Building highly sensitive dye assemblies for biosensing from molecular building blocks

Energy transfer mediated fluorescence from blended conjugated polymer nanoparticles

Nanoparticles consisting of a derivative of the blue-emitting conjugated polymer polyfluorene doped with green-, yellow-, and red-emitting conjugated polymers were prepared by a reprecipitation method. The nanoparticles can be described as a system of densely packed chromophores that exhibit efficient energy transfer from the host to the dopant polymers. Fluorescence quenching analysis of the host polymer as a function of the dopant concentration indicates that one energy acceptor molecule can effectively quench 90% of the fluorescence of a nanoparticle consisting of 100-200 host conjugated polymer molecules. A nanoparticle energy transfer model was developed that successfully describes the quenching behavior of a small number of highly efficient energy acceptors per nanoparticle. The fluorescence brightness of the blended polymer nanoparticles was determined to be much higher than that of inorganic quantum dots and dye-loaded silica particles of similar dimensions. The combination of high fluorescence brightness and tunable fluorescence of these blended nanoparticles is promising for ultrasensitive fluorescence-based assays.

Chiral Supramolecular Assemblies of a Squaraine Dye in Solution and Thin Films: Concentration-, Temperature-, and Solvent-Induced Chirality Inversion

We prepared novel cholesterol-appended squaraine dye 1 and model squaraine dye 2 and investigated their aggregation behavior in solution and thin films using photophysical, chiroptical, and microscopic techniques. Investigations on the dependence of aggregation on solvent composition (good/poor, CHCl3/CH3CN) demonstrated that squaraine dye 1 forms two novel H-type chiral supramolecular assemblies with opposite chirality at different good/poor solvent compositions. Model compound 2 formed J-type achiral assemblies under similar conditions. The supramolecular assembly of 1 observed at lower fractions of the poor solvent could be assigned to the thermodynamically stable form, while a kinetically controlled assembly is formed at higher fractions of the poor solvent. This assignment is evidenced by temperature- and concentration-dependent experiments. With increasing temperature, the chirality of the kinetically controlled aggregate was lost and, on cooling, the aggregate with the opposite chirality was formed. On further heating and cooling the aggregates thus formed resulted in no significant changes in chirality, that is they are thermodynamically stable. Similarly, at lower concentrations, the thermodynamically stable form exists, but at higher concentration aggregation was found to proceed with kinetic control. Based on these observations it can be assumed that formation of the kinetically controlled assembly might be largely dependent on the presence of the nonpolar cholesterol moiety as well as the amount of poor solvent present. However, under solvent-free conditions, structurally different aggregates were observed when drop cast from solutions containing monomer, whereas a left-handed CD signal corresponding to the thermodynamically controlled assemblies was observed from pre-aggregated solutions.

Preparation of an ordered array of cyanine complex microdomes by a simple dewetting method

We demonstrate a simple method for fabricating a two-dimensional array of microdomes that consist of cyanine dye complexes. Investigation of the morphology and the fluorescence emission of microdomes was carried out before/after annealing. The principal of microdome formation is "dewetting," which is a self-organization phenomena. Generally, one can observe dewetting when a liquid film breaks spontaneously on a nonwettable substrate, leaving droplets or patterns on the substrate. A cyanine dye complex was prepared from a cationic cyanine dye and an anionic amphiphile, or vice versa, an anionic dye and a cationic amphiphile. When a chloroform solution of the cyanine complex was spread on a glass substrate by a roller, microdomes of the cyanine dye complex formed in dewetted films. The roller draws the three-phase line (the air-solid-liquid boundary of the droplet of the chloroform solution) with a constant rate. Thus dewetting can be controlled and leads to a two-dimensional ordered array of uniform sized microdomes. The diameter and height of microdomes decrease with increasing roller speed. Fluorescence microscopy shows that the cyanine dye complex formed J-aggregates. Annealing caused transformation of the dome morphology and a change of the fluorescence spectra. The microdome transformed into anisotropic crystals or became amorphous depending on the molecular structure of the cyanine dye.

