Ultrafast Single-Molecule Fluorescence Measured by Femtosecond Double-Pulse Excitation Photon Antibunching.

Most measurements of fluorescence lifetimes on the single-molecule level are carried out using avalanche photon diodes (APDs). These single-photon counters are inherently slow, and their response shows a strong dependence on photon energy, which can make reconvolution of the instrument response function (IRF) challenging. An ultrafast time resolution in single-molecule fluorescence is crucial, e.g., in determining donor lifetimes in donor-acceptor couples which undergo energy transfer, or in plasmonic antenna structures, where the radiative rate and non-radiative rates are enhanced. We introduce a femtosecond double-excitation (FeDEx) photon correlation technique, which measures the degree of photon antibunching as a function of time delay between two excitation pulses. In this boxcar integration, the time resolution of fluorescence transients is limited solely by the laser pulse length and is independent of the detector IRF. The versatility of the technique is demonstrated with a custom-made donor-acceptor complex with one donor and two acceptors and with single dye molecules positioned accurately between two gold nanoparticles using DNA origami. The latter structures show ∼75-fold radiative-rate enhancement and fluorescence lifetimes down to 19 ps, which is measured without the need for any reconvolution. With the potential of measuring subpicosecond fluorescence lifetimes, plasmonic antenna structures can now be optimized further.

Nanostructuring of the conjugated polyelectrolyte poly[9,9-bis(4-sulfonylbutoxyphenyl)fluorene-2,7-diyl-2,2'-bithiophene] in liquid crystalline C12E4 in bulk water and aligned thin films.

We report on the conjugated polyelectrolyte 12 mM poly[9,9-bis(4-sulfonylbutoxyphenyl) fluorene-2,7-diyl-2,2'-bithiophene] (PBS-PF2T) mixed in concentrated aqueous 680 mM tetraethylene glycol monododecyl ether (C12E4) in bulk and thin films. A blue-shift in the fluorescence spectrum demonstrates breakup of PBS-PF2T aggregates in bulk aqueous C12E4. Small-angle X-ray scattering data indicate that this mixture follows a very similar phase behaviour to binary mixtures of a pure surfactant with water, including a micellar phase below about 20 °C, a lamellar phase in between about 20 and 70 °C and a proposed coexistence of water and the liquid surfactant solution above 70 °C. Molecular dynamics simulations reproduce these transitions and suggest that PBS-PF2T is incorporated into the surfactant headgroup region, and is, on average, perpendicular to the alkyl chains. In wet thin films, grazing-incidence small-angle X-ray scattering shows that the phase window for the lamellar phase becomes much narrower, located at about 30-34 °C. Weakly ordered phases exist both below and above these temperatures. These phases are isotropic, but lamellae become aligned in a stacked manner on the surface whether approached from low or high temperatures. Dry films are disordered but can be reversibly ordered and disordered and aligned and misaligned by maintaining the temperature at 30-34 °C and switching relative outside humidity between 32% and 100%.

Photophysical and structural characterisation of in situ formed quantum dots.

Conjugated polymer-semiconductor quantum dot (QD) composites are attracting increasing attention due to the complementary properties of the two classes of materials. We report a convenient method for in situ formation of QDs, and explore the conditions required for light emission of nanocomposite blends. In particular we explore the properties of nanocomposites of the blue emitting polymer poly[9,9-bis(3,5-di-tert-butylphenyl)-9H-fluorene] together with cadmium sulphide (CdS) and cadmium selenide (CdSe) precursors. We show the formation of emissive quantum dots of CdSe from thermally decomposed precursor. The dots are formed inside the polymer matrix and have a photoluminescence quantum yield of 7.5%. Our results show the importance of appropriate energy level alignment, and are relevant to the application of organic-inorganic systems in optoelectronic devices.

Systematic variation in gene expression patterns in human cancer cell lines.

We used cDNA microarrays to explore the variation in expression of approximately 8,000 unique genes among the 60 cell lines used in the National Cancer Institute's screen for anti-cancer drugs. Classification of the cell lines based solely on the observed patterns of gene expression revealed a correspondence to the ostensible origins of the tumours from which the cell lines were derived. The consistent relationship between the gene expression patterns and the tissue of origin allowed us to recognize outliers whose previous classification appeared incorrect. Specific features of the gene expression patterns appeared to be related to physiological properties of the cell lines, such as their doubling time in culture, drug metabolism or the interferon response. Comparison of gene expression patterns in the cell lines to those observed in normal breast tissue or in breast tumour specimens revealed features of the expression patterns in the tumours that had recognizable counterparts in specific cell lines, reflecting the tumour, stromal and inflammatory components of the tumour tissue. These results provided a novel molecular characterization of this important group of human cell lines and their relationships to tumours in vivo.

A gene expression database for the molecular pharmacology of cancer.

We used cDNA microarrays to assess gene expression profiles in 60 human cancer cell lines used in a drug discovery screen by the National Cancer Institute. Using these data, we linked bioinformatics and chemoinformatics by correlating gene expression and drug activity patterns in the NCI60 lines. Clustering the cell lines on the basis of gene expression yielded relationships very different from those obtained by clustering the cell lines on the basis of their response to drugs. Gene-drug relationships for the clinical agents 5-fluorouracil and L-asparaginase exemplify how variations in the transcript levels of particular genes relate to mechanisms of drug sensitivity and resistance. This is the first study to integrate large databases on gene expression and molecular pharmacology.

Solvent dependent assembly of a polyfluorene-polythiophene "rod-rod" block copolyelectrolyte: influence on photophysical properties.

We report the solvent-driven assembly of a polyelectrolytic polyfluorene-polythiophene diblock copolymer-poly[9,9-bis(2-ethylhexyl)fluorene]-b-poly[3-(6-trimethylammoniumhexyl)thiophene] (PF2/6-b-P3TMAHT)-in tetrahydrofuran (THF), water, their 1:1 mixture and in subsequently prepared thin films, as investigated using a combination of scattering, microscopic and photoluminescence techniques. In solution PF2/6-b-P3TMAHT forms large (>100 nm) aggregates which undergo a transition from objects with surface fractal interface (THF) to ones with a significant planar component due to the presence of the 2-dimensionally merged ribbon-like aggregates or fused walls of the observed vesicular aggregates [THF-water (1:1)]. In THF-water and water the blocks are loosely segregated into P3TMAHT and PF2/6 rich domains, with PF2/6 dominating the aggregate interior. Depending on solvent, the spun films contain either aggregates with a crystalline interior (THF) or large 200 nm-2 microm vesicular aggregates embedded in a featureless matrix (THF-water and water). Structural variations are concomitant with distinctive solvatochromic changes in the photophysical properties including a color change from deep red (THF) to pale orange (THF-water and water) in solution, a decrease in fluorescence quantum yield with increasing water content, and a shift from photoluminescence of individual PF2/6 blocks (THF) to efficient PF2/6 --> P3TMAHT energy transfer (THF-water and water).

Improving the performance of doped pi-conjugated polymers for use in organic light-emitting diodes

Organic light-emitting diodes (OLEDs) represent a promising technology for large, flexible, lightweight, flat-panel displays. Such devices consist of one or several semiconducting organic layer(s) sandwiched between two electrodes. When an electric field is applied, electrons are injected by the cathode into the lowest unoccupied molecular orbital of the adjacent molecules (simultaneously, holes are injected by the anode into the highest occupied molecular orbital). The two types of carriers migrate towards each other and a fraction of them recombine to form excitons, some of which decay radiatively to the ground state by spontaneous emission. Doped pi-conjugated polymer layers improve the injection of holes in OLED devices; this is thought to result from the more favourable work function of these injection layers compared with the more commonly used layer material (indium tin oxide). Here we demonstrate that by increasing the doping level of such polymers, the barrier to hole injection can be continuously reduced. The use of combinatorial devices allows us to quickly screen for the optimum doping level. We apply this concept in OLED devices with hole-limited electroluminescence (such as polyfluorene-based systems), finding that it is possible to significantly reduce the operating voltage while improving the light output and efficiency.

Excited state properties of oligophenyl and oligothienyl swivel cruciforms.

A comprehensive study has been undertaken of the electronic spectral and photophysical properties of two oligophenyl (BPH and BPHF) and one oligothienyl (BTF) swivel cruciforms involving measurements of absorption, fluorescence, and phosphorescence spectra, quantum yields of fluorescence (phiF), phosphorescence (phiPh) and triplet formation (phiT), lifetimes of fluorescence (tauF) and of the triplet state (tauT), and quantum yields of singlet oxygen production (phiDelta). From these, all radiative kF and radiationless rate constants, kIC and kISC, have been obtained in solution. The energies of the lowest lying singlet and triplet excited states were also determined at 293 K. Several of the above properties have also been obtained at low temperature and in the solid state (thin films). In general, for the phenyl oligophenyl (BPH) and for the oligothienyl (BTF) compounds, the radiationless decay channels (phiIC+phiISC) are the dominant pathway for the excited-state deactivation, whereas with the fluorene based oligophenyl BPHF the radiative route prevails. In contrast to the general rule found for related oligomers (and polymers) where radiative emission from T1 is absent, with the compounds studied, phosphorescence has been observed for all of the compounds, indicating that this type of functionalization can lead to emissive triplets. Time-resolved fluorescence decays with picosecond resolution revealed multiexponential (bi- and triexponential) decay laws compatible with the existence of more than one species or conformation in the excited state. These results are discussed on the basis of conformational flexibility in the excited state.

Control over phase behavior and solution structure of hairy-rod polyfluorene by means of side-chain length and branching.

We present guidelines on how the solution structure of pi -conjugated hairy-rod polyfluorenes is controlled by the side-chain length and branching. First, the semiquantitative mean-field theory is formulated to predict the phase behavior of the system as a function of side-chain beads (N). The phase transition at N=N{ *} separates a lyotropic phase with solvent coexistence (NN{ *}). The membrane phase transforms into the isotropic phase of dissolved rodlike polymers at the temperature T_{mem}{ *}(N), which decreases both with N and with the degree of side-chain branching. This picture is complemented by polymer demixing with the transition temperature T_{IN}{ *}(N), which decreases with N . For NN{ *}, stable membranes are predicted for T_{IN}{ *}N{ *}. T_{mem}{ *}(N) decreases from 340 K to 280 K for N > or = 8 . For copolymers, the membrane phase is found when the fraction of F8 units is at least 90%, T_{mem}{ *} decreasing with this fraction. The membrane phase contains three material types: loose sheets of two polymer layers, a better packed beta phase, and dissolved polymer. For N > or = 7 and T

Conjugated polymers for photocatalysis.

The photocatalytic properties of the conjugated polymers have been investigated for the first time. Degradation of various textile dyes such as Alizarin S, Alizarin G, Orange G, and Remazol brilliant blue were studied under UV radiation. The experimental data indicated that the photocatalytic activity of the conjugated polymers was significantly higher than that of Degussa P-25 under similar conditions. The conjugated polymers were characterized by photoluminescent, UV-visible, and IR spectroscopies before and after photocatalytic reactions. The degradation of phenol was also carried out to study the reaction pathway of degradation.

Spectral and photophysical studies on cruciform oligothiophenes in solution and the solid state.

