Bulge-like Asymmetric Heterodye Clustering in DNA Duplex Results in Efficient Quenching of Background Emission Based on the Maximized Excitonic Interaction

Asymmetric dye clusters with a single fluorophore (Cy3) and multiple quenchers (4'-methylthioazobenzene-4-carboxylate, methyl red, and 4'-dimethylamino-2-nitroazobenzene-4-carboxylate) were prepared. The dye and one-to-five quenchers were tethered through D-threoninol to opposite strands of a DNA duplex. NMR analysis revealed that the clusters with a single fluorophore and two quenchers formed a sandwich-like structure (antiparallel H-aggregates). The melting temperatures of all the heteroclusters were almost the same, although structural distortion should become larger, as the number of quenchers increased. An asymmetric heterocluster of a single fluorophore and two quenchers showed larger excitonic interaction (i.e., hypochromicity of Cy3), than did a single Cy3 and a single quencher. Due to the larger exciton coupling between the dyes, the 1:2 heterocluster suppressed the background emission more efficiently than the 1:1 cluster. However, more quenchers did not enhance quenching efficiency due to the saturation of exciton coupling with two quenchers. Finally, this asymmetric 1:2 heterocluster was introduced into the stem region of a molecular beacon (MB; also known as an in-stem MB) targeting the fusion site in the L6 BCR-ABL fusion gene. With this MB design, the signal/background ratio was as high as 68 due to efficient suppression of background emission resulting from the maximized excitonic interaction.     

A Complex Comprising a Cyanine Dye Rotaxane and a Porphyrin Nanoring as a Model Light‐Harvesting System

A nanoring‐rotaxane supramolecular assembly with a Cy7 cyanine dye (hexamethylindotricarbocyanine) threaded along the axis of the nanoring was synthesized as a model for the energy transfer between the light‐harvesting complex LH1 and the reaction center in purple bacteria photosynthesis. The complex displays efficient energy transfer from the central cyanine dye to the surrounding zinc porphyrin nanoring. We present a theoretical model that reproduces the absorption spectrum of the nanoring and quantifies the excitonic coupling between the nanoring and the central dye, thereby explaining the efficient energy transfer and demonstrating similarity with structurally related natural light‐harvesting systems.     

Separation‐free single‐base extension assay with fluorescence resonance energy transfer for rapid and convenient determination of DNA methylation status at specific cytosine and guanine dinucleotide sites

A separation‐free single‐base extension (SBE) assay utilizing fluorescence resonance energy transfer (FRET) was developed for rapid and convenient interrogation of DNA methylation status at specific cytosine and guanine dinucleotide sites. In this assay, the SBE was performed in a tube using an allele‐specific oligonucleotide primer (i.e., extension primer) labeled with Cy3 as a FRET donor fluorophore at the 5′‐end, a nucleotide terminator (dideoxynucleotide triphosphate) labeled with Cy5 as a FRET acceptor, a PCR amplicon derived from bisulfite‐converted genomic DNA, and a DNA polymerase. A single base‐extended primer (i.e., SBE product) that was 5′‐Cy3‐ and 3′‐Cy5‐tagged was formed by incorporation of the Cy5‐labeled terminator into the 3′‐end of the extension primer, but only if the terminator added was complementary to the target nucleotide. The resulting SBE product brought the Cy3 donor and the Cy5 acceptor into close proximity. Illumination of the Cy3 donor resulted in successful FRET and excitation of the Cy5 acceptor, generating fluorescence emission from the acceptor. The capacity of the developed assay to discriminate as low as 10% methylation from a mixture of methylated and unmethylated DNA was demonstrated at multiple cytosine and guanine dinucleotide sites.     

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.     

