DNA hybridization detection with water-soluble conjugated polymers and chromophore-labeled single-stranded DNA

Amplified quenching of a conjugated polyelectrolyte by cyanine dyes

The conjugated polyelectrolyte PPESO3 features a poly(phenylene ethynylene) backbone substituted with anionic 3-sulfonatopropyloxy groups. PPESO3 is quenched very efficiently (KSV > 10(6) M(-1)) by cationic energy transfer quenchers in an amplified quenching process. In the present investigation, steady-state and picosecond time-resolved fluorescence spectroscopy are used to examine amplified quenching of PPESO3 by a series of cyanine dyes via singlet-singlet energy transfer. The goal of this work is to understand the mechanism of amplified quenching and to characterize important parameters that govern the amplification process. Steady-state fluorescence quenching of PPESO3 by three cationic oxacarbocyanine dyes in methanol solution shows that the quenching efficiency does not correlate with the Forster radius computed from spectral overlap of the PPESO3 fluorescence with the cyanines' absorption. The quenching efficiency is controlled by the stability of the polymer-dye association complex. When quenching studies are carried out in water where PPESO3 is aggregated, changes observed in the absorption and fluorescence spectra of 1,1',3,3,3',3'-hexamethylindotricarbocyanine iodide (HMIDC) indicate that the polymer templates the formation of a J-aggregate of the dye. The fluorescence dynamics in the PPESO3/HMIDC system were probed by time-resolved upconversion and the results show that PPESO3 to HMIDC energy transfer occurs on two distinctive time scales. At low HMIDC concentration, the dynamics are dominated by an energy transfer pathway with a time scale faster than 4 ps. With increasing HMIDC concentration, an energy pathway with a time scale of 0.1-1 ns is active. The prompt pathway (tau < 4 ps) is attributed to quenching of delocalized PPESO3 excitons created near the HMIDC association site, whereas the slow phase is attributed to intra- and interchain exciton diffusion to the HMIDC.

DNA-PEG-DNA triblock macromolecules for reagentless DNA detection

The sandwich assay is the most common design for electrochemical DNA sensors. This assay consists of three individual DNA components: an immobilized capture strand, a target strand, and a probe strand containing a redox-active reporter group. We report a simplified DNA assay where two strands of ssDNA, the capture and probe strands, are linked together via a flexible poly(ethylene glycol) (PEG) spacer forming an ABA triblock macromolecule. We have developed an electrochemical assay where the detection signal arises as a consequence of a large structural change induced upon hybridization with target DNA. In this system, the DNA-PEG-DNA macromolecule folds or wraps around the target DNA, bringing the ferrocene probe in close proximity to the electrode, affording an electrochemical response.

Label-free colorimetric detection of specific sequences in genomic DNA amplified by the polymerase chain reaction

We document the surprising result that single-stranded DNA adsorbs on negatively charged gold nanoparticles (Au-nps) with a rate that depends on sequence length and temperature. After ss-DNA adsorbs on Au-nps, we find that the particles are stabilized against salt-induced aggregation. These observations can be rationