Excitonic interaction: another photophysical process for fluorescence‐controlled nucleic acid sensing

An excitonic interaction caused by the H‐aggregation of fluorescent dyes is a new type of useful photophysical process for fluorescence‐controlled nucleic acid sensing. We designed a fluorescence‐labeled nucleotide in which two thiazole orange dyes were linked covalently. A DNA strand containing this fluorescence‐labeled nucleotide showed absorption at 480 nm before hybridization, whereas an absorption band at 510 nm became predominant when the DNA was hybridized with the complementary strand. The shift in the absorption bands shows the existence of an excitonic interaction between dyes in the nucleotide, and as a result, emission from the doubly thiazole orange‐labeled DNA was well controlled. This clear change in fluorescence intensity depending on hybridization is applicable to multicolor RNA imaging in living cells. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 10: 188–196; 2010: Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.201000003     

UV–vis photodegradation of dyes in the presence of colloidal Q-CdS

The interaction of the dyes Safranin-O (SO) and Orange II (OII) with aqueous colloidal Q-CdS clusters, which emit single fluorescence bands with maximum wavelengths at 481 nm (excitonic band) or 559 nm (trapped band), has been studied. This was carried out by monitoring both the photodegradation of the dye in the presence of the clusters and the quenching of the clusters fluorescence by the dyes. The photolysis experiments were carried out by excitation either at 520 nm (the wavelength at which the dyes, but not the clusters absorb light) or at 350 nm (the wavelength at which the clusters strongly absorb light, and the dyes have absorbance minima). At 520 nm, photodegradation of SO could be observed, which follows a first-order kinetics (for trapped-band clusters) and a second-order kinetics (for excitonic-band clusters). For the excitation wavelength of 350 nm, photodegradation of either of the dyes could not be observed. The Stern–Volmer plots for the quenching of the excitonic band-clusters fluorescence by SO show an upward curvature, pointing to the occurrence of more than one species acting as the fluorescence quencher, whereas the Stern–Volmer plots for the quenching of the trapped band-clusters fluorescence by SO are linear, indicating that only one species acts as a fluorescence quencher. Lambert–Beer type plots (absorbance vs. concentration) are linear for SO in water and in trapped band-clusters solutions, but a similar study of SO in excitonic band-clusters solution show the occurrence of a new band, which can be assigned to a ground-state dimer of the dye. The latter can be used to explain both the upward curvature of the Stern–Volmer plots and the second-order kinetics observed for SO photodegradation in the SO-excitonic band-clusters system. The Stern–Volmer plots for the quenching of both fluorescence bands by OII are linear.     

Analysis of Coherent Heteroclustering of Different Dyes by Use of Threoninol Nucleotides for Comparison with the Molecular Exciton Theory

To test the molecular exciton theory for heterodimeric chromophores, various heterodimers and clusters, in which two different dyes were stacked alternately, were prepared by hybridizing two oligodeoxyribonucleotides (ODNs), each of which tethered a different dye on D ‐threoninol at the center of the strand. NMR analyses revealed that two different dyes from each strand were stacked antiparallel to each other in the duplex, and were located adjacent to the 5′‐side of a natural nucleobase. The spectroscopic behavior of these heterodimers was systematically examined as a function of the difference in the wavelength of the dye absorption maxima (Δλ_max). We found that the absorption spectrum of the heterodimer was significantly different from that of the simple sum of each monomeric dye in the single strand. When azobenzene and Methyl Red, which have λ_max at 336 and 480 nm, respectively, in the single strand (Δλ_max=144 nm), were assembled on ODNs, the band derived from azobenzene exhibited a small hyperchromism, whereas the band from Methyl Red showed hypochromism and both bands shifted to a longer wavelength (bathochromism). These hyper‐ and hypochromisms were further enhanced in a heterodimer derived from 4′‐methylthioazobenzene and Methyl Red, which had a much smaller Δλ_max (82 nm; λ_max=398 and 480 nm in the single‐strand, respectively). With a combination of 4′‐dimethylamino‐2‐nitroazobenzene and Methyl Red, which had an even smaller Δλ_max (33 nm), a single sharp absorption band that was apparently different from the sum of the single‐stranded spectra was observed. These changes in the intensity of the absorption band could be explained by the molecular exciton theory, which has been mainly applied to the spectral behavior of H‐ and/or J‐aggregates composed of homo dyes. However, the bathochromic band shifts observed at shorter wavelengths did not agree with the hypsochromism predicted by the theory. Thus, these data experimentally verify the molecular exciton theory of heterodimerization. This coherent coupling among the heterodimers could also partly explain the bathochromicity and hypochromicity that were observed when the dyes were intercalated into the duplex.     

