Fluorescence properties and photophysics of the sulfoindocyanine Cy3 linked covalently to DNA

The sulfoindocyanine Cy3 is one of the most commonly used fluorescent dyes in the investigation of the structure and dynamics of nucleic acids by means of fluorescence methods. In this work, we report the fluorescence and photophysical properties of Cy3 attached covalently to single-stranded and duplex DNA. Steady-state and time-resolved fluorescence techniques were used to determine fluorescence quantum yields, emission lifetimes, and fluorescence anisotropy decays. The existence of a transient photoisomer was investigated by means of transient absorption techniques. The fluorescence quantum yield of Cy3 is highest when attached to the 5' terminus of single-stranded DNA (Cy3-5' ssDNA), and decreases by a factor of 2.4 when the complementary strand is annealed to form duplex DNA (Cy3-5' dsDNA). Substantial differences were also observed between the 5'-modified strands and strands modified through an internal amino-modified deoxy uridine. The fluorescence decay of Cy3 became multiexponential upon conjugation to DNA. The longest lifetime was observed for Cy3-5' ssDNA, where about 50% of the decay is dominated by a 2.0-ns lifetime. This value is more than 10 times larger than the fluorescence lifetime of the free dye in solution. These observations are interpreted in terms of a model where the molecule undergoes a trans-cis isomerization reaction from the first excited state. We observed that the activation energy for photoisomerization depends strongly on the microenvironment in which the dye is located. The unusually high activation energy measured for Cy3-5' ssDNA is an indication of dye-ssDNA interactions. In fact, the time-resolved fluorescence anisotropy decay of this sample is dominated by a 2.5-ns rotational correlation time, which evidences the lack of rotational freedom of the dye around the linker that separates it from the terminal 5' phosphate. The remarkable variations in the photophysical properties of Cy3-DNA constructs demonstrate that caution should be used when Cy3 is used in studies employing DNA conjugates.     

Understanding Photophysical Effects of Cucurbituril Encapsulation: A Model Study with Acridine Orange in the Gas Phase

Encapsulation of dyes by cucurbituril macrocycles has proven profitable as a strategy to alter fluorescence characteristics in useful ways. Encapsulation generally results in longer fluorescence lifetimes, enhanced brightness, and solvatochromic effects not normally seen in the condensed phase. These effects have been attributed variously to both the removal of interactions with solvent molecules and to the confined environment of extremely low polarizability provided by the cucurbituril interior. It is difficult to disentangle these effects in solution. Here, we present results from gas‐phase experiments designed to separate these effects, using cucurbit[7]uril (CB7), and the cationic dye acridine orange (AOH⁺) as a probe. Fluorescence properties of gaseous AOH⁺ are compared with those of the gaseous AOH⁺‐CB7 complex and with the properties of the dye and complex in aqueous solution. The dependence on the local environment of several spectroscopic properties is discussed, including the fluorescence excitation and emission maxima, the size of the Stokes shift, fluorescence lifetime and relative brightness. An understanding of the modulation of fluorescence properties by the local environment, such as that promoted by this work, will aid in the rational design of improved fluorophores and fluorescent sensors.     

Electrochemical Modulation of the Fluorescence of Cyanine Dye Cy5

Organic fluorescent dyes are widely used in single molecule localization microscopy, where their performances are determined by the photophysical properties. Herein, we utilized a sensitive method to modulate the fluorescence of organic dyes by external potentials using a combination of electrochemical cell and super‐resolution fluorescent microscopy. Cy5 (cyanine dye) was chosen as a model molecule considering its wide application and commercial availability. We applied different potentials on the Au electrode to change the Coulombic charge microenvironment of Cy5. When the electrode potential was adjusted negatively, Cy5 displayed a better photostability. This method is proved effective in adjusting the fluorescence of organic dyes.     

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.     

Fluorescent signal amplification of carbocyanine dyes using engineered viral nanoparticles

We report enhancement in the fluorescent signal of the carbocyanine dye Cy5 by using an engineered virus as a scaffold to attach >40 Cy5 reporter molecules at fixed locations on the viral capsid. Although cyanine dye loading is often accompanied by fluorescence quenching, our results demonstrate that organized spatial distribution of Cy5 reporter molecules on the capsid obviates this commonly encountered problem. In addition, we observe energy transfer from the virus to adducted dye molecules, resulting in a highly fluorescent viral nanoparticle. We have used this enhanced fluorescence for the detection of DNA-DNA hybridization. When compared with the most often used detection methods in a microarray-based genotyping assay for Vibrio cholerae O139, these viral nanoparticles markedly increased assay sensitivity, thus demonstrating their applicability for existing DNA microarray protocols.     