The photophysical and spectroscopic properties of a new class of oligothiophene derivatives, designated as cruciform oligomers, have been investigated in solution (room and low temperature) and in the solid state (as thin films in Zeonex matrixes). The study comprises absorption, emission, and triplet-triplet absorption spectra, together with quantitative measurements of quantum yields (fluorescence, intersystem crossing, internal conversion, and singlet oxygen formation) and lifetimes. The overall data allow the determination of the rate constants for all decay processes. From these, several conclusions are drawn. First, in solution, the main deactivation channels for the compounds are the radiationless processes: S(1) --> S(0) internal conversion and S(1) --> T(1) intersystem crossing. Second, in general, in the solid state, the fluorescence quantum yields decrease relative to solution. A comparison is made with the analogous linear alpha-oligothiophenes, revealing a lower fluorescence quantum efficiency and, in contrast to the normal oligothiophenes, that internal conversion is an important channel for the deactivation of the singlet excited state. Replacement of thiophene by 1,4-phenylene units in the longer-sized cruciform oligomer increases the fluorescence efficiency. The highly efficient generation of singlet oxygen through energy transfer from the triplet state (S(Delta) approximately 1) provides support for the measured intersystem crossing quantum yields and suggests that reaction with this may be an important pathway to consider for degradation of devices produced with these compounds.

Triplet-state and singlet oxygen formation in fluorene-based alternating copolymers.

Data are reported on the triplet states of a series of fluorene-based A-alt-B type alternating copolymers based on pulse radiolysis-energy transfer and flash photolysis experiments. From the pulse radiolysis experiments, spectra are given for eight copolymers involving phenylene, thiophene, benzothiadiazole, and oligothienylenevinylene groups. Quantum yields for triplet-state formation (PhiT) have been obtained by flash photolysis following laser excitation and in one case by photoacoustic calorimetry. In addition, yields of sensitized formation of singlet oxygen have been determined by time-resolved phosphorescence and are, in general, in excellent agreement with the PhiT values. In all cases, the presence of thiophene units is seen to increase intersystem-crossing quantum yields, probably because of the presence of the heavy sulfur atom. However, with the poly[2,7-(9,9-bis(2'-ethylhexyl)fluorene)-alt-1,4-phenylene] (PFP), thiophene S,S-dioxide (PFTSO2) and benzothiadiazole (F8BT) copolymers, low yields of triplet formation are observed. With three of the copolymers, the energies of the triplet states have been determined. With PFP, the triplet energy is virtually identical to that of poly[2,7-(9,9-bis(2'-ethylhexyl)fluorene)]. In contrast, with fluorene-thiophene copolymers PFaT and PF3T, the triplet energies are closer to those of thiophene oligomers, indicating that there is significant conjugation between fluorene and thiophene units but also that there is a more localized triplet state than with the homopolymers.

Effect of side-chain asymmetry on the intermolecular structure and order-disorder transition in alkyl-substituted polyfluorenes.

We study relations among the side-chain asymmetry, structure, and order-disorder transition (ODT) in hairy-rod-type poly(9,9-dihexylfluorene) (PF6) with two identical side chains and atactic poly(9-octyl-9-methyl-fluorene) (PF1-8) with two different side chains per repeat. PF6 and PF1-8 organize into alternating side-chain and backbone layers that transform into an isotropic phase at T^{ODT}(PF6) and T_{bi}^{ODT}(PF1-8). We interpret polymers in terms of monodisperse and bidisperse brushes and predict scenarios T^{ODT}

Interaction between the water soluble poly{1,4-phenylene-[9,9-bis(4-phenoxy butylsulfonate)]fluorene-2,7-diyl} copolymer and ionic surfactants followed by spectroscopic and conductivity measurements.

The interaction has been studied in aqueous solutions between a negatively charged conjugated polyelectrolyte poly{1,4-phenylene-[9,9-bis(4-phenoxybutylsulfonate)]fluorene-2,7-diyl} copolymer (PBS-PFP) and several cationic tetraalkylammonium surfactants with different structures (alkyl chain length, counterion, or double alkyl chain), with tetramethylammonium cations and with the anionic surfactant sodium dodecyl sulfate (SDS) by electronic absorption and emission spectroscopy and by conductivity measurements. The results are compared with those previously obtained on the interaction of the same polymer with the nonionic surfactant C12E5. The nature of the electrostatic or hydrophobic polymer-surfactant interactions leads to very different behavior. The polymer induces the aggregation with the cationic surfactants at concentrations well below the critical micelle concentration, while this is inhibited with the anionic SDS, as demonstrated from conductivity measurements. The interaction with cationic surfactants only shows a small dependence on alkyl chain length or counterion and is suggested to be dominated by electrostatic interactions. In contrast to previous studies with the nonionic C12E5, both the cationic and the anionic surfactants quench the PBS-PFP emission intensity, leading also to a decrease in the polymer emission lifetime. However, the interaction with these cationic surfactants leads to the appearance of a new emission band (approximately 525 nm), which may be due to energy hopping to defect sites due to the increase of PBS-PFP interchain interaction favored by charge neutralization of the anionic polymer by cationic surfactant and by hydrophobic interactions involving the surfactant alkyl chains, since the same green band is not observed by adding either tetramethylammonium hydroxide or chloride. This effect suggests that the cationic surfactants are changing the nature of PBS-PFP aggregates. The nature of the polymer and surfactant interactions can, thus, be used to control the spectroscopic and conductivity properties of the polymer, which may have implications in its applications.

