Highly sensitive biological and chemical sensors based on reversible fluorescence quenching in a conjugated polymer

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.

Characterization of tectoRNA assembly with cationic conjugated polymers

Association between RNAs with preprogrammed molecular recognition units can be quantified by using cationic, water-soluble conjugated polymers. The method uses a fluorophore-labeled probe RNA (RNA-F*), which is treated with a target structure (RNA-T). Heterodimer formation, (RNA-T/RNA-F*), increases the total negative charge on the F*-bearing macromolecule and reduces the number of negatively charged molecules (relative to unbound RNA-T+ RNA-F*). On the basis of electrostatic interactions, we anticipated more effective binding between CCP and (RNAT/RNA-F*), a reduction of the average CCP- - -F* distance, and more effective FRET upon excitation of the conjugated polymer. The resulting signals benefit from the optical amplification characteristic of emissive conjugated polymers. Solution dissociation constants can be determined by monitoring F* intensity changes as a function of [RNA-F*] and the ratio: [I(T) - I(NB)]/I(NB), where I(T) and I(NB) are the F* intensities in the presence of the target RNA (RNA-T) and a nonbinding RNA (RNA-NB), respectively, while keeping the concentration of the conjugated polymer constant. By focusing on [I(T) - I(NB)]/I(NB) as a function of RNA concentration, one can detect the concentration range wherein increased fluorescence is the result of dimerization.

High-Efficiency, Environment-Friendly Electroluminescent Polymers with Stable High Work Function Metal as a Cathode: Green- and Yellow-Emitting Conjugated Polyfluorene Polyelectrolytes and Their Neutral Precursors

A series of aminoalkyl-substituted polyfluorene copolymers with benzothiadiazole (BTDZ) of different content were synthesized by Suzuki coupling reaction, and their quaternized ammonium polyelectrolyte derivatives were obtained through a postpolymerization treatment on the terminal amino groups. Copolymers are soluble in environmentally friendlier solvents, such as alcohols. It was found that the efficient energy transfer occurs by exciton trapping on the narrow band gap BTDZ site under UV illumination. Only 1% of BTDZ content is needed to completely quench a fluorene emission for both the neutral and the quaternized copolymers in the neat film. Absolute PL efficiencies of copolymer films were greatly enhanced as a result of the suppression of excimer formation. Light-emitting devices fabricated from these copolymers show high external quantum efficiencies over 3% and 1% for the neutral precursor and the quaternized copolymers, respectively, with high work function metals such as Al as a cathode. To the best of our knowledge, this is the first report on an electroluminescent polymer which bears the high EL efficiency, the electron-injection ability from high work function metals, and the solubility in environment-friendly solvents at the same time. These features make them a promising candidate for the next generation of light-emitting copolymers in PLED flat panel display application.

Time-resolved energy transfer in DNA sequence detection using water-soluble conjugated polymers: the role of electrostatic and hydrophobic interactions

We have investigated the energy transfer processes in DNA sequence detection by using cationic conjugated polymers and peptide nucleic acid (PNA) probes with ultrafast pump-dump-emission spectroscopy. Pump-dump-emission spectroscopy provides femtosecond temporal resolution and high sensitivity and avoids interference from the solvent response. The energy transfer from donor (the conjugated polymer) to acceptor (a fluorescent molecule attached to a PNA terminus) has been time resolved. The results indicate that both electrostatic and hydrophobic interactions contribute to the formation of cationic conjugated polymers/PNA-C/DNA complexes. The two interactions result in two different binding conformations. This picture is supported by the average donor-acceptor separations as estimated from time-resolved and steady-state measurements. Electrostatic interactions dominate at low concentrations and in mixed solvents.