Probing the interaction between fluorophores and DNA nucleotides by fluorescence correlation spectroscopy and fluorescence quenching

We have investigated the association interactions between the fluorescent dyes TAMRA, Cy3B and Alexa-546 and the DNA deoxynucleoside monophosphates by means of fluorescence quenching and fluorescence correlation spectroscopy (FCS). The interactions of Cy3B and TAMRA with the nucleotides produce a decrease in the apparent diffusion coefficient of the dyes, which result in a shift toward longer times in the FCS autocorrelation decays. Our results with Cy3B demonstrate the existence of Cy3B-nucleotide interactions that do not affect the fluorescence intensity or lifetime of the dye significantly. The same is true for TAMRA in the presence of dAMP, dCMP and dTMP. In contrast, the diffusion coefficient of Alexa 546 remains practically unchanged even at high concentrations of nucleotide. These results demonstrate that interactions between this dye and the four dNMPs are not significant. The presence of the negatively charged sulfonates and the bulky chlorine atoms in the phenyl group of Alexa 546 possibly prevent strong interactions that are otherwise possible for TAMRA. The characterization of dye-DNA interactions is important in biophysical research because they play an important role in the interpretation of energy transfer experiments, and because they can potentially affect the structure and dynamics of the DNA.     

Ratiometric fluorescence transduction by hybridization after isothermal amplification for determination of zeptomole quantities of oligonucleotide biomarkers with a paper-based platform and camera-based detection

Paper is a promising platform for the development of decentralized diagnostic assays owing to the low cost and ease of use of paper-based analytical devices (PADs). It can be challenging to detect on PADs very low concentrations of nucleic acid biomarkers of lengths as used in clinical assays. Herein we report the use of thermophilic helicase-dependent amplification (tHDA) in combination with a paper-based platform for fluorescence detection of probe-target hybridization. Paper substrates were patterned using wax printing. The cellulosic fibers were chemically derivatized with imidazole groups for the assembly of the transduction interface that consisted of immobilized quantum dot (QD)–probe oligonucleotide conjugates. Green-emitting QDs (gQDs) served as donors with Cy3 as the acceptor dye in a fluorescence resonance energy transfer (FRET)-based transduction method. After probe-target hybridization, a further hybridization event with a reporter sequence brought the Cy3 acceptor dye in close proximity to the surface of immobilized gQDs, triggering a FRET sensitized emission that served as an analytical signal. Ratiometric detection was evaluated using both an epifluorescence microscope and a low-cost iPad camera as detectors. Addition of the tHDA method for target amplification to produce sequences of ∼100 base length allowed for the detection of zmol quantities of nucleic acid targets using the two detection platforms. The ratiometric QD-FRET transduction method not only offered improved assay precision, but also lowered the limit of detection of the assay when compared with the non-ratiometric QD-FRET transduction method. The selectivity of the hybridization assays was demonstrated by the detection of single nucleotide polymorphism.     

Improved photostability and fluorescence properties through polyfluorination of a cyanine dye

[structure: see text] A polyfluorinated cyanine dye has been synthesized and characterized. Compared with the nonfluorinated analogue, the dye exhibits significantly reduced aggregation in aqueous media, enhanced fluorescence quantum yield, greater resistance to photobleaching upon direct irradiation, and reduced reactivity toward singlet oxygen. All of these properties are favorable for use of cyanine dyes as fluorescent labels and point toward fluorination as a general strategy for improving performance in imaging applications.     

Use of the Cy3 and Cy5 Fluorescent Labels to Protect a DNA Strand from Degradation under λ Exonuclease Treatment

λ Exonuclease hydrolyzes a 5′-phosphorylated strand of double-stranded DNA in the 5′–3′ direction. In this paper, the activity of the enzyme with respect to DNA substrates containing Cy3 and Cy5 fluorescent labels at their 5′ ends is studied for the first time. It is demonstrated using the fluorescence procedure for measuring the exonuclease activity that double-stranded DNA, of which both the 5′ ends contain these fluorophores, is not destroyed under the action of λ exonuclease. Using the electrophoretic separation of DNA in polyacrylamide gel, the process of obtaining single-stranded DNA from double-stranded precursors containing different labels at the 5′ ends is studied. It is shown that the introduction of Cy3 and Cy5 fluorophores to the 5′ end of the DNA strand protects this strand from enzyme damage both in the duplex and in single-stranded form, and these labels can be used to produce fluorescently labeled single-stranded DNA.     