Dissecting the General Physicochemical Properties of Noncovalent Interactions Involving Tyrosine Side Chain as a Second-Shell Ligand in Biomolecular Metal-Binding Site Mimetics: An Experimental Study Combining Fluorescence,13C NMR Spectroscopy and ESI Mass Spectrometry

Detailed physicochemical features inherent in the dynamic cation-pi interactions of aromatic amino acid side chains in the secondary coordination spheres around metal ions were extracted and mapped by intrinsic tyrosine fluorescence titration experiments with two homologous, artificially engineered metal-binding scaffolds which mimic metal-binding sites in metalloproteins. A newly formulated method for the treatment of fluorescence titration data allows straightforward assessment of both the magnitudes and properties of metal-chelation-assisted cation-aromatic interactions (K2) underlying a proposed two-step metallosupramolecular association process. The unprecedented linear platform-motif correlations between the two contrasting scaffolds in their changes in tyrosine fluorescence on binding of 3d metal cations help to elucidate the properties of general cation-arene recognition corresponding to the metal-responsive characteristics of the second-shell Tyr residue surrounding the metal-binding sites in the supramolecular context, and thereby define a new noncovalent design principle for metal-ion recognition in aqueous solution. As supported by NMR spectroscopic and ESI-MS analyses and molecular mechanics force field calculations, the systematic study exemplifies the concept of using steady-state tyrosine fluorescence as a powerful tool for comprehensive descriptions of cation-pi interactions in the extended environment of a metal-binding site. We established that the physicochemical properties pertaining to indirect metal-arene interactions are highly dependent on the electronic properties of the metal ions. This work suggests that second-shell cation-pi interactions may play more diverse roles, including modulation of structure, reactivity, and function of metal-binding sites, than the previously well-established direct cation-pi interactions involving hard cations (e.g., alkali metal ions). Moreover, such a study will continue to complement theoretical predications and/or the early experimental investigations in organic solvents.

Modification of the Nanoscale Structure of the J-Aggregate of a Sulfonate-Substituted Amphiphilic Carbocyanine Dye through Incorporation of Surface-Active Additives

The amphiphilic dye 3,3'-bis(2-sulfopropyl)-5,5',6,6'-tetrachloro-1,1'-dioctylbenzimidacarbocyanine (C8S3) self-aggregates in aqueous solution to form tubular J-aggregates with a diameter of 17.0 +/- 0.5 nm, a wall thickness of approximately 4 nm, and a length exceeding several hundred nanometers. The absorption spectrum shows the typical features expected for tubular J-aggregates with several sharp and red-shifted absorption bands. Morphological investigations using cryo-transmission electron microscopy (cryo-TEM) and spectroscopic investigations reveal a high stability of the tubular morphology but a tendency of the aggregates to assemble into ropelike bundles after several weeks of storage. It is found that aggregation in solutions containing additives such as alcohols or surfactants results in the formation of new types of aggregates. A second type of tubular aggregate with a diameter of 13.0 +/- 0.5 nm is observed when the solutions contain more than 10 wt % MeOH. On the time scale of days these tubular aggregates transform into ribbonlike structures characterized by a new absorption spectrum, and they convert after several weeks into giant tubes with diameters of up to 500 nm.

β-1,3-Glucan Polysaccharide (Schizophyllan) Acting as a One-Dimensional Host for Creating Supramolecular Dye Assemblies

We have demonstrated that one-dimensional supramolecular dye assemblies with a uniform diameter can be created by utilizing schizophyllan (SPG) as a one-dimensional host. In the supramolecular nanofibers, the dye molecules are assembled into the different aggregation modes depending on the preparation procedures. The findings establish that SPG is useful for creating the supramolecular nanofibers, where temporal superstructures can be stabilized by the SPG-specific helical higher-order structure. [structure: see text].

Controlled Formation of the Two-Dimensional TTBC J-Aggregates in an Aqueous Solution

Strong experimental and theoretical evidence was provided on the controlled formation of the two-dimensional J-aggregates that were assembled in the herringbone morphology. The exciton-band structure formation of 1,1',3,3'-tetraethyl-5,5',6,6'-tetrachlorobenzimidazolocarbocyanine (TTBC) J-aggregates was investigated in ionic (NaOH) aqueous solution at room temperature. The control was achieved by changing the [TTBC] at a given [NaOH], or vice versa, and was monitored through the changes in the absorption, fluorescence excitation, and emission spectra. Specific attention was paid to expose the excited-state structure and dynamics through simulations of the excitonic properties, which included diagonal energetic disorder and phonon-assisted exciton relaxation. Aggregates were characterized by an asymmetrically split Davydov pair, an H-band (approximately 500 nm, 1300 cm(-1) wide, Lorentzian-like) and a J-band (approximately 590 nm, 235 cm(-1) wide, with a band shape typical of a one-dimensional J-aggregate), whose relative intensities showed a strong dependence on the [TTBC]/[NaOH]. The H-band is favored by high [TTBC] or high [NaOH]. An explanation of the control on the aggregate formation was given by correlating the changes in the absorption with the structural modifications and the subsequent changes in the dynamics, which were induced by variations in the dye and NaOH concentrations. The J-band shape/width was attributed to disorder and disorder-induced intraband phonon-assisted exciton relaxation. The intraband processes in both bands were estimated to occur in the same time scale (about a picosecond). It has been suggested that the wide energetic gap between the Davydov split bands (3000 cm(-1)) could get bridged by the excitonic states of the loosely coupled chains, in addition to the monomeric species at low [TTBC]. Phonon-assisted interband relaxation, through the band gap states and/or directly from the H- to the J-band, are suggested for accounting the difference between the bandwidths and shapes of the two bands. Energy transfer between the H-band and the monomeric species is suggested as crucial for tuning the relative strengths of the two bands.