Large-scale gene expression analysis in molecular target discovery.

The evolution of simple arrays consisting of a few genes to ones composed of thousands of genes and/or ESTs has allowed investigators unprecedented views of the molecular mechanisms within cells. Due to the enormous quantities of information derived from microarray analysis, new types of problems have surfaced, such as where to store all of the data. The ability to solve database or statistical problems has required the bench biologist to collaborate with database developers, software designers and statisticians to determine solutions for storage, analysis and interpretation of microarray data. The collaborative effort between these extremely diverse disciplines has led to the development of creative database query and gene expression analysis tools, producing significant reductions in the time required by researchers to filter through the datasets and discover the key processes perturbed by the diseases of interest. Both unsupervised and supervised analysis methods have been applied to gene expression data leading to the discovery of novel therapeutic targets and diagnostic markers. Furthermore, tumor classification based on their respective molecular fingerprints has led to the classification of cancer subtypes and the discovery of novel molecular taxonomies that may eventually lead to improved patient stratification and superior therapeutic strategies.

Cytotoxic and antitumor activity of a recombinant tumor necrosis factor-B1(Fv) fusion protein on LeY antigen-expressing human cancer cells.

We have constructed a fusion protein composed of tumor necrosis factor alpha (TNF-alpha) fused at its COOH terminus to the scFv region of monoclonal antibody (mAb) B1, an antibody that recognizes LeY antigen present on many human cancer cells. Our rationale for fusing the scFv to the COOH terminus of TNF was to diminish the binding of the fusion protein to TNF receptors because the COOH terminus of TNF is involved in binding, and thus to partially inactivate (detoxify) the molecule. The Fv region should then target and accumulate the fusion protein on cancer cells, which should compensate for the reduced binding affinity of the TNF moiety and lead to selective killing of TNF-sensitive antigen-expressing cancer cells. The fusion protein was expressed in Escherichia coli and found in insoluble inclusion bodies. After refolding and purification by anion exchange, Ni-NTA affinity, and size-exclusion chromatography, we obtained monomeric TNF-B1(Fv). This molecule binds to LeY antigen on cancer cells with the same affinity as B1(scFv) and B1(scFv) immunotoxins but with significantly lower affinity to the TNF receptor compared to the TNF trimer. TNF-B1(Fv) is very toxic to LeY antigen-expressing cancer cells that are sensitive to TNF (e.g., MCF-7 breast or CRL-1739 gastric cancer cells). This cytotoxicity is antibody targeted and TNF mediated because it can be prevented (as shown on MCF-7 cells) by an antibody competing for LeY antigen binding and by an antibody that neutralizes TNF-alpha. TNF-B1(Fv) kills TNF-alpha-sensitive cells that do not express the target antigen only at much higher doses than TNF trimer, and it does not kill LeY-bearing but TNF-alpha-resistant cells. TNF-B1(Fv) can cause significant tumor regression of MCF-7 tumor xenografts in mice at doses that are not toxic to the mice. Thus, the reduced binding of the TNF moiety to TNF receptors, combined with binding of the B1(Fv) portion to LeY antigen, makes TNF-B1(Fv) an agent for selective killing of LeY-expressing TNF-sensitive cancer cells.