Amplified fluorescence sensing of protease activity with conjugated polyelectrolytes

Fluorescent conjugated polyelectrolytes with pendant ionic sulfonate and carboxylate groups are used to sense protease activity. Inclusion of the fluorescent conjugated polyelectrolyte into the assay scheme leads to amplification of the sensory response. The sensing mechanism relies on an electrostatic interaction between the conjugated polyelectrolyte and a peptide substrate that is labeled with a fluorescence quencher. Enzyme activity and hydrolysis kinetics are measured in real time by using fluorescence spectroscopy. Two approaches are presented. In the first approach, a fluorescence turn-on sensor was developed that is based on the use of p-nitroanilide-labeled peptide substrates. In this system enzyme-catalyzed peptide hydrolysis is signaled by an increase in the fluorescence from the conjugated polyelectrolyte. The turn-on system was used to sense peptidase and thrombin activity when the concentrations of the enzyme and substrate are in the nanomolar regime. Kinetic parameters were recovered from real-time assays. In the second approach, a fluorescence turn-off sensor was developed that relies on a peptide-derivatized rhodamine substrate. In the turn-off system enzyme-catalyzed peptide hydrolysis is signaled by a decrease in the fluorescence intensity of the conjugated polyelectrolyte.

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.

Interpolyelectrolyte complexes of conjugated copolymers and DNA: platforms for multicolor biosensors

Interchain interactions modulate the frequency of emission from a cationic water-soluble conjugated polymer. The polymer, PFPB, is obtained by a Suzuki copolymerization of p-phenylenebisboronic acid with a 95:5 mixture of 2,7-dibromo-9,9-bis(6'-bromohexyl)fluorene and 4,7-dibromo-2,1,3-benzothiadiazole, followed by quarternization of the pendant groups by addition of NMe3. The structure of PFPB contains 5% of the 2,1,3-benzothiadiazole (BT) chromophore within a cationic poly(fluorene-co-phenylene) polymer chain. The emission of PFPB is blue under dilute conditions (<1 x 10-6 M in repeat units) and green at higher concentrations. Energy transfer to dye-labeled ss-DNA is more efficient, relative to the parent polymer poly(9,9-bis(6'-N,N,N,-trimethylammonium)hexyl)fluorene-co-alt-1,4-phenylene) dibromide (PFP), as a result of improved spectral overlap. By using a peptide nucleic acid (PNA-C*) labeled with a red-emitting chromophore one can obtain three different emission colors, depending on the nature of the substrate under interrogation. If no ss-DNA is present, the solution emits blue. With a ss-DNA that is noncomplementary to PNA-C*, green emission is observed. Red emission occurs upon addition of ss-DNA complementary to the PNA sequence.

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.

Fluorescent Polymeric Transducer for the Rapid, Simple, and Specific Detection of Nucleic Acids at the Zeptomole Level

We report the specific detection of a few hundred molecules of genetic material using a fluorescent polythiophene biosensor. Such recognition is based on simple electrostatic interactions between a cationic polymeric optical transducer and the negatively charged nucleic acid target and can be done in less than 1 h, simply and affordably, and without any chemical reaction. This simple system is versatile enough to detect nucleic acids of various lengths, including a segment from the RNA genome of the Influenza virus.

Optical Sensors Based on Hybrid Aptamer/Conjugated Polymer Complexes

Single-stranded DNA (aptamer) can specifically bind potassium ions or human alpha-thrombin. When binding takes place, the aptamer undergoes a conformational transition from an unfolded to a folded structure. This conformational change of the negatively charged oligonucleotide can be detected by adding a water-soluble, cationic polythiophene derivative, which transduces the new complex formation into an optical (colorimetric or fluorometric) signal without any labeling of the probe or of the target. This simple and rapid methodology has enabled the detection of human thrombin in the femtomole range. This new biophotonic tool can easily be applied to the detection of various other proteins as well as being useful in the high-throughput screening of new drugs.

Enhanced photoluminescence from poly(phenylene vinylene) ∶ dendrimer polyelectrolyte assemblies in solution

Poly(2,5-methoxy-propyloxy sulfonate phenylene vinylene)(MPS-PPV) and DAB-Am-16, a generation 3.0 polypropylenimine hexadecamine dendrimer (DAB), are shown to form a tunable photoresponsive polyelectrolyte assembly in aqueous solution with an enhanced emission signal of up to 18-times that of MPS-PPV alone.