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.     

Two‐Photon‐Induced Fluorescence in New π‐Expanded Diketopyrrolopyrroles

Structurally unique π‐expanded diketopyrrolopyrroles (EDPP) were designed and synthesized. Strategic placement of a fluorene scaffold at the periphery of a diketopyrrolopyrrole through tandem Friedel–Crafts‐dehydration reactions resulted in dyes with supreme solubility. The structure of the dyes was confirmed by X‐ray crystallography verifying a nearly flattened arrangement of the ten fused rings. Despite the extended ring system, the dye still preserved good solubility and was further functionalized by using Pd‐catalyzed coupling reactions, such as the Buchwald–Hartwig amination. Photophysical studies of these new functional dyes revealed that they possess enhanced properties when compared with expanded DPPs in terms of two‐photon absorption cross‐section. It is further demonstrated that in addition to the initial diacetals, the final electrophilic cyclization step can also be applied to diketones. By placing two amine groups at peripheral positions of the resulting dyes, values of two‐photon absorption cross‐section on the level of 2000 GM around 1000 nm were achieved, which in combination with high fluorescence quantum yield (Φ_fl), generated a two‐photon brightness of approximately 1600 GM. These characteristics in combination with strong red emission (665 nm) make these new π‐expanded diketopyrrolopyrroles of major promise as two‐photon dyes for bioimaging applications. Finally, the corresponding N‐alkylated DPPs displayed a solid‐state fluorescence.     

Nanocrystallization of oligosilanes by a reprecipitation method: easy fabrication of H-aggregates of linear-chain oligosilane molecules

Nanocrystals of several oligosilanes have been fabricated easily by using a reprecipitation method. The nanocrystals reveal an intense absorption band at the UVB region (280 to 320 nm) and a fluorescence band with large Stokes shift. These photophysical properties show that the nanocrystals exhibit an excitonic interaction of the H-aggregate type.     

Doubly thiazole orange-labeled cytidine for functional expansion of a hybridization-sensitive probe

A 2′-deoxycytidine derivative modified by two thiazole orange dyes has been designed for functional expansion of hybridization-sensitive fluorescence probes. This nucleotide was synthesized by a procedure that included protection of the cytosine amino group by di(n-butyl)formamidine formation, followed by incorporation into DNA. The fluorescence of the synthesized DNA was controlled by excitonic interaction, showing strong fluorescence upon hybridization with the target nucleic acid and effective quenching in a single-stranded state of the probe.     

Rational Design of a Near‐infrared Fluorescence Probe for Ca2+ Based on Phosphorus‐substituted Rhodamines Utilizing Photoinduced Electron Transfer

Fluorescence imaging in the near‐infrared (NIR) region (650–900 nm) is useful for bioimaging because background autofluorescence is low and tissue penetration is high in this range. In addition, NIR fluorescence is useful as a complementary color window to green and red for multicolor imaging. Here, we compared the photoinduced electron transfer (PeT)‐mediated fluorescence quenching of silicon‐ and phosphorus‐substituted rhodamines (SiRs and PRs) in order to guide the development of improved far‐red to NIR fluorescent dyes. The results of density functional theory calculations and photophysical evaluation of a series of newly synthesized PRs confirmed that the fluorescence of PRs was more susceptible than that of SiRs to quenching via PeT. Based on this, we designed and synthesized a NIR fluorescence probe for Ca²⁺, CaPR‐1 , and its membrane‐permeable acetoxymethyl derivative, CaPR‐1 AM , which is distributed to the cytosol, in marked contrast to our previously reported Ca²⁺ far‐red to NIR fluorescence probe based on the SiR scaffold, CaSiR‐1 AM , which is mainly localized in lysosomes as well as cytosol in living cells. CaPR‐1 showed longer‐wavelength absorption and emission (up to 712 nm) than CaSiR‐1 . The new probe was able to image Ca²⁺ at dendrites and spines in brain slices, and should be a useful tool in neuroscience research.     

