Anthracene–BODIPY Cassettes: Syntheses and Energy Transfer

Functionalization of boron dipyrrin (BODIPY) dyes through iridium and rhodium catalysis: a complementary approach to alpha- and beta-substituted BODIPYs

Iridium-catalyzed direct borylation has been applied to meso-substituted dipyrromethane and boron dipyrrin (BODIPY) dyes. Borylation is highly regioselective and complementary: it occurs exclusively at the alpha position for meso-mesityldipyrromethane and at the beta positions for meso-mesityl BODIPY dye. This regioselective borylation enables a variety of alpha- and beta-substituted BODIPY dyes to be synthesized. Introduction of alpha,beta-enoate and alpha,beta,gamma,delta-dienoate functions into BODIPY dyes at the alpha or beta positions was achieved by rhodium-catalyzed Heck-type addition of the borylated compounds to acrylate and 2,4-pentadienoate esters. This functionalization has a significant effect on the electronic properties of BODIPY dyes, as seen in substantial redshift of the absorption and emission spectra. Comparative studies showed that the alpha- and beta-substituted series of BODIPY dyes show substantially different photophysical properties, and thus the importance of the position to be functionalized is highlighted.

Photon upconversion in homogeneous fluorescence-based bioanalytical assays

Upconverting phosphors (UCPs) are very attractive reporters for fluorescence resonance energy transfer (FRET)-based bioanalytical assays. The large anti-Stokes shift and capability to convert near-infrared to visible light via sequential absorption of multiple photons enable complete elimination of autofluorescence, which commonly impairs the performance of fluorescence-based assays. UCPs are ideal donors for FRET, because their very narrow-banded emission allows measurement of the sensitized acceptor emission, in principle, without any crosstalk from the donor emission at a wavelength just tens of nanometers from the emission peak of the donor. In addition, acceptor dyes emitting at visible wavelengths are essentially not excited by near-infrared, which further emphasizes the unique potential of upconversion FRET (UC-FRET). These characteristics result in favorable assay performance using detection instrumentation based on epifluorometer configuration and laser diode excitation. Although UC-FRET is a recently emerged technology, it has already been applied in both immunoassays and nucleic acid hybridization assays. The technology is also compatible with optically difficult biological samples, such as whole blood. Significant advances in assay performance are expected using upconverting lanthanide-doped nanocrystals, which are currently under extensive research. UC-FRET, similarly to other fluorescence techniques based on resonance energy transfer, is strongly distance dependent and may have limited applicability, for example in sandwich-type assays for large biomolecules, such as viruses. In this article, we summarize the essentials of UC-FRET, describe its current applications, and outline the expectations for its future potential.

The chemistry of fluorescent bodipy dyes: versatility unsurpassed

The world of organic luminophores has been confined for a long time to fairly standard biological labeling applications and to certain analytical tests. Recently, however, the field has undergone a major change of direction, driven by the dual needs to develop novel organic electronic materials and to fuel the rapidly emerging nanotechnologies. Among the many diverse fluorescent molecules, the Bodipy family, first developed as luminescent tags and laser dyes, has become a cornerstone for these new applications. The near future looks extremely bright for "porphyrin's little sister".

Pyrene-modified guanosine as fluorescent probe for DNA modulated by charge transfer

8-(Pyren-1-yl)-2'-deoxyguanosine (Py-G) was incorporated synthetically as a modified DNA base and optical probe into oligonucleotides. A variety of Py-G-modified DNA duplexes have been investigated by methods of optical spectroscopy. The DNA duplex hybridization can be observed by both fluorescence and absorption spectroscopy since the Py-G group exhibits altered properties in single strands versus double strands for both spectroscopy methods. The fluorescence enhancement upon DNA hybridization can be improved significantly by the presence of 7-deazaguanin as an additional modification and charge acceptor three bases away from the Py-G modification site. Moreover, Py-G in DNA can be applied as a photoinducable donor for charge transfer processes when indol is present as an artificial DNA base and charge acceptor. Correctly base-paired duplexes can be discriminated from mismatched ones by comparison of their fluorescence quenching.