Adsorption of Cyanine Dyes on Gold Nanoparticles and Formation of J-Aggregates in the Nanoparticle Assembly

This paper describes the results of an investigation of the interparticle interactions and reactivities in the assembly of gold nanoparticles mediated by cyanine dyes. The combination of the positively charged indolenine cyanine dyes and the negatively charged gold nanoparticles is shown to form a J-aggregate bridged assembly of nanoparticles, in addition to hydrophobic interparticle and electrostatic dye-particle interactions. Such interparticle interactions and reactivities are studied by probing the absorption of J-aggregates and fluorescence from the dyes and the surface plasmon resonance absorption from the nanoparticles. The J-aggregation of the dyes adsorbed on the nanoparticles is shown to play an important role in the assembly of nanoparticles. The spectral evolution of the J-band of the dyes and the surface plasmon resonance band of the nanoparticles was found to be sensitive to the nature of the charge and the structure of the dyes. The fluorescence quenching for the dyes was shown to be quantitatively related to the surface coverage of the dyes on the nanocrystal surfaces. These findings have provided important information for assessing a two-step process involving a rapid adsorption of the dyes on the nanoparticles and a subsequent assembly of the nanoparticles involving a combination of interparticle J-aggregation and hydrophobic interactions of the adsorbed dyes. The results are discussed in terms of the structural effects of the dyes, and the interparticle molecular interactions and reactivities, which provide important physical and chemical insights into the design of dye-nanoparticle structured functional nanomaterials.

Superquenching as a detector for microsphere-based flow cytometric assays

BACKGROUND

Fluorescent conjugated polymers display high fluorescence quantum yields and enhanced sensitivity to quenching (superquenching) by oppositely charged quenchers through energy or electron transfer. Fluorescent polymers and their quenchers are used in bead-based biosensor applications where the polymers are coated on particles. In this work, we investigate a detection method that utilizes superquenching on microspheres, which can be used for flow cytometric assays.

METHODS

Microspheres were coated with the fluorescent cationic polyelectrolyte poly(p-phenylene-ethynylene) (PPE), and its superquenching by 9,10-anthraquinone-2,6-disulfonic acid (AQS) was examined by fluorometric methods in presence and in absence of a barrier to superquenching in the form of an anionic lipid bilayer.

RESULTS

Flow cytometry detected superquenching of PPE on microspheres (MS-PPE) by AQS where high levels of reduction in fluorescence were observed. Adding different concentrations of AQS to MS-PPE yielded a Stern-Volmer quenching constant of 0.8x10(6) M-1. While forming an anionic lipid bilayer around the MS-PPE acted as a barrier to superquenching by AQS, disrupting the lipid bilayer allowed superquenching to take place.

CONCLUSIONS

The sensitivity of flow cytometry in detecting fluorescence of microspheres and the amplified quenching sensitivity of fluorescent conjugated polymers both offer advantages over other fluorometric methods and conventional quenching detection. This study used superquenching of fluorescent polymers as a new tool in flow cytometry, thus combining the advantages offered by both method and detector. In addition, we employed the formation and the disruption of a supported lipid bilayer in mediating superquenching to offer new biosensing applications.

High-throughput kinase assays with protein substrates using fluorescent polymer superquenching

BACKGROUND

High-throughput screening is used by the pharmaceutical industry for identifying lead compounds that interact with targets of pharmacological interest. Because of the key role that aberrant regulation of protein phosphorylation plays in diseases such as cancer, diabetes and hypertension, kinases have become one of the main drug targets. With the exception of antibody-based assays, methods to screen for specific kinase activity are generally restricted to the use of small synthetic peptides as substrates. However, the use of natural protein substrates has the advantage that potential inhibitors can be detected that affect enzyme activity by binding to a site other than the catalytic site. We have previously reported a non-radioactive and non-antibody-based fluorescence quench assay for detection of phosphorylation or dephosphorylation using synthetic peptide substrates. The aim of this work is to develop an assay for detection of phosphorylation of chemically unmodified proteins based on this polymer superquenching platform.