Spectral Properties of Fluorogenic Thiophene‐derived Triarylmethane Dyes

Spectral properties and fluorogenic behaviors of five novel thiophene variants of malachite green (MG), termed MGTs, were determined. Appreciable changes as a function of homologation and substitution pattern, including absorption band positions and intensities and fluorescence quantum yields were observed. In particular, the shorter wavelength y‐band absorption was found to shift over a nearly 200 nm range based on aryl group variation, allowing fine‐tuning of the excitation wavelength for these dyes. In addition, the fluorescence intensity of some MGTs increased significantly (up to 4600‐fold) when the dye was bound to a cognate protein partner, which is potentially useful for cell imaging studies.     

Spectroscopic studies of a near-infrared absorbing pH sensitive aminodienone-carbocyanine dye system

Synthetic red and near-infrared absorbing dyes may be used as probe molecules in a large number of applications. Dyes exhibiting spectral changes with hydrogen ion concentration are useful as pH probes. Those dyes which have their absorption and fluorescence maxima in the long wavelength region of the visible spectral region are specially valuable because of decreased interference and semiconductor laser applications. In this paper we have evaluated an aminodienone dyes 1 which demostrates pH dependent absorption and fluorescence spectra as well as solvent polarity dependence. In organic solvents the long wavelength absorption band of the dye is in the reduced interference region. The absorption maximum is at 535 nm in neutral or alkaline solutions in methanol. The absorption spectra undergo a strong bathochromic shift in the presence of acids (lambda(max) = 709 nm) with a concomitant change in the fluorescence spectra. This pH sensitive dye was found to be specially especially useful for organic solvents. The analytical utility of this and similar near-infrared absorbing dyes is discussed.     

5‐(Pyren‐1‐yl)uracil as a Base‐Discriminating Fluorescent Nucleobase in Pyrrolidinyl Peptide Nucleic Acids

A pyrene‐labeled uridine (U^Py) monomer for a pyrrolidinyl peptide nucleic acid with an alternating proline/2‐aminocyclopentanecarboxylic acid backbone (acpcPNA) was synthesized and incorporated into the PNA. The U^Py base in acpcPNA could specifically recognize the base A in its complementary DNA strand as determined by thermal denaturation (T_m) experiments. The fluorescence of the U^Py‐containing single‐stranded acpcPNA was very weak in aqueous buffer. In the presence of a complementary DNA target, the fluorescence was enhanced significantly (2.7–41.9 folds, depending on sequences). The fluorescence enhancement was specific to the pairing between U^Py and dA, making the U^Py‐modified acpcPNA useful as a hybridization‐responsive fluorescence probe for DNA‐sequence determination.     

NUCLEIC ACID HYBRIDIZATION ACCOMPANIED WITH EXCIMER FORMATION FROM TWO PYRENE-LABELED PROBES

Abstract— We developed a novel nucleic acid hybridization method based on excimer formation. We used two different 16-mer oligonucleotide probes that had a combined continuous-sequence run that was complementary to a target 32-mer. Prior to hybridization, the adjacent terminal ends (i.e. the 3'-terminal of one probe and the 5'-terminal of the other probe) were each labeled with one pyrene residue. When these probes simultaneously hybridized to the target, a 495 nm broad fluorescence band was produced. The intensity of this band increased as the intensity of the pyrene monomer bands decreased, indicating that the 495 nm band was attributed to the pyrene excimer. The excimer fluorescence, easily differentiated from the monomer bands for emission wavelength, opens up a new way to perform homogeneous hybridization assays and in vivo imaging of nucleic acids.     

