Design and synthesis of an enzyme-cleavable sensor molecule for phosphodiesterase activity based on fluorescence resonance energy transfer

Ratiometric measurement is a technique that can provide precise data and even quantitative detection. To carry out ratiometric measurements, it is necessary that the sensor molecule exhibits a large shift in its emission or excitation spectrum after reaction with the target molecule. Fluorescence resonance energy transfer (FRET) is one mechanism used to obtain a large spectral shift. In this study, our aim was to develop a ratiometric fluorescent sensor molecule for phosphodiesterase activity based on FRET. We designed and synthesized CPF4 with a coumarin donor, a fluorescein acceptor, and two phenyl linkers having the phosphodiester moiety interposed between them. In the emission spectrum of CPF4 in aqueous buffer excited at 370 nm, the emission of the coumarin donor was strongly quenched and the emission of the fluorescein acceptor was observed. This emission spectrum demonstrates that energy transfer from the coumarin donor to the fluorescein acceptor proceeds efficiently. Addition of a phosphodiesterase to an aqueous solution of CPF4 resulted in an increase in the donor fluorescence and a decrease in the acceptor fluorescence. CPF4 exhibited a large shift in its emission spectrum after the hydrolysis of the phosphodiester group by the enzyme. This large shift of the emission spectrum indicates that ratiometric measurements can be made by using CPF4. The method described in this paper for designing enzyme-cleavable sensor molecules based on FRET should be readily applicable to other hydrolytic enzymes.     

Correlations of structure and rates of energy transfer for through-bond energy-transfer cassettes

Fluorescent DNA-labeling cassettes are designed to have a common absorbing chromophore matched to a single exciting laser wavelength, but up to four different emitters. Experiments reported here have examined the energy-transfer rates and fluorescence polarization characteristics for two different types of cassette, involving three distinct relative orientations of the donor and acceptor transition moments and the axis of the rigid linker. Energy-transfer times range from <200 fs to approximately 20 ps, the fastest transfer times occurring when the transition moments of the donor and acceptor species are aligned parallel to the linker axis. Experimental evidence is presented that supports a through-bond energy-transfer mechanism, in contrast with a commercial DNA-labeling agent, which exhibits much slower transfer times controlled by FRET. These rigid cassettes also exhibit polarized fluorescence from the acceptor species, so that this particular type of DNA-labeling probe has some of the advantages of single-molecule probes such as rhodamine and coumarin dyes.     

FRET-based modified graphene quantum dots for direct trypsin quantification in urine

A versatile nanoprobe was developed for trypsin quantification with fluorescence resonance energy transfer (FRET). Here, fluorescence graphene quantum dot is utilized as a donor while a well-designed coumarin derivative, CMR2, as an acceptor. Moreover, bovine serum albumin (BSA), as a protein model, is not only served as a linker for the FRET pair, but also a fluorescence enhancer of the quantum dots and CMR2. In the presence of trypsin, the FRET system would be destroyed when the BSA is digested by trypsin. Thus, the emission peak of the donor is regenerated and the ratio of emission peak of donor/emission peak of acceptor increased. By the ratiometric measurement of these two emission peaks, trypsin content could be determined. The detection limit of trypsin was found to be 0.7 μg/mL, which is 0.008-fold of the average trypsin level in acute pancreatitis patient's urine suggesting a high potential for fast and low cost clinical screening.     

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.     

Coumarin Modified Rhodamine Derivative： Fluorescent Chemosensor Selectively Recognizing Al^3＋ and Ca^2＋

A fluorescent probe with a coumarin moiety bound to rhodamine 6G hydrazide（l） was synthesized. Its sensing behavior toward various metal ions was investigated with fluorescence methods. Compound I displays different fluorescence emission responses to Al^3＋ and Ca^2＋ at the same excitation wavelength in the visible light region, while no changes occur after the addition of other metal ions. The binding ratios of the complexs of 1-Al^3＋ and 1-Ca^2＋ are both 2：1 according to the Job plot and high resolution mass spectrometer（HRMS） experiments. Moreover, emission spectrum of 1-Ca^2＋ complex and absorption spectrum of the rbodamine dyes overlap largely. When Al^3＋ was added to the 1-Ca2＋ system, calcium in complex 1-Ca2＋ can be displaced by Al^3＋, resulting in the output of another ratiometric sensing signal, which demonstrates that the 1-Ca^2＋ complex can be served as a new and effective fluorescence resonance energy transfer（FRET） donor for rhodamine derivatives.     

Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection

We report the design, synthesis, and characterization of binary oligonucleotide probes for mRNA detection. The probes were designed to avoid common problems found in standard binary probes such as direct excitation of the acceptor fluorophore and overlap between the donor and acceptor emission spectra. Two different probes were constructed that contained an array of either two or three dyes and were characterized using steady-state fluorescence spectroscopy, time-resolved fluorescence spectroscopy, and fluorescence depolarization measurements. The three-dye binary probe (BP-3d) consists of a Fam fluorophore which acts as a donor, collecting light and transferring it as energy to Tamra, which subsequently transfers energy to Cy5 when the two probes are hybridized to mRNA. This design allows the use of 488 nm excitation, which avoids the direct excitation of Cy5 and at the same time provides a good fluorescence resonance energy transfer (FRET) efficiency. The two-dye binary probe system (BP-2d) was constructed with Alexa488 and Cy5 fluorophores. Although the overlap between the fluorescence of Alexa488 and the absorption of Cy5 is relatively low, FRET still occurs due to their close physical proximity when the probes are hybridized to mRNA. This framework also decreases the direct excitation of Cy5 and reduces the fluorescence overlap between the donor and the acceptor. Picosecond time-resolved spectroscopy showed a reduction in the fluorescence lifetime of donor fluorophores after the formation of the hybrid between the probes and target mRNA. Interestingly, BP-2d in the presence of mRNA shows a slow rise in the fluorescence decay of Cy5 due to a relatively slow FRET rate, which together with the reduction in the Alexa488 lifetime provides a way to improve the signal to background ratio using time-resolved fluorescence spectra (TRES). In addition, fluorescence depolarization measurements showed complete depolarization of the acceptor dyes (Cy5) for both BP-3d (due to sequential FRET steps) and BP-2d (due to the relatively low FRET rate) in the presence of the mRNA target.     

Development of FRET-based dual-excitation ratiometric fluorescent pH probes and their photocaged derivatives

Dual-excitation ratiometric fluorescent probes allow the measurement of fluorescence intensities at two excitation wavelengths, which should provide a built-in correction for environmental effects. However, most of the small-molecule dual-excitation ratiometric probes that have been reported thus far have shown rather limited separation between the excitation wavelengths (20-70 nm) and/or a very small molar absorption coefficient at one of the excitation wavelengths. These shortcomings can lead to cross-excitation and thus to errors in the measurement of fluorescence intensities and ratios. Herein, we report a FRET-based molecular strategy for the construction of small-molecule dual-excitation ratiometric probes in which the donor and acceptor excitation bands exhibit large separations between the excitation wavelengths and comparable excitation intensities, which is highly desirable for determining the fluorescence intensities and signal ratios with high accuracy. Based on this strategy, we created a coumarin-rhodamine FRET platform that was then employed to develop the first class of FRET-based dual-excitation ratiometric pH probes that have two well-resolved excitation bands (excitation separations>160 nm) and comparable excitation intensities. In addition, these pH probes may be considered as in a kind of "secured ratioing mode". As a further application of these pH probes, the dual-excitation ratiometric pH probes were transformed into the first examples of photocaged dual-excitation ratiometric pH probes to improve the spatiotemporal resolution. It is expected that the modular nature of our FRET-based molecular strategy should render it applicable to other small-molecule dual-dye energy-transfer systems based on diverse fluorescent dyes for the development of a wide range of dual-excitation ratiometric probes with outstanding spectral features, including large separations between the excitation wavelengths and comparable excitation intensities.     