Photophysical and theoretical investigations of oligo(p-phenyleneethynylene)s: effect of alkoxy substitution and alkyne-aryl bond rotations

The unique photophysical, conformational, and electronic properties of two model phenyleneethynylene-based rigid rod molecular systems, possessing dialkoxy substitutions, are reported in comparison with an unsubstituted system. Twisting of the phenyl rings along the carbon-carbon triple bond is almost frictionless in these systems giving rise to planar as well as several twisted ground-state conformations, and this results in broad structureless absorption in the spectral region of 250-450 nm. In the case of 1,4-bis(phenylethynyl)benzene, a broad absorption band was observed due to the HOMO-LUMO transition, whereas dialkoxy-substituted compounds possess two well-separated bands. Dialkoxy substitution in the 2,5-position of the phenyl ring in phenyleneethynylenes alters its central arene pi-orbitals through the resonance interaction with oxygen lone pairs resulting in similar orbital features for HOMO and HOMO-1/HOMO-2. Electronic transition from the low-lying HOMO-1/HOMO-2 orbital to LUMO results in the high-energy band, and the red-shifted band originates from the HOMO-LUMO transition. The first excited-state transition energies at different dihedral angles, calculated by the TDDFT method, indicate that the orthogonal conformation has the highest excitation energy with an energy difference of 15 kcal/mol higher than the low-lying planar conformation. The emission of these compounds originates preferentially from the more relaxed planar conformation resulting in well-defined vibronic features. The fluorescence spectral profile and lifetimes were found to be independent of excitation wavelengths, confirming the existence of a single emitting species.

Excited-State Dynamics of Donor−Acceptor Bridged Systems Containing a Boron−Dipyrromethene Chromophore: Interplay between Charge Separation and Reorientational Motion

The excited-state dynamics of a series of electron donor-acceptor bridged systems (DABS) consisting of a boron-dipyrromethene chromophore covalently linked to a dinitro-substituted triptycene has been investigated using femtosecond time-resolved spectroscopy. The chromophores differ by the number of bromine atom substituents. The fluorescence lifetime of the DABS without any bromine atom is strongly reduced when going from toluene to polar solvents, this shortening being already present in chloroform. This effect is about 10 times weaker with a single bromine atom and negligible with two bromine atoms on the chromophore. The excited-state lifetime shortening is ascribed to a charge transfer from the excited chromophore to a nitrobenzene moiety, the driving force of this process depending on the number of bromine substituents. The occurrence of this process is further confirmed by the investigation of the excited-state dynamics of the chromophore alone in pure nitrobenzene. Surprisingly, no correlation between the charge separation time constant and the dielectric properties of the solvents could be observed. However, a good correlation between the charge separation time constant and the diffusional reorientation time of the chromophore alone, measured by fluorescence anisotropy, was found. Quantum chemistry calculations suggest that quasi-free rotation about the single bond linking the chromophore to the triptycene moiety permits a sufficient coupling of the donor and the acceptor to ensure efficient charge separation. The charge separation dynamics in these molecules is thus controlled by the reorientational motion of the donor relative to the acceptor.

Convenient Synthesis of Green Diisoindolodithienylpyrromethene−Dialkynyl Borane Dyes

[structure: see text] Versatile dyes based on diisoindolodithienylpyrromethene substituted at the boron center by alkynylaryl chromophores have been developed that efficiently fluorescence in the near infrared. Fast intramolecular energy transfer from the appended alkynyl units to the central core provides Stokes shifts above 16,000 cm(-1).

Syntheses, Photophysical Properties, and Application of Through-Bond Energy-Transfer Cassettes for Biotechnology

We have designed fluorescent "through-bond energy-transfer cassettes" that can harvest energy of a relatively short wavelength (e.g., 490 nm), and emit it at appreciably longer wavelengths without significant loss of intensity. Probes of this type could be particularly useful in biotechnology for multiplexing experiments in which several different outputs are to be observed from a single excitation source. Cassettes 1-4 were designed, prepared, and studied as model systems to achieve this end. They were synthesized through convergent routes that feature coupling of specially prepared fluorescein- and rhodamine-derived fragments. The four cassettes were shown to emit strongly, with highly efficient energy transfer. Their emission maxima cover a broad range of wavelengths (broader than the four dye cassettes currently used for most high-throughput DNA sequencing), and they exhibit faster energy-transfer rates than a similar through-space energy-transfer cassette. Specifically, energy-transfer rates in these cassettes is around 6-7 ps, in contrast to a similar through-space energy-transfer system shown to have a decay time of around 35 ps. Moreover, the cassettes are considerably more stable to photobleaching than fluorescein, even though they each contain fluorescein-derived donors. This was confirmed by bulk fluorescent measurements, and in single-molecule-detection studies. Modification of a commercial automated DNA-sequencing apparatus to detect the emissions of these four energy-transfer cassettes enabled single-color dye-primer sequencing.