Highly selective oxidative cross‐coupling polymerization with copper(I)‐bisoxazoline catalysts

The asymmetric oxidative coupling polymerization of methyl 6,6′‐dihydroxy‐2,2′‐binaphthalene‐7‐carboxylate with the copper‐diamine catalysts under an O₂ atmosphere was carried out. As is the case with the CuCl‐2,2′‐(S)‐isopropylidenbis(4‐phenyl‐2‐oxazoline) [(S)IPhO] catalyst, a polymer with a high cross‐coupling selectivity of 96% was obtained in 71% yield, whose THF‐soluble part had a number‐average molecular weight of 4.5 × 10³. To estimate the enantioselectivity with respect to the cross‐coupling linkage in the obtained polymer, the model asymmetric oxidative cross‐coupling reaction with CuCl‐(S)IPhO was also conducted, and the products showed a 94% cross‐coupling selectivity and enantioselectivity of 31% ee (S). © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 6287–6294, 2005     

A Complex Comprising a Cyanine Dye Rotaxane and a Porphyrin Nanoring as a Model Light-Harvesting System

A nanoring-rotaxane supramolecular assembly with a Cy7 cyanine dye (hexamethylindotricarbocyanine) threaded along the axis of the nanoring was synthesized as a model for the energy transfer between the light-harvesting complex LH1 and the reaction center in purple bacteria photosynthesis. The complex displays efficient energy transfer from the central cyanine dye to the surrounding zinc porphyrin nanoring. We present a theoretical model that reproduces the absorption spectrum of the nanoring and quantifies the excitonic coupling between the nanoring and the central dye, thereby explaining the efficient energy transfer and demonstrating similarity with structurally related natural light-harvesting systems.     

Mechanism of Intramolecular Photostabilization in Self‐Healing Cyanine Fluorophores

Organic fluorophores, which are popular labels for microscopy applications, intrinsically suffer from transient and irreversible excursions to dark‐states. An alternative to adding photostabilizers at high concentrations to the imaging buffer relies on the direct linkage to the fluorophore. However, the working principles of this approach are not yet fully understood. In this contribution, we investigate the mechanism of intramolecular photostabilization in self‐healing cyanines, in which photodamage is automatically repaired. Experimental evidence is provided to demonstrate that a single photostabilizer, that is, the vitamin E derivative Trolox, efficiently heals the cyanine fluorophore Cy5 in the absence of any photostabilizers in solution. A plausible mechanism is that Trolox interacts with the fluorophore through intramolecular quenching of triplet‐related dark‐states, which is a mechanism that appears to be common for both triplet‐state quenchers (cyclooctatetraene) and redox‐active compounds (Trolox, ascorbic acid, methylviologen). Additionally, the influence of solution‐additives, such as cysteamine and procatechuic acid, on the self‐healing process are studied. The results suggest the potential applicability of self‐healing fluorophores in stochastic optical reconstruction microscopy (STORM) with optical super‐resolution. The presented data contributes to an improved understanding of the mechanism involved in intramolecular photostabilization and has high relevance for the future development of self‐healing fluorophores, including their applications in various research fields.     

Intramolecular dimers: a new strategy to fluorescence quenching in dual-labeled oligonucleotide probes

Many genomics assays use profluorescent oligonucleotide probes that are covalently labeled at the 5' end with a fluorophore and at the 3' end with a quencher. It is generally accepted that quenching in such probes without a stem structure occurs through F?rster resonance energy transfer (FRET or FET) and that the fluorophore and quencher should be chosen to maximize their spectral overlap. We have studied two dual-labeled probes with two different fluorophores, the same sequence and quencher, and with no stem structure: 5'Cy3.5-beta-actin-3'BHQ1 and 5'FAM-beta-actin-3'BHQ1. Analysis of their absorption spectra, relative fluorescence quantum yields, and fluorescence lifetimes shows that static quenching occurs in both of these dual-labeled probes and that it is the dominant quenching mechanism in the Cy3.5-BHQ1 probe. Absorption spectra are consistent with the formation of an excitonic dimer, an intramolecular heterodimer between the Cy3.5 fluorophore and the BHQ1 quencher.     