Linewidth-limited energy transfer in single conjugated polymer molecules

Using low temperature single molecule spectroscopy on rigid-rod conjugated polymers we are able to identify homogeneously broadened, strongly polarized emission from individual chromophore units on a single chain. Gated fluorescence spectroscopy allows real time imaging of intramolecular energy transfer as the chain behaves as a series of weakly interacting chromophores. Energy transfer is controlled by the chromophoric spectral linewidth, which depends on temperature. Linewidths exceeding intramolecular disorder lead to incoherent chromophore coupling and collective fluorescence phenomena.

Shape-Adaptable Water-Soluble Conjugated Polymers

Cationic water-soluble conjugated polymers with a non "rigid-rod" aspect ratio can be prepared by Suzuki coupling condensation polymerization of 2,7-dibromo-9,9-bis(6'-bromohexyl)fluorene and varying ratios of p- and m-phenyl diboronic acids, followed by reaction with trimethylamine. The resulting polymers are designated MnPm+, where the subscripts in Mn and Pm correspond to the ratio of meta and para linkages, respectively. Absorption and fluorescence spectra indicate facile energy transfer via interachain or intrachain mechanisms. The emission of MnPm+ with m > 50 matches that of M0P100+. Excitations ultimately reside in the polymer segments with largest number of para linkages. FRET experiments show that the polymers with a more flexible structure are better donors to fluorescein-labeled double-stranded DNA. Similar results are obtained when intercalated ethidium bromide is used as the acceptor. These results indicate that there is better spatial registry between the flexible conjugated polymers and the secondary structure of DNA.

Self-assembly of synthetic peptides control conformation and optical properties of a zwitterionic polythiophene derivative

The optical transitions of a chiral, three-substituted polythiophene with an amino acid function can be tuned by interactions with synthetic peptides. The addition of a positively charged peptide with a random-coil formation will force the polymer to adopt a nonplanar conformation, and the intensity of the emitted light is increased and blue-shifted. After the addition of a negatively charged peptide with a random-coil conformation, the backbone of the polymer adopts a planar conformation and an aggregation of the polymer chains occurs, seen as a red shift and a decrease of the intensity of the emitted light. By adding the positively charged peptide designed to form a four-helix bundle with the negatively charged peptide, the polymer aggregates are disrupted and the intensity of the emitted light is increased because of separation of the polymer chains. This technique could be used as a platform for making novel sensors and biomolecular switches.

A Comparison of Crystalline- and Graft Polymer-Based Chemosensors

Herein, we report a highly sensitive luminescent thin film chemosensor constructed out of a small-molecule donor/acceptor system. Two types of films were compared: one using a small-molecule crystalline donor/acceptor pair and the other using a donor-graft polymer/small-molecule acceptor pair. The acceptor selected for this proof of concept responds to acid, causing its absorption and emission bands to red-shift, which increases spectral overlap with the donor. This increase in overlap greatly enhances energy transfer from the acceptor to the donor. Signal amplification was ascertained by measuring the ratio of acceptor fluorescence when the donor was excited versus direct excitation of the acceptor. Both types of films exhibited large amplification. For the polymeric system, the mechanism of energy migration was investigated by the use of steady-state fluorescence spectroscopy. The mechanism was determined to be dominated by an exciton-hopping process.

Effect of chromophore-charge distance on the energy transfer properties of water-soluble conjugated oligomers

The synthesis of 1,4-bis(9,9'-bis(3"-(N,N,N-trimethylammonium)-propyl)-2'-fluorenyl)benzene tetrabromide (C3), 1,4-bis(9,9'-bis(4"-(N,N,N-trimethylammonium)-butyl)-2'-fluorenyl)benzene tetrabromide (C4), 1,4-bis(9,9'-bis(6"-(N,N,N-trimethylammonium)-hexyl)-2'-fluorenyl)benzene tetrabromide (C6), and 1,4-bis(9,9'-bis(8"-(N,N,N-trimethylammonium)-octyl)-2'-fluorenyl)benzene tetrabromide (C8) is reported. Fluorescence energy transfer experiments between C3-C8 and the acceptors pentasodium 1,4-bis(4'(2",4"-bis(butoxysulfonate)-styryl)styryl)-2-(butoxysulfonate)-5-methoxybenzene (3), fluorescein labeled single-stranded DNA and fluorescein labeled double-stranded DNA in water, buffer, and methanol reveal the importance of hydrophobic and electrostatic forces in determining chromophore-chromophore close proximity. In water, the oligomers with longer side chain length show better energy transfer, as well as higher Stern-Volmer quenching constants (K(sv)), largely due to a stronger hydrophobic attraction between the optically active components. In methanol, the differences in energy transfer are leveled, and the oligomers with shorter side chain lengths show higher K(sv) values. Compounds C3, C4, C6, and C8 were also used to dissect the different contributors to DNA hybridization assays based on cationic conjugated polymers.