Convenient and efficient FRET platform featuring a rigid biphenyl spacer between rhodamine and BODIPY: transformation of 'turn-on' sensors into ratiometric ones with dual emission

We have connected a borondipyrromethene (BODIPY) donor to the 5′ position of a tetramethylrhodamine (TMR) acceptor to form a high efficiency (over 99 %) intramolecular fluorescence resonance energy transfer (FRET) cassette, BODIPY–rhodamine platform (BRP). While the good spectral overlap between the emission of BODIPY and the absorption of TMR was one favorable factor, another feature of this FRET system was the rigid and short biphenyl spacer that favored efficient through‐bond energy transfer. More importantly, in this system, the 2′‐carboxyl group of the rhodamine unit was preserved for the further modifications, which was as convenient as those carbonyl groups on the original rhodamines without connection to donors. For this reason, BRP is clearly differentiated from the previous ratiometric sensors based on donor rhodamine systems. To illustrate its value as a versatile platform, we introduced typical Hg²⁺ receptors into BRP, through convenient one‐pot reactions on the 2′‐carboxyl group, and successfully developed two ratiometric sensors, BRP‐1 and BRP‐2, with different spirocyclic receptors that recognized Hg²⁺ on different reaction mechanisms. Upon excitation at a single wavelength (488 nm), at which only BODIPY absorbed, both of the FRET sensors exhibited clear Hg²⁺‐induced changes in the intensity ratio of the two strong emission bands of BODIPY and rhodamine. It should be noted that these ratiometric Hg²⁺ sensors exhibited excellent sensitivity and selectivity Hg²⁺, as well as pH insensitivity, which was similar to the corresponding ‘turn‐on’ rhodamine sensors. While both ratiometric probes were applicable for Hg²⁺ imaging in living cells, BRP‐1 exhibited higher sensitivity and faster responses than BRP‐2. Our investigation indicated that on a versatile platform, such as BRP, a large number of highly efficient ratiometric sensors for transition‐metal ions could be conveniently developed.     

CdS量子点与曙红Y间的荧光共振能量转移研究

在水溶液中,量子点与有机荧光染料之间可能发生荧光共振能量转移(FRET)。本文以发射波长470nm的Cd S量子点为供体,曙红Y为受体,建立了Cd S量子点-曙红Y的FRET体系,研究了该体系的FRET参数。该体系受体供体数目比为8,猝灭效率为45.6%,增强效率为20.1%;供体-受体间的距离为4.4nm;临界能量转移距离为2.4nm。     

A New Robust and Highly Sensitive FRET Donor–Acceptor Pair: Synthesis,Characterization, and Application in a Thrombin Assay

The synthesis of a new, robust fluorescence‐resonance‐energy‐transfer (FRET) system is described. Its donor chromophore is derived from an N‐allyl‐substituted quinolinone attached to 4‐bromophenylalanine via Heck cross‐coupling. The resulting Fmoc‐protected derivative 11 was used as building block in solid‐phase peptide synthesis (SPPS). As FRET acceptor, a sulfonylated ruthenium(II)–bathophenanthroline complex with a peripheral COOH function was prepared for covalent attachment to target molecules. The UV/VIS absorption and emission spectra of peptides bearing only the donor (D) or acceptor (A) dye showed a good overlap of the emission band of the donor with the absorption band of the acceptor. The fluorescence spectra of a peptide bearing both dyes revealed an additional emission after excitation of the donor, which is due to indirect excitation of the acceptor via FRET. The long fluorescence lifetime of the Ru^II complex (0.53 μs) makes it well‐suited for time‐resolved measurements. As a first application of this new FRET system, the peptide 18 , with the recognition sequence for the protease thrombin, flanked by the two dyes, was synthesized and successfully cleaved by the enzyme. The change in the ratio of the fluorescence intensities could be determined.     

Ratiometric fluorescence chemosensors for copper(II) and mercury(II) based on FRET systems

A system based on FRET mechanism, comprising a coumarin donor and a rhodamine acceptor, was developed for the selective and quantitative detection of metal ions. Fluorescent chemosensors RCs, linked by 1,2-diethylamine, exhibit significant fluorescence enhancement and excellent selectivity toward Cu²⁺. Fluorescent probes CRB and CR6G, linked by hydrazide, function as ratiometric receptors for Cu²⁺ chromogentically and fluorogentically in organic-aqueous media. Furthermore, the characteristic rhodamine-based fluorescence response of CRB (excitation at 550 nm) exhibits high selectivity for Hg(II). The construction of this kind of universal FRET system opens a broader prospect for future design of ratiometric fluorescent probes.     