Construction of Three Single‐Chain Antibody Fragment Variable Fusion Structures for Sensitive Detection of Nucleocapsid Protein of Hantaan Virus

Abstract

Three single‐chain fragment variable (scFv) fusion structures were constructed for use in rapid and sensitive detection of nucleocapsid protein (NP) of Hantaan virus. The detection of NPs on glass chips was signalized by enzyme labeling or fluorescence dye Cy3, or Cy5 cluster nanoparticles. The sensitivity of the methods with different signal systems was evaluated and compared. The detection limits of scFv‐alkaline phosphatase fusion, fluorescence labeling (scFv‐Cy3), and nanoparticles labeling (scFv‐SBP‐streptavidin‐nanoparticle) were 0.1 µg/mL, 1 ng/mL, and 0.1 ng/mL NP, respectively, which were all lower than that in a conventional enzyme‐linked immunosorbent assay (ELISA) (1 µg/mL). Twenty Hantaan virus isolates were detected using the proposed methods.     

DNA scaffold supports long-lived vibronic coherence in an indodicarbocyanine (Cy5) dimer

Vibronic coupling between pigment molecules is believed to prolong coherences in photosynthetic pigment–protein complexes. Reproducing long-lived coherences using vibronically coupled chromophores in synthetic DNA constructs presents a biomimetic route to efficient artificial light harvesting. Here, we present two-dimensional (2D) electronic spectra of one monomeric Cy5 construct and two dimeric Cy5 constructs (0 bp and 1 bp between dyes) on a DNA scaffold and perform beating frequency analysis to interpret observed coherences. Power spectra of quantum beating signals of the dimers reveal high frequency oscillations that correspond to coherences between vibronic exciton states. Beating frequency maps confirm that these oscillations, 1270 cm⁻¹ and 1545 cm⁻¹ for the 0-bp dimer and 1100 cm⁻¹ for the 1-bp dimer, are coherences between vibronic exciton states and that these coherences persist for ∼300 fs. Our observations are well described by a vibronic exciton model, which predicts the excitonic coupling strength in the dimers and the resulting molecular exciton states. The energy spacing between those states closely corresponds to the observed beat frequencies. MD simulations indicate that the dyes in our constructs lie largely internal to the DNA base stacking region, similar to the native design of biological light harvesting complexes. Observed coherences persist on the timescale of photosynthetic energy transfer yielding further parallels to observed biological coherences, establishing DNA as an attractive scaffold for synthetic light harvesting applications.

Dyes coupled to DNA display distance-dependent vibronic couplings that prolongs quantum coherences detected with 2D spectroscopy.     

Using circularly polarized luminescence to probe exciton coherence in disordered helical aggregates

Circularly polarized emission from helical MOPV4 aggregates is studied theoretically based on a Hamiltonian including excitonic coupling, exciton phonon coupling, and site disorder. The latter is modeled via a Gaussian distribution of site energies. The frequency dependence of the circularly polarized luminescence dissymmetry g(lum)(omega) contains structural information about the low-energy-neutral (excitonic) polaron from which emission originates. Near the 0-0 emission frequency, g(lum)(omega) provides a measure of the exciton coherence length, while at lower energies, in the vicinity of the sideband frequencies, g(lum)(omega) probes the polaron radius. The present work focuses on how the 0-0 dissymmetry, g(lum)(0-0), relates to the emitting exciton's coherence function, from which the coherence length is deduced. In the strong disorder limit where the exciton is localized on a single chromophore, g(lum)(0-0) is zero. As disorder is reduced and the coherence function expands, /g(lum)(0-0)/ increases more rapidly than the sideband dissymmetries, resulting in a pronounced surge in g(lum)(omega) near the 0-0 transition frequency. The resulting spectral shape of g(lum)(omega) is in excellent agreement with recent experiments on MOPV4 aggregates. In the limit of very weak disorder, corresponding to the motional narrowing regime, the coherence function extends over the entire helix. In this region, g(lum)(0-0) undergoes a surprising sign reversal but only for helices which are between n+12 and n+1 complete turns (n = 0,1,...). This unusual sign change is due to the dependence of the rotational line strength on long-range exciton coherences which are also responsible for a heightened sensitivity of g(lum)(omega) to long-range excitonic coupling.     