Chip and solution detection of DNA hybridization using a luminescent zwitterionic polythiophene derivative

Electronic polymers in aqueous media may offer bioelectronic detection of biospecific interactions. Here we report a fluorometric DNA hybridization detection method based on non-covalent coupling of DNA to a water-soluble zwitterionic polythiophene derivative. Introduction of a single-stranded oligonucleotide will induce a planar polymer and aggregation of the polymer chains, detected as a decrease of the intensity and a red-shift of the fluorescence. On addition of a complementary oligonucleotide, the intensity of the emitted light is increased and blue-shifted. The detection limit of this method is at present approximately 10(-11) moles. The method is highly sequence specific, and a single-nucleotide mismatch can be detected within five minutes without using any denaturation steps. The interaction with DNA and the optical phenomena persists when the polymer is deposited and patterned on a surface. This offers a novel way to create DNA chips without using covalent attachment of the receptor or labelling of the analyte.

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.

Conjugated polymers as molecular materials: how chain conformation and film morphology influence energy transfer and interchain interactions

The electronic structure of conjugated polymers is of current interest because of the wide range of potential applications for such materials in optoelectronic devices. It is increasingly clear that the electronic properties of conjugated polymers depend sensitively on the physical conformation of the polymer chains and the way the chains pack together in films. This article reviews the evidence that interchain electronic species do form in conjugated polymer films, and that their number and chemical nature depend on processing conditions; the chain conformation, degree of interchain contact, and rate of energy transfer can be controlled by factors such as choice of solvent, polymer concentration, thermal annealing, presence of electrically charged side groups, and encapsulation of the polymer chains in mesoporous silica. Taken together, the results reconcile many contradictions in the literature and provide a prescription for the optimization of conjugated polymer film morphology for device applications.

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.

Water-soluble oligomer dimers based on paracyclophane: a new optical platform for fluorescent sensor applications

Water soluble paracyclophane chromophore dimers provide optical reporters that show little sensitivity to surfactants and thus are ideal for biosensor design. Strong intramolecular delocalization circumvents complications from intermolecular delocalization in spontaneously formed aggregates. The synthesis of 2 involves a novel TBAT deprotection/butane sultone ring-opening sequence, which should be general for the preparation of water-soluble conjugated oligomers and polymers.

Saccharide Detection Based on the Amplified Fluorescence Quenching of a Water-Soluble Poly(phenylene ethynylene) by a Boronic Acid Functionalized Benzyl Viologen Derivative

The amplified quenching of an anionic conjugated polymer, sulfonated poly(phenylene ethynylene) (PPE-SO3 -), by a cationic quencher comprising a boronic acid functionalized benzyl viologen (p-BV2+), has been used to optically detect sugars. In the absence of sugar, a strong polymer/quencher interaction leads to superlinear quenching. In the presence of sugar at pH 7.4, the dicationic viologen derivative forms a neutral zwitterionic species, reducing its ability to complex with and quench the anionic polymer's emission. Addition of sugar to the polymer/quencher system leads a large increase in the fluorescence intensity (up to 70-fold in one case). Spectral data, quenching parameters, and sugar titration curves are presented and discussed in terms of future development of glucose sensors.