Ultrafast fluorescence resonance energy transfer in a reverse micelle: excitation wavelength dependence

Fluorescence resonance energy transfer (FRET) from coumarin 480 (C480) to fluorescein 548 (F548) in a sodium dioctyl sulfosuccinate (AOT) reverse micelle is studied by picosecond and femtosecond emission spectroscopy. In bulk water, at the low concentration of the donor (C480) and the acceptor (F548), no FRET is observed. However, when the donor (C480) and the acceptor (F548) are confined in a AOT reverse micelle very fast FRET is observed. The time constants of FRET were obtained from the rise time of the emission of the acceptor (F548). In a AOT microemulsion, FRET is found to occur in multiple time scales--3, 200, and 2700 ps. The 3 ps component is assigned to FRET in the water pool of the reverse micelle with a donor-acceptor distance, 16 A. The 200 ps component corresponds to a donor-acceptor distance of 30 A and is ascribed to the negatively charged acceptor inside the water pool and the neutral donor inside the alkyl chains of AOT. The very long 2700 ps component may arise due to FRET from a donor outside the micelle to an acceptor inside the water pool and also from diffusion of the donor from bulk heptane to the reverse micelle. With increase in the excitation wavelength from 375 to 405 nm the relative contribution of the FRET due to C480 in the AOT reverse micelle (the 3 and 200 ps components) increases.     

A FRET-based approach to ratiometric fluorescence detection of hydrogen peroxide

We report the synthesis, properties, and biological applications of Ratio-Peroxyfluor-1 (RPF1), a new ratiometric fluorescent reporter for hydrogen peroxide. RPF1 is comprised of a two-fluorophore cassette, where the spectral overlap between coumarin donor and fluoran/fluorescein acceptor partners can be controlled by the chemoselective peroxide-mediated deprotection of boronic ester pendants on the acceptor dye. RPF1 features good selectivity for hydrogen peroxide over a variety of reactive oxygen species, including superoxide and nitric oxide, a ca. 8-fold increase in fluorescence intensity ratio (lambda517/lambda464) upon H2O2 reaction, and excitation and emission profiles in the visible region. Experiments with viable yeast mitochondria show that RPF1 can monitor and quantify endogenous production of H2O2, establishing the potential utility of this approach for probing peroxide biology in living systems.     

Through bond energy transfer (TBET)-based fluorescent chemosensors

Excitation energy transfer is one of the crucial issues in photophysical and photochemical process of any muti-chromophoric molecular systems, such as energy harvester and fluorescent chemosensor. Through bond energy transfer (TBET)-based fluorescent chemosensors are composed of three main parts: energy donor, energy acceptor, and rigid linker. Comparing with the often used Förster resonance energy transfer (FRET) mechanism, TBET does not require spectral overlap, thus it may enable more possible combination of energy donors and acceptors to be employed and afford higher sensitivity toward targets through ratiometric fluorescence. In this review, we highlight the recent progress in the design and biological applications of the organic TBET-based fluorescent chemosensors during 2014–2019, which will provide profound guidance for designing powerful chemosensors as well as exploring further biological applications.     

A Peptide‐Cyclodextrin Hybrid System Capable of Detecting Guest Molecules Utilizing Fluorescence Resonance Energy Transfer

Summary: A cyclodextrin‐peptide hybrid bearing coumarin and fluorescein on the peptide side chain has been designed and synthesized as a novel chemosensor molecule utilizing fluorescence resonance energy transfer (FRET). Inclusion of coumarin into β‐cyclodextrin protects this system against fluorescent quenching, so that FRET occurs though donor and acceptor moieties nearby. FRET is diminished upon the addition of various guest compounds, suggesting that this system is useful for detecting molecules in aqueous solution.

A cyclodextrin‐peptide hybrid bearing coumarin and fluorescein on the peptide side chain.     

A FRET-based ultraviolet to near-infrared frequency converter

The synthesis and photophysical characterization of a generation 1 dendrimer containing four coumarin 2 laser dyes at the periphery and a perylenebis(dicarboximide) derivative at the core are described. It was found that 99% of the UV light absorbed by the peripheral coumarin 2 donor chromophores is transferred through fluorescence resonance energy transfer (FRET) to the core acceptor. Emission from the core via FRET is observed in the near-infrared with a 6.2-fold amplification relative to direct excitation.     