Carbon nanotube-quenched fluorescent oligonucleotides: probes that fluoresce upon hybridization

We report an effective, novel self-assembled single-wall carbon nanotube (SWNT) complex with an oligonucleotide and demonstrate its feasibility in recognizing and detecting specific DNA sequences in a single step in a homogeneous solution. The key component of this complex is the hairpin-structured fluorescent oligonucleotide that allows the SWNT to function as both a "nanoscaffold" for the oligonucleotide and a "nanoquencher" of the fluorophore. Given this functionality, this carbon nanotube complex represents a new class of universal fluorescence quenchers that are substantially different from organic quenchers and should therefore have many applications in molecular engineering and biosensor development. Competitive binding of a DNA target and SWNTs with the oligonucleotide results in fluorescence signal increments relative to the fluorescence without a target as well as in marked fluorescence quenching. In contrast to the common loop-and-stem configuration of molecular beacons (MBs), this novel fluorescent oligonucleotide needs only one labeled fluorophore, yet the emission can be measured with little or no background interference. This property greatly improves the signal-to-background ratio compared with those for conventional MBs, while the DNA-binding specificity is still maintained by the MB. To test the interaction mechanisms of the fluorescent oligonucleotide with SWNTs and target DNA, thermodynamic analysis and fluorescence anisotropy measurements, respectively, were applied. Our results show that MB/SWNT probes can be an excellent platform for nucleic acid studies and molecular sensing.     

EXAT: EXcitonic analysis tool

We introduce EXcitonic Analysis Tool (EXAT), a program able to compute optical spectra of large excitonic systems directly from the output of quantum mechanical calculations performed with the popular Gaussian 16 package. The software is able to combine in an excitonic scheme the single‐chromophore properties and exciton couplings to simulate energies, coefficients, and excitonic spectra (UV‐vis, CD, and LD). The effect of the environment can also be included using a Polarizable Continuum Model. EXAT also presents a simple graphical user interface, which shows on‐screen both site and exciton properties. To show the potential of the method, we report two applications on a a chiral perturbed BODIPY system and DNA G‐quadruplexes, respectively. The program is available online at http://molecolab.dcci.unipi.it/tools/ . © 2017 Wiley Periodicals, Inc.     

Synthesis,Structure, and Magnetic Properties of a Copper(II) Metal‐Organic Framework with Biphenyl‐2,2′,4,4′‐tetracarboxylic Acid

The 2D Cu^II metal‐organic framework [Cu₂(bptc)(H₂O)₄]_n · 4nH₂O ( 1 ) (H₄bptc = biphenyl‐2,2′,4,4′‐tetracarboxylic acid) was hydrothermally synthesized and characterized by single‐crystal X‐ray diffraction and magnetic measurements. In the structure, bptc^4– serves as a twisted Π‐shaped organic building block to connect paddlewheel [Cu₂(COO)₄] dinuclear units and mononuclear units through 2‐/2′‐carboxylate and 4‐/4′‐carboxylate, respectively. According to the magnetic analysis using a dimer‐plus‐monomer model, strong antiferromagnetic coupling is operative within the dinuclear unit (J = –311 cm^–1 based on H = –J S ₁ S ₂), and the compound behaves like a mononuclear molecule at low temperature.     