Influence of molecular weight on the phase behavior and structure formation of branched side-chain hairy-rod polyfluorene in bulk phase.

We report on an experimental study of the self-organization and phase behavior of hairy-rod pi -conjugated branched side-chain polyfluorene, poly[9,9-bis(2-ethylhexyl)-fluorene-2,7-diyl]-i.e., poly[2,7-(9,9-bis(2-ethylhexyl)fluorene] (PF2/6) -as a function of molecular weight (M(n)) . The results have been compared to those of phenomenological theory. Samples for which M(n) =3-147 kg/mol were used. First, the stiffness of PF2/6 , the assumption of the theory, has been probed by small-angle neutron scattering in solution. Thermogravimetry has been used to show that PF2/6 is thermally stable over the conditions studied. Second, the existence of nematic and hexagonal phases has been phenomenologically identified for lower and higher M(n) (LMW, M(n) < M(*)(n) and HMW, M(n) > M(*)(n) ) regimes, respectively, based on free-energy argument of nematic and hexagonal hairy rods and found to correspond to the experimental x-ray diffraction (XRD) results for PF2/6 . By using the lattice parameters of PF2/6 as an experimental input, the nematic-hexagonal transition has been predicted in the vicinity of glassification temperature (T(g)) of PF2/6 . Then, by taking the orientation parts of the free energies into account the nematic-hexagonal transition has been calculated as a function of temperature and M(n) and a phase diagram has been formed. Below T(g) of 80 degrees C only (frozen) nematic phase is observed for M(n)< M(*)(n) = 10(4) g/mol and crystalline hexagonal phase for M(n) > M(*)(n) . The nematic-hexagonal transition upon heating is observed for the HMW regime depending weakly on M(n) , being at 140-165 degrees C for M(n) > M(*)(n). Third, the phase behavior and structure formation as a function of M(n) have been probed using powder and fiber XRD and differential scanning calorimetry and reasonable semiquantitative agreement with theory has been found for M(n) >or=3 kg/mol. Fourth, structural characteristics are widely discussed. The nematic phase of LMW materials has been observed to be denser than high-temperature nematic phase of HMW compounds. The hexagonal phase has been found to be paracrystalline in the (ab0) plane but a genuine crystal meridionally. We also find that all these materials including the shortest 10-mer possess the formerly observed rigid five-helix hairy-rod molecular structure.

MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling.

The trend toward high-throughput techniques in molecular biology and the explosion of online scientific data threaten to overwhelm the ability of researchers to take full advantage of available information. This problem is particularly severe in the rapidly expanding area of gene expression experiments, for example, those carried out with cDNA microarrays or oligonucleotide chips. We present an Internet-based hypertext program, MedMiner, which filters and organizes large amounts of textual and structured information returned from public search engines like GeneCards and PubMed. We demonstrate the value of the approach for the analysis of gene expression data, but MedMiner can also be extended to other areas involving molecular genetic or pharmacological information. More generally still, MedMiner can be used to organize the information returned from any arbitrary PubMed search.

Geometry-dependent electronic properties of highly fluorescent conjugated molecules

We present a combined experimental/theoretical study of the electronic properties of conjugated para-phenylene type molecules under high pressure up to 80 kbar. Pressure is used as a tool to vary the molecular geometry and intermolecular interaction. The influence of the latter two on singlet and triplet excitons as well as polarons is monitored via optical spectroscopy. We have performed band structure calculations for the planar poly(para-phenylene) and calculated the dielectric function. By varying the intermolecular distances and the length of the polymer repeat unit the observed pressure effects can be explained.

Polarized photoluminescence and spectral narrowing in an oriented polyfluorene thin film.

The oriented polyfluorene 1 is a promising candidate for a blue polarized emitter in organic optoelectronic devices. By examination of the anisotropic luminescence of thin films of 1, polarization-dependent spectral narrowing was found at high excitation densities, which is of particular interest in reducing the threshold for optically pumped polymer lasers. Femtosecond pump­probe experiments show optical gain at this spectral position.