π‐Expanded α,β‐Unsaturated Ketones: Synthesis,Optical Properties,and Two‐Photon‐Induced Polymerization

A library of π‐expanded α,β‐unsaturated ketones was designed and synthesized. They were prepared by a combination of Wittig reaction, Sonogashira reaction, and aldol condensation. It was further demonstrated that the double aldol condensation can be performed effectively for highly polarized styrene‐ and diphenylacetylene‐derived aldehydes. The strategic placement of two dialkylamino groups at the periphery of D ‐π‐A‐π‐D molecules resulted in dyes with excellent solubility. These ketones absorb light in the region 400–550 nm. Many of them display strong solvatochromism so that the emission ranges from 530–580 nm in toluene to the near‐IR region in benzonitrile. Ketones based on cyclobutanone as central moieties display very high fluorescence quantum yields in nonpolar solvents, which decrease drastically in polar media. Photophysical studies of these new functional dyes revealed that they possess an enhanced two‐photon absorption cross section when compared with simpler ketone derivatives. Due to strong polarization of the resulting dyes, values of two‐photon absorption cross sections on the level of 200–300 GM at 800 nm were achieved, and thanks to that as well as the presence of the keto group, these new two‐photon initiators display excellent performance so that the operating region is 5–75 mW in some cases.     

Assessment of Luminescent Downshifting Layers for the Improvement of Light‐Harvesting Efficiency in Dye‐Sensitized Solar Cells

Luminescence downshifting (LDS) of light can be a practical photon management technique to compensate the narrow absorption band of high‐extinction‐coefficient dyes in dye‐sensitized solar cells (DSSCs). Herein, an optical analysis on the loss mechanisms in a reflective LDS (R‐LDS)/DSSC configuration is reported. For squaraine dye (550–700 nm absorption band) and CaAlSiN₃:Eu²⁺ LDS material (550–700 nm emission band), the major loss channels are found to be non‐unity luminescence quantum efficiency (QE) and electrolyte absorption. By using an ideal LDS layer (QE=100 %), a less absorbing electrolyte (Co‐based), and antireflection coatings, approximately 20 % better light harvesting is obtained. If the absorption/emission band of dye/LDS is shifted to 800 nm, a maximal short‐circuit current density (J_sc) of 22.1 mA cm^?2 can be achieved. By putting the LDS layer in front of the DSSC (transmissive mode), more significant loss channels are observed, and hence a lower overall efficiency than the R‐LDS configuration.     

Synthesis and Electronic Properties of 1,2‐Hemisquarimines and Their Encapsulation in a Cucurbit[7]uril Host

The synthesis of a new class of robust squaraine dyes, colloquially named 1,2‐hemisquarimines (1,2‐HSQiMs), through the microwave‐assisted condensation of aniline derivatives with the 1,2‐squaraine core is reported. In CH₃CN, 1,2‐HSQiMs show a broad absorption band with a high extinction coefficient and a maximum at around λ=530 nm, as well as an emission band centered at about λ=574 nm, that are pH dependent. Protonation of the imine nitrogen causes a redshift of both absorption and emission maxima, with a concomitant increase in the lifetime of the emitting excited state. Encapsulation of the chromophore into a cucurbit[7]uril host revealed fluorescence enhancement and increased photostability in water. The redox characteristics of 1,2‐HSQiMs indicate that charge injection into TiO₂ is possible; this opens up promising perspectives for their use as photosensitizers for solar energy conversion.     

Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout

By using (S)‐2‐amino‐1,3‐propanediol as a linker, thiazole orange (TO) was incorporated in a dimeric form into DNA. The green fluorescence (λ=530 nm) of the intrastrand TO dimer is quenched, whereas the interstrand TO dimer shows a characteristic redshifted orange emission (λ=585 nm). Steady‐state optical spectroscopic methods reveal that the TO dimer fluorescence is independent of the sequential base contexts. Time‐resolved pump–probe measurements and excitation spectra reveal the coexistence of conformations, including mainly stacked TO dimers and partially unstacked ones, which yield exciton and excimer contributions to the fluorescence, respectively. The helicity of the DNA framework distorts the excitonic coupling. In particular, the interstrand TO dimer could be regarded as an excitonically interacting base pair with fluorescence readout for DNA hybridization. Finally, the use of this fluorescent readout was representatively demonstrated in molecular beacons.     