Verification and Biophysical Characterization of a New Three‐Color Förster Resonance‐Energy‐Transfer (FRET) System in DNA

We report on a new three‐color FRET system consisting of three fluorescent dyes, i.e., of a carbostyril (=quinolin‐2(1H)‐one)‐derived donor D, a (bathophenanthroline)ruthenium complex as a relay chromophore A₁, and a Cy dye as A₂ (FRET=Förster resonance‐energy‐transfer) (cf. Fig. 1). With their widely matching spectroscopic properties (cf. Fig. 2), the combination of these dyes yielded excellent FRET efficiencies. Furthermore, fluorescence lifetime measurements revealed that the long fluorescence lifetime of the Ru complex was transferred to the Cy dye offering the possibility to measure the whole system in a time‐resolved mode. The FRET system was established on double‐stranded DNA (cf. Fig. 3) but it should also be generally applicable to other biomolecules.     

Encapsulation of Trimethine Cyanine in Cucurbit[8]uril: Solution versus Solid-State Inclusion Behavior

Inclusion of polymethine cyanine dyes in the cavity of macrocyclic receptors is an effective strategy to alter their absorption and emission behavior in aqueous solution. In this paper, the effect of the host-guest interaction between cucurbit[8]uril (CB[8]) and a model trimethine indocyanine (Cy3) on dye spectral properties and aggregation in water is investigated. Solution studies, performed by a combination of spectroscopic and calorimetric techniques, indicate that the addition of CB[8] disrupts Cy3 aggregates, leading to the formation of a 1 : 1 host-guest complex with an association constant of 1.5×10⁶ M⁻¹. At concentrations suitable for NMR experiments, the slow formation of a supramolecular polymer was observed, followed by precipitation. Single crystals X-ray structure elucidation confirmed the formation of a polymer with 1 : 1 stoichiometry in the solid state.     

Fluorescence resonance energy transfer (FRET) for DNA biosensors: FRET pairs and Förster distances for various dye-DNA conjugates

Fluorescence resonance energy transfer (FRET) between the extrinsic dye labels Cyanine 3 (Cy3), Cyanine 5 (Cy5), Carboxytetramethyl Rhodamine (TAMRA), Iowa Black Fluorescence Quencher (IabFQ), and Iowa Black RQ (IabRQ) has been studied. The F?rster distances for these FRET-pairs in single- and double-stranded DNA conjugates have been determined. In particular, it should be noted that the quantum yield of the donors Cy3 and TAMRA varies between single- and double-stranded DNA. While this alters the F?rster distance for a donor-acceptor pair, this also allows for detection of thermal denaturation events with a single non-intercalating fluorophore. The utility of FRET in the development of nucleic acid biosensor technology is illustrated by using TAMRA and IabRQ as a FRET pair in selectivity experiments. The differential quenching of TAMRA fluorescence by IabRQ in solution has been used to discriminate between 0 and 3 base pair mismatches at 60 degrees C for a 19 base sequence. At room temperature, the quenching of TAMRA fluorescence was not an effective indicator of the degree of base pair mismatch. There appears to be a threshold of duplex stability at room temperature which occurs beyond two base pair mismatches and reverses the observed trend in TAMRA fluorescence prior to that degree of mismatch. When this experimental system is transferred to a glass surface through covalent coupling and organosilane chemistry, the observed trend in TAMRA fluorescence at room temperature is similar to that obtained in bulk solution, but without a threshold of duplex stability. In addition to quenching of fluorescence by FRET, it is believed that several other quenching mechanisms are occurring at the surface.     

A theoretical and experimental study of two thiazole orange derivatives with single- and double-stranded oligonucleotides, polydeoxyribonucleotides and DNA