RESULTS

Using a modified QTL Lightspeed assay, phosphorylation of native protein was quantified by the interaction of the phosphorylated proteins with metal-ion coordinating groups co-located with fluorescent polymer deposited onto microspheres. The binding of phospho-protein inhibits a dye-labeled "tracer" peptide from associating to the phosphate-binding sites present on the fluorescent microspheres. The resulting inhibition of quench generates a "turn on" assay, in which the signal correlates with the phosphorylation of the substrate. The assay was tested on three different proteins: Myelin Basic Protein (MBP), Histone H1 and Phosphorylated heat- and acid-stable protein (PHAS-1). Phosphorylation of the proteins was detected by Protein Kinase Calpha (PKCalpha) and by the Interleukin -1 Receptor-associated Kinase 4 (IRAK4). Enzyme inhibition yielded IC50 values that were comparable to those obtained using peptide substrates. Statistical parameters that are used in the high-throughput community to determine assay robustness (Z'-value) demonstrate the suitability of this format for high-throughput screening applications for detection of inhibitors of enzyme activity.

CONCLUSION

The QTL Lightspeed protein detection system provides a simple mix and measure "turn on" assay for the detection of kinase activity using natural protein substrates. The platform is robust and allows for identification of inhibitors of kinase activity.

Exciton Migration in Rigid-Rod Conjugated Polymers: An Improved Förster Model

The dynamics of interchain and intrachain excitation energy transfer taking place in a polyindenofluorene endcapped with perylene derivatives is explored by means of ultrafast spectroscopy combined with correlated quantum-chemical calculations. The experimental data indicate faster exciton migration in films with respect to solution as a result of the emergence of efficient channels involving hopping between chains in close contact. These findings are supported by theoretical simulations based on an improved Forster model. Within this model, the rates are expressed according to the Fermi golden rule on the basis of (i) electronic couplings that take account of the detailed shape of the excited-state wave functions (through the use of a multicentric monopole expansion) and (ii) spectral overlap factors computed from the simulated acceptor absorption and donor emission spectra with explicit coupling to vibrations (considered within a displaced harmonic oscillator model); inhomogeneity is taken into account by assuming a distribution of chromophores with different conjugation lengths. The calculations predict faster intermolecular energy transfer as a result of larger electronic matrix elements and suggest a two-step mechanism for intrachain energy transfer with exciton hopping along the polymer backbone as the limiting step. Injecting the calculated hopping rates into a set of master equations allows the modeling of the dynamics of exciton transport along the polyindenofluorene chains and yields ensemble-averaged energy-transfer rates in good agreement with experiment.

Metal ion-mediated polymer superquenching for highly sensitive detection of kinase and phosphatase activities

An assay technology for high-throughput screening of kinase and phosphatase activities is introduced. The format is based upon superquenching of fluorescent-conjugated polymers by dye-labeled kinase/phosphatase peptide substrates. The sensor platform is composed of highly fluorescent-conjugated polyelectrolytes colocated with the phosphate coordinating metal ion gallium on microspheres. Phosphorylated peptide substrates containing a quencher bind specifically to the metal ions by means of phosphate groups, resulting in quench of polymer fluorescence. The modulation of fluorescence signal is proportional to kinase or phosphatase activity and is monitored as a turn-off or turn-on signal, respectively. The assay is homogeneous and simple and can be run either as an endpoint measurement or in a kinetic mode. The assay meets the sensitivity required for high-throughput screening of kinase or phosphatase inhibitors and is a valuable tool for drug discovery. A modified version of the assay allows for the detection of protein phosphorylation.

Selective growth of metal tips onto semiconductor quantum rods and tetrapods

We show the anisotropic selective growth of gold tips onto semiconductor (cadmium selenide) nanorods and tetrapods by a simple reaction. The size of the gold tips can be controlled by the concentration of the starting materials. The new nanostructures display modified optical properties caused by the strong coupling between the gold and semiconductor parts. The gold tips show increased conductivity as well as selective chemical affinity for forming self-assembled chains of rods. Such gold-tipped nanostructures provide natural contact points for self-assembly and for electrical devices and can solve the difficult problem of contacting colloidal nanorods and tetrapods to the external world.