Relaxation Kinetics of Excitonic States in ZnSe Quantum Dots: A Femtosecond Laser Spectroscopy Study

Relaxation processes in ZnSe quantum dots upon excitation by a 30-fs pulse at a wavelength of 360 nm have been studied by broadband femtosecond absorption spectroscopy. The diameter of ZnSe nanoparticles was 3.7 ± 0.6 nm. A colloidal solution of ZnSe in cyclohexane was used. In the differential spectra, a bleaching band at the edge of the excitonic absorption band of ZnSe, an absorption band of the biexcitonic transition with a peak at about 420 nm, and a broad structureless absorption band in the region from 440 to 750 nm have been revealed. From the analysis of the absorption and luminescence spectra, the shift of the excitonic luminescence band δ_XX = 127 meV has been measured. From the femtosecond photolysis data, an estimate of the biexcitonic interaction Δ_XX ≈ 75 meV has been obtained. It has been shown that the relaxation kinetics of the differential spectra is described by three-exponential dependences with time constants and corresponding amplitude contributions of 1 ps (42%), 13 ps (22%), and 91 ps (17%). The kinetic component of 1 ps (42%) is presumably due to hole transport to surface traps. The kinetic components of 13 ps (22%) and 91 ps (17%) apparently describe the processes of electron transport to shallow and deep traps.     

Capillary electrophoresis,a method for the determination of nucleic acid ligands covalently attached to quantum dots representing a donor of Förster resonance energy transfer

The synthesis and determination of the structure of a Förster resonance energy transfer probe intended for the detection of specific nucleic acid sequences are described here. The probe is based on the hybridization of oligonucleotide modified quantum dots with a fluorescently labeled nucleic acid sample resulting in changes of the fluorescence emission due to the energy transfer effect. The stoichiometry distribution of oligonucleotides conjugated to quantum dots was determined by capillary electrophoresis separation. The results indicate that one to four molecules of oligonucleotide are conjugated to the surface of a single nanoparticle. This conclusion is confirmed by the course of the dependence of Förster resonance energy transfer efficiency on the concentration of fluorescently labeled complementary single‐stranded nucleic acid, showing saturation. While the energy transfer efficiency of the probe hybridized with complementary nucleic acid strands was 30%, negligible efficiency was observed with a noncomplementary strand.     

On the Non‐Metallicity of 2.2 nm Au246(SR)80 Nanoclusters

The transition from molecular to plasmonic behaviour in metal nanoparticles with increasing size remains a central question in nanoscience. We report that the giant 246‐gold‐atom nanocluster (2.2 nm in gold core diameter) protected by 80 thiolate ligands is surprisingly non‐metallic based on UV/Vis and femtosecond transient absorption spectroscopy as well as electrochemical measurements. Specifically, the Au₂₄₆ nanocluster exhibits multiple excitonic peaks in transient absorption spectra and electron dynamics independent of the pump power, which are in contrast to the behaviour of metallic gold nanoparticles. Moreover, a prominent oscillatory feature with frequency of 0.5 THz can be observed in almost all the probe wavelengths. The phase and amplitude analysis of the oscillation suggests that it arises from the wavepacket motion on the ground state potential energy surface, which also indicates the presence of a small band‐gap and thus non‐metallic or molecular‐like behaviour.     

Fluorescence-quenching phenomenon by photoinduced electron transfer between a fluorescent dye and a nucleotide base.

Fluorescently labeled oligonucleotide probes have been widely used in biotechnology, and fluorescence quenching by the interaction between the dyes and a nucleobase has been pointed out. This quenching causes big problem in analytical methods, but is useful in some other cases. Therefore, it is necessary to estimate the fluorescence quenching intensity under various conditions. We focused on the redox properties of some commercially available fluorescent dyes, and investigated dye-nucleotide interactions between a free dye and a nucleotide in aqueous solution by electrochemical and spectroscopic techniques. Our results suggested that the quenching was accompanied by photoinduced electron transfer between a thermodynamically quenchable excited dye and a specific base. Several kinds of fluorescent dyes labeled to the 5'-end of oligonucleotide C10T6 were prepared, and their quenching ratios compared upon hybridization with the complementary oligonucleotide A6G10. The quenching was completely reversible and their efficiencies depended on the attached fluorophore types. The fluorescence of 5-FAM, BODIPY FL or TAMRA-modified probe was strongly quenched by hybridization.