved fluorescence spectra of arterial fluorescent compounds: reconstruction with the Laguerre expansion technique

The time-resolved fluorescence spectra of the main arterial fluorescent compounds were retrieved using a new algorithm based on the Laguerre expansion of kernels technique. Samples of elastin, collagen and cholesterol were excited with a pulsed nitrogen laser and the emission was measured at 29 discrete wavelengths between 370 and 510 nm. The expansion of the fluorescence impulse response function on the Laguerre basis of functions was optimized to reproduce the observed fluorescence emission. Collagen lifetime (5.3 ns at 390 nm) was substantially larger than that of elastin (2.3 ns) and cholesterol (1.3 ns). Two decay components were identified in the emission decay of the compounds. For collagen, the decay components were markedly wavelength dependent and hydration dependent such that the emission decay became shorter at higher emission wavelengths and with hydration. The decay characteristics of elastin and cholesterol were relatively unchanged with wavelength and with hydration. The observed variations in the time-resolved spectra of elastin, collagen and cholesterol were consistent with the existence of several fluorophores with different emission characteristics. Because the compounds are present in different proportions in healthy and atherosclerotic arterial walls, characteristic differences in their time-resolved emission spectra could be exploited to assess optically the severity of atherosclerotic lesions.