The effect of interaction with DNA and oligonucleotides on the photophysical properties of two thiazole orange (TO) derivatives, with different side chains (-(CH2)3-N+(CH3)3 and -(CH2)6-I)) linked to the nitrogen of the quinoline ring of the thiazole orange, is presented here. The first one called TO-PRO1 is a commercially available dye, whereas the second one called TO-MET has been specially synthesized for further covalent binding to oligonucleotides with the aim of being used for specific in situ detection of biomolecular interactions. Both photophysical measurements and molecular calculations have been done to assess their possible mode of interaction with DNA. When dissolved in buffered aqueous solutions both derivatives exhibit very low fluorescence quantum yields of 8 x 10(-5) and 2 x 10(-4), respectively. However, upon binding to double-stranded DNA, large spectroscopic changes result and the quantum yield of fluorescence is enhanced by four orders of magnitude, reaching values up to phi F = 0.2 and 0.3, respectively, as a result of an intercalation mechanism between DNA base pairs. A modulation of the quantum yield is observed as a function of the base sequence. The two derivatives also bind with single-stranded oligonucleotides, but the fluorescence quantum yield is not so great as that when bound to double-stranded samples. Typical fluorescence quantum yields of 7 x 10(-3) to 3 x 10(-2) are observed when the dyes interact with short oligonucleotides, whereas the fluorescence quantum yield remains below 10(-2) when interacting with single-stranded oligonucleotides. This slight but significant quantum-yield increase is interpreted as a folding of the single strand around the dye, which reduces the internal rotation of the two heterocycles around the central methine bridge that links the two moieties of the dye. From these properties, it is proposed to link monomer covalently to oligonucleotides for the subsequent detection of target sequences within cells.     

Thiazole orange and Cy3: improvement of fluorescent DNA probes with use of short range electron transfer

Thiazole orange was synthetically incorporated into oligonucleotides by using the corresponding phosphoramidite as the building block for automated DNA synthesis. Due to the covalent fixation of the TO dye as a DNA base surrogate, the TO-modified oligonucleotides do not exhibit a significant increase of fluorescence upon hybridization with the counterstrand. However, if 5-nitroindole (NI) is present as a second artificial DNA base (two base pairs away from the TO dye) a fluorescence increase upon DNA hybridization can be observed. That suggests that a short-range photoinduced electron transfer causes the fluorescence quenching in the single strand. The latter result represents a concept that can be transferred to the commercially available Cy3 label. It enables the Cy3 fluorophore to display the DNA hybridization by a fluorescence increase that is normally not observed with this dye.     

Label‐Free Detection of MicroRNA: Two‐Step Signal Enhancement with a Hairpin‐Probe‐Based Graphene Fluorescence Switch and Isothermal Amplification

A label‐free approach with multiple enhancement of the signal for microRNA detection has been introduced. The key idea of this strategy is achieved by taking advantage of a novel graphene oxide (GO)/intercalating dye based fluorescent hairpin probe (HP) and an isothermal polymerization reaction. In this paper, we used microRNA‐21 (mir‐21) as the target to examine the desirable properties of this assay. When the target, as a “trigger”, was hybridized with the HP and caused a conformation change, an efficient isothermal polymerization reaction was activated to achieve the first step of the “signal” amplification. After incubation with the platform of GO/intercalating dye, the formed complex of DNA interacted with the high‐affinity dye and then detached from the surface of the GO, a process that was accompanied by distinguishable fluorescence recovery. Further signal enhancement has been accomplished by a mass of intercalating dye inserting into the minor groove of the long duplex replication product. Due to the efficient and multiple amplification steps, this approach exerted a substantial enhancement in sensitivity and could be used for rapid and selective detection of Mir‐21 at attomole levels. Proof‐of‐concept evidence has been provided for the proposed cost‐effective strategy; thus, this strategy could expand the application of GO‐material‐based bioanalysis for nucleic acid studies.     

Optically active dendrimers with a binaphthyl core and phenylene dendrons: light harvesting and enantioselective fluorescent sensing

Optically active dendrimers containing a 1,1'-binaphthyl core and cross-conjugated phenylene dendrons were synthesized and characterized. The chiral optical properties of these phenylene-based dendrimers are different from the previously reported phenyleneethynylene-based dendrimers probably because of the increased steric interaction between the adjacent phenylene units. UV and fluorescence spectroscopic studies demonstrate that the energy harvested by the periphery of the dendrimers can be efficiently transferred to the more conjugated core, generating much enhanced fluorescence signal at higher generation. The fluorescence of these dendrimers can be quenched both efficiently and enantioselectively by chiral amino alcohols. The energy migration and light-harvesting effects of the dendrimers make the higher generation dendrimer more sensitive to fluorescent quenchers than the lower ones. Thus, the dendritic structure provides a signal amplification mechanism. These materials are potentially useful in the enantioselective recognition of chiral organic molecules.     