Fabrication of Novel Polymer Nanoparticle-Based Fluorescence Resonance Energy Transfer Systems and their Tunable Fluorescence Properties

In this study, two hydrophobic fluorescent dyes, nitrobenzoxadiazolyl (NBD) and 9-(diethylamino)benzo[a]phenoxazin-5-one (NR) with different doping ratios were incorporated into polymer nanoparticles to constitute novel polymer nanoparticle-based fluorescence resonance energy transfer (FRET) systems via a facile one-step mini-emulsion polymerization. Spectroscopic characteristics demonstrate that the two fluorophores have been successfully embedded into the nanoparticles, and the fluorescence emission intensity of the two hydrophobic dyes can be greatly enhanced in aqueous media. The as-prepared fluorescent nanoparticles also display a uniform small size (ca. 55 nm), high dye load, intense fluorescence, as well as controllable amount and ratio of the two dyes. The observed FRET efficiencies (16.0–75.2%), as well as the distance (r) between NBD (donor) and NR (acceptor), is closely correlated to the doping ratio of two dyes. Moreover, by varying the doping ratio of two dyes, the fluorescent nanoparticles would exhibit multicolor through FRET upon a single wavelength excitation, and the fluorescence emission signals of the dye-doped nanoparticles could be accurately tuned. These results indicate that the as-prepared uniform FRET-mediated nanoparticles are of high interest in multiplexed bioanalysis.     

Bidirectional switching of near IR emitting boradiazaindacene fluorophores

Two novel distyryl-boradiazaindacene dyes with dimethylaminostyryl and pyridylethenyl substituents display opposite spectral shifts on protonation with TFA in organic solvents. This bidirectional switching of the dyes can be shown to be directly related to ICT donor and acceptor characteristics of the substituents attached to the BODIPY core. The observed spectral response of these dyes could be very useful in the design of novel NIR fluorescent ratiometric probes for pH.     

Diheteroarylethenes as thermally stable photoswitchable acceptors in photochromic fluorescence resonance energy transfer (pcFRET)

We have employed diheteroarylethenes as acceptors for photochromic FRET (pcFRET), a technique introduced for the quantitative determination of fluorescence resonance energy transfer (FRET). In pcFRET, the fluorescent emission of the donor is modulated by cyclical transformations of a photochromic acceptor. Light induces a reversible change in the structure and, concomitantly, in the absorption properties of the acceptor. Only the closed forms of the selected diheteroarylethenes 2a and 2b have an absorption band overlapping the emission band of the donor, 1. The corresponding variation in the overlap integral (and thus critical transfer distance R(o)) between the two states provides the means for reversibly switching the process of FRET on and off, allowing direct and repeated evaluation of the relative changes in the donor fluorescence quantum yield. The diheteroarylethenes demonstrate excellent stability in aqueous media, an absence of thermal back reactions, and negligible fatigue. The equilibration of these systems after exposure to near-UV or visible light follows simple monoexponential kinetics. We developed a general conceptual scheme for such coupled photochromic-FRET reactions, allowing quantitative interpretations of the photostationary and kinetic data, from which the quantum yields for the cyclization and cycloreversion reactions of the photochromic acceptor were calculated.     

Dual fluorophore PNA FIT-probes - extremely responsive and bright hybridization probes for the sensitive detection of DNA and RNA

Fluorescently labeled oligonucleotides are commonly employed as probes to detect specific DNA or RNA sequences in homogeneous solution. Useful probes should experience strong increases in fluorescent emission upon hybridization with the target. We developed dual labeled peptide nucleic acid probes, which signal the presence of complementary DNA or RNA by up to 450-fold enhancements of fluorescence intensity. This enabled the very sensitive detection of a DNA target (40 pM LOD), which was detectable at less than 0.1% of the beacon concentration. In contrast to existing DNA-based molecular beacons, this PNA-based method does not require a stem sequence to enforce dye-dye communication. Rather, the method relies on the energy transfer between a "smart" thiazole orange (TO) nucleotide, which requires formation of the probe-target complex in order to become fluorescent, and terminally appended acceptor dyes. To improve upon fluorescence responsiveness the energy pathways were dissected. Hydrophobic, spectrally mismatched dye combinations allowed significant (99.97%) decreases of background emission in the absence of a target. By contrast, spectral overlap between TO donor emission and acceptor excitation enabled extremely bright FRET signals. This and the large apparent Stokes shift (82 nm) suggests potential applications in the detection of specific RNA targets in biogenic matrices without the need of sample pre-processing prior to detection.