Linear absorbance of the pheophorbide-a butanediamine dendrimer P(4) in solution: computational studies using a mixed quantum classical methodology

The linear absorbance of a particular chromophore complex P(4) dissolved in ethanol is computed. P(4) is formed by a butanediamine dendrimer to which four pheophorbide-a molecules are covalently linked. The computations utilize a mixed quantum classical methodology and different approximations are compared. The electronic states of the P(4) chromophores which form Frenkel excitons in the excited states are treated quantum mechanically, whereas the intramolecular, intermolecular, as well as solvent coordinates are described classically. The computations use an improved exciton model, where the charge and transition densities of the chromophores are described by atomic partial charges, derived from a fit of the respective ab initio electrostatic potentials. Room temperature molecular dynamics simulations of all nuclear coordinates result in a time-dependent exciton model. It includes modulations of chromophore excitation energies due to charge density coupling between all chromophores as well as between the chromophores and solvent molecules, and, finally, modulations of the interchromophore excitonic couplings. The different approximations to the absorbance agree rather well. In particular, they confirm the reliability of adiabatic excitonic states which energies and oscillator strengths are altered by the overall temporal evolution of P(4) conformations. The fluctuations of solute-solvent interactions have a significantly larger effect on the absorbance broadening than the excitonic couplings but cannot completely explain the measured spectrum. The additional account for intrachromophore vibrations overcomes this discrepancy.     

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.     

Coherent Exciton-Phonon Coupling in CdSe/ZnS Nanocrystals Studied by Two-Dimensional Electronic Spectroscopy

Coherent exciton-phonon coupling in CdSe/ZnS nanocrystals have been investigated by temperature-dependent two-dimensional electronic spectroscopy (2DES) measurements. Benefiting from the ability of 2DES to dissect assembles in nanocrystal films, we have clearly identified experimental evidences of coherent coupling between exciton and phonon in CdSe/ZnS nanocrystals. In time domain, 2DES signals of excitonic transitions beat at a frequency resonant to a longitudinal optical phonon mode; in energy domain, phonon side bands are distinct at both Stokes and anti-Stokes sides. When temperature increases, phonon-induced exciton dephasing is observed with dramatic broadening of homogeneous linewidth. The results suggest exciton-phonon coupling is essential in elucidating the quantum dynamics of excitonic transitions in semiconductor nanocrystals.     

Asymmetric Synthesis and Characterization of Chiral 2,2′‐Diamino‐3,3′‐diethoxycarbonyl‐8,8′‐diphenyl‐1,1′‐biazulene

Abstract

rac‐2,2′‐Diamino‐3,3′‐diethoxycarbonyl‐8,8′‐diphenyl‐1,1′‐biazulene was synthesized from diethyl 2‐aminoazulene‐1,3‐dicarboxylate and was optically resolved into two enantiomers of S‐form and R‐form. The enantioselective oxidative couplings with two chiral amines [(?)‐sparteine and (R)‐(+)‐α‐methylbenzylamine] and ferric chloride catalyst, and the asymmetric couplings with two chiral oxovanadium(IV) complexes of ethyl 2‐amino‐4‐phenylazulene‐1‐carboxylate, easily yielded chiral 2,2′‐diamino‐3,3′‐diethoxycarbonyl‐8,8′‐diphenyl‐1,1′‐biazulene. Therefore, the introduction of two phenyl groups at the 8‐ and 8′‐postions of each azulene ring using phenyl magnesium bromide via an addition–oxidation–decarboxylation mechanism resulted in 1,1′‐biazulene forming a chiral C₂ axis.     

Dynamics of Fluorescent Dyes Attached to G‐Quadruplex DNA and their Effect on FRET Experiments

FRET spectroscopy is a promising approach for investigating the dynamics of G‐quadruplex DNA folds and improving the targeting of G‐quadruplexes by potential anticancer compounds. To better interpret such experiments, classical and replica‐exchange molecular dynamics simulations and fluorescence‐lifetime measurements are used to understand the behavior of a range of Cy3‐based dyes attached to the 3′ end of G‐quadruplex DNA. The simulations revealed that the dyes interact extensively with the G‐quadruplex. Identification of preferred dye positions relative to the G‐quadruplex in the simulations allows the impact of dye–DNA interactions on FRET results to be determined. All the dyes show significant deviations from the common approximation of being freely rotating and not interacting with the host, but one of the Cy3 dye analogues is slightly closer to this case.