Spectroscopic Investigations on the Interaction of Crystal Violet with Nonionic Micelles of Brij and Igepal Surfactants in Aqueous Media

The behavior of the triphenylmethane dye crystal violet in aqueous solutions containing polyoxyethylene nonionic surfactants was investigated using absorption and fluorescence spectroscopic techniques. The interactions of the dye were examined in micellar media in order to prevent dye aggregation and to ensure maximum dye and surfactant interaction. The relative fluorescence enhancements and the binding constants of the dye to the surfactant micelles were determined. The micropolarities of the micellar environment sensed by the pyrene probe were estimated from the I ₁/I ₃ intensity ratios of the fluorescence spectra of pyrene. The fluorescence quenching of pyrene by hexadecylpyridinium chloride was investigated in aqueous surfactant mixtures at a fixed concentration of surfactant in order to determine the aggregation numbers. Attempts were made to correlate the binding constants obtained in this investigation to various micellar parameters.     

吲哚类菁染料Cy3嵌入的核壳荧光纳米颗粒的制备及其性质研究

以蛋白质或多肽修饰的吲哚类菁染料Cy3为内核, 采用实验条件简单的油包水反相微乳液方法成核, 通过正硅酸乙酯水解形成的网状二氧化硅包壳的方法制备吲哚类菁染料Cy3嵌入的核壳荧光纳米颗粒. 考察了以不同等电点的蛋白质和多肽修饰的Cy3为内核材料对吲哚类菁染料Cy3嵌入的核壳荧光纳米颗粒制备的影响. 结果表明, 分别采用人免疫球蛋白(IgG)或多聚赖氨酸修饰的Cy3为内核材料, 都能制备荧光强度高、荧光稳定性强和染料泄漏极少的Cy3嵌入的核壳荧光纳米颗粒. 进一步对Cy3嵌入的核壳荧光纳米颗粒进行了表征, 并将基于这一新型的荧光纳米颗粒建立起来的生物标记方法初步应用于流感病毒DNA的检测, 其检测线性范围为3.18×10-10～1.27×10-9 mol/L, 检测下限为3.51×10-10 mol/L, 相关系数r为0.986 5.     

Interaction of surfactants and aminoindophenol dye

The interaction of dye and surfactants was studied by their spectroscopic and surface properties. Large bathochromic shift (15 nm) in the absorption spectrum was found for aminoindophenol dye at high pH in cationic surfactant, while there is no significant shift in anionic, zwitterionic and nonionic surfactant solutions. The static and dynamic surface properties show there is strong interaction in mixture of cationic surfactant and aminoindophenol dye. Interaction of dye and surfactants on surface and in solution is correlated to the intensity of dye deposition on fiber. The charge complex formation between cationic surfactant and aminoindophenolic dye delays the dye diffusion into keratin fiber. The stronger is the dye/surfactant interaction, the lower dye deposition and diffusion become.     

Spectral studies of N-nonyl acridine orange in anionic, cationic and neutral surfactants

The spectroscopic and photophysical properties of N-nonyl acridine orange - a metachromatic dye useful as a mitochondrial probe in living cells - are reported in water and microheterogeneous media: anionic sodium dodecylsulfate (SDS), cationic cetyltrimethylammonium bromide (CTAB) and neutral octylophenylpolyoxyethylene ether (TX-100). The spectral changes of N-nonyl acridine orange were observed in the presence of varying amount of SDS, CTAB and TX-100 and indicated formation of a dye-surfactant complex. The spectral changes were also regarded to be caused by the incorporation of dye molecules to micelles. It was proved by calculated values K(b) and f in the following order: K(bTX-100)>K(bCTAB)>K(bSDS) and f(TX-100)>f(CTAB)>f(SDS). NAO binds to the micelle regardless the micellar charge. There are two types of interactions between NAO and micelles: hydrophobic and electrostatic. The hydrophobic interactions play a dominant role in binding of the dye to neutral TX-100. The unexpected fact of the binding NAO to cationic CTAB can be explained by a dominant role of hydrophobic interactions over electrostatic repulsion. Therefore, the affinity of NAO to CTAB is smaller than TX-100. Electrostatic interactions play an important role in binding of NAO to anionic micelles SDS. We observed a prolonged fluorescence lifetime after formation of the dye-surfactant complex tau(SDS)>tau(TX-100)>tau(CTAB)>tau(water), the dye being protected against water in this environment. TX-100 is found to stabilize the excited state of NAO which is more polar than the ground state. Spectroscopic and photophysical properties of NAO will be helpful for a better understanding of the nature of binding and distribution inside mammalian cells.