Interchain vs. intrachain energy transfer in acceptor-capped conjugated polymers

The energy-transfer processes taking place in conjugated polymers are investigated by means of ultrafast spectroscopy and correlated quantum-chemical calculations applied to polyindenofluorenes end-capped with a perylene derivative. Comparison between the time-integrated luminescence and transient absorption spectra measured in solution and in films allows disentangling of the contributions arising from intrachain and from interchain energy-migration phenomena. Intrachain processes dominate in solution where photoexcitation of the polyindenofluorene units induces a rather slow energy transfer to the perylene end moieties. In films, close contacts between chains favors interchain transport of the excited singlet species (from the conjugated bridge of one chain to the perylene unit of a neighboring one); this process is characterized by a 1-order-of-magnitude increase in transfer rate with respect to solution. This description is supported fully by the results of quantum-chemical calculations that go beyond the usual point-dipole model approximation and account for geometric relaxation phenomena in the excited state before energy migration. The calculations indicate a two-step mechanism for intrachain energy transfer with hopping along the conjugated chains as the rate-limiting step; the higher efficiency of the interchain transfer process is mainly due to larger electronic coupling matrix elements between closely lying chains.

DNA detection using water-soluble conjugated polymers and peptide nucleic acid probes

The light-harvesting properties of cationic conjugated polymers are used to sensitize the emission of a dye on a specific peptide nucleic acid (PNA) sequence for the purpose of homogeneous, "real-time" DNA detection. Signal transduction is controlled by hybridization of the neutral PNA probe and the negative DNA target. Electrostatic interactions bring the hybrid complex and cationic polymer within distances required for Förster energy transfer. Conjugated polymer excitation provides fluorescein emission >25 times higher than that obtained by exciting the dye, allowing detection of target DNA at concentrations of 10 pM with a standard fluorometer. A simple and highly sensitive assay with optical amplification that uses the improved hybridization behavior of PNA/DNA complexes is thus demonstrated.

Biosensors from conjugated polyelectrolyte complexes

A charge neutral complex (CNC) was formed in aqueous solution by combining an orange light emitting anionic conjugated polyelectrolyte and a saturated cationic polyelectrolyte at a 1:1 ratio (per repeat unit). Photoluminescence (PL) from the CNC can be quenched by both the negatively charged dinitrophenol (DNP) derivative, (DNP-BS(-)), and positively charged methyl viologen (MV(2+)). Use of the CNC minimizes nonspecific interactions (which modify the PL) between conjugated polyelectrolytes and biopolymers. Quenching of the PL from the CNC by the DNP derivative and specific unquenching on addition of anti-DNP antibody (anti-DNP IgG) were observed. Thus, biosensing of the anti-DNP IgG was demonstrated.

Building highly sensitive dye assemblies for biosensing from molecular building blocks

Fluorescence superquenching is investigated for polyelectrolytes consisting of cyanine dye pendant polylysines ranging in number of polymer repeat units (N(PRU)) from 1 to 900, both in solution and after adsorption onto silica nanoparticles. As N(PRU) increases, the absorption and fluorescence evolve from monomer spectra to red-shifted features indicative of molecular J aggregates. In solution, the superquenching sensitivity toward an anionic electron acceptor increases by more than a millionfold over the N(PRU) range from 1 to 900. The dramatic increase is attributed to enhanced equilibrium constants for binding the quenchers, and the amplified quenching of a delocalized exciton of approximately 100 polymer repeat units. The self-assembly of monomer onto silica and clay nanoparticles leads to formation of J aggregates, and surface-activated superquenching enhanced 10,000x over the monomer in solution, indicating the formation of "self-assembled polymers" on the nanoparticle surface. Utilization of these self-assembled polymers as high-sensitivity biosensors is demonstrated.

Emission of a single conjugated polymer chain isolated in its single crystal monomer matrix

The excitonic luminescence of a highly ordered single conjugated polymer chain is studied by microphotoluminescence. At T< or =10 K it consists of a single Lorentzian line. The linewidth increases linearly with T between 6 and 60 K, from 350 microeV at 6 K, indicating a pure dephasing time of approximately 2 ps. Above 10 K, other neighboring regions along the chain direction start to emit at a slightly higher (by approximately 1 meV) energy. This indicates very small inhomogeneous broadening, very long chains ( > or =10 microm), and a long range and very rapid exciton energy transfer ( >10 microm in <100 ps).