Fluorescent-conjugated polymer superquenching facilitates highly sensitive detection of proteases

Sensor formats have been developed for detecting the activity of proteolytic enzymes based on fluorescent conjugated polymer superquenching. These sensors employ a reactive peptide sequence within a tether linking a quencher to a biotin. The peptide binds to sensors containing colocated biotin-binding protein and fluorescent polymer by means of biotin-biotin binding protein interactions, resulting in a strong quenching of polymer fluorescence. Enzyme-mediated cleavage of the peptide results in a reversal of the fluorescence quenching. These assays for protease activity are simple, sensitive, fast, and have the specificity required for screening chemical libraries for novel protease inhibitors in a high-throughput screening assay environment. These assays have been demonstrated for enterokinase, caspase-3/7, and beta-secretase.

Applications of Fluorescent Polymer Superquenching to High Throughput Screening Assays for Protein Kinases

Protein kinases are involved in the regulation of cellular metabolism, growth, differentiation, and proliferation. Aberrations in their function can lead to diseases such as cancer and inflammation. Protein kinases are therefore possible targets for drug therapies. To address the need for high throughput screening of potential inhibitors, QTL has developed a homogeneous and robust kinase assay for use in multiwell plate format. The QTL Lightspeed fluorescence superquenching-based kinase assays do not require specialized equipment, nor do they involve the use of radioactive hazardous materials or antibodies. QTL Lightspeed kinase assays directly measure the enzymatic activity of the target and do not involve secondary (detector) enzyme. In this article, we compare QTL Lightspeed protein kinase assays using Protein Kinase A, Protein Kinase Balpha/Akt1, and ribosomal S6 kinase-2 as examples with other commercially available kinase kits. Our data show that QTL Lightspeed kinase assays offer significant advantages over the current commercial kits in terms of both sensitivity and performance. The QTL Lightspeed kinase assay also offers a kinetic assay mode where the substrate phosphorylation can be monitored in real-time.

Selective cell targeting with light-absorbing microparticles and nanoparticles

We describe a new method for selective cell targeting based on the use of light-absorbing microparticles and nanoparticles that are heated by short laser pulses to create highly localized cell damage. The method is closely related to chromophore-assisted laser inactivation and photodynamic therapy, but is driven solely by light absorption, without the need for photochemical intermediates (particularly singlet oxygen). The mechanism of light-particle interaction was investigated by nanosecond time-resolved microscopy and by thermal modeling. The extent of light-induced damage was investigated by cell lethality, by cell membrane permeability, and by protein inactivation. Strong particle size dependence was found for these interactions. A technique based on light to target endogenous particles is already being exploited to treat pigmented cells in dermatology and ophthalmology. With exogenous particles, phamacokinetics and biodistribution studies are needed before the method can be evaluated against photodynamic therapy for cancer treatment. However, particles are unique, unlike photosensitizers, in that they can remain stable and inert in cells for extended periods. Thus they may be particularly useful for prelabeling cells in engineered tissue before implantation. Subsequent irradiation with laser pulses will allow control of the implanted cells (inactivation or modulation) in a noninvasive manner.

Beyond superquenching: hyper-efficient energy transfer from conjugated polymers to gold nanoparticles

Gold nanoparticles quench the fluorescence of cationic polyfluorene with Stern-Volmer constants (KSV) approaching 1011 M-1, several orders of magnitude larger than any previously reported conjugated polymer-quencher pair and 9-10 orders of magnitude larger than small molecule dye-quencher pairs. The dependence of KSV on ionic strength, charge and conjugation length of the polymer, and the dimensions (and thus optical properties) of the nanoparticles suggests that three factors account for this extraordinary efficiency: (i) amplification of the quenching via rapid internal energy or electron transfer, (ii) electrostatic interactions between the cationic polymer and anionic nanoparticles, and (iii) the ability of gold nanoparticles to quench via efficient energy transfer. As a result of this extraordinarily high KSV, quenching can be observed even at subpicomolar concentrations of nanoparticles, suggesting that the combination of conjugated polymers with these nanomaterials can potentially lead to improved sensitivity in optical biosensors.

Capture and detection of a quencher labeled oligonucleotide by poly(phenylene ethynylene) particles

Fluorescence quenching of poly(phenylene ethynylene) (PPE) particles by a Cy-5 labeled oligonucleotide is 2 orders of magnitude more sensitive than direct excitation of the Cy-5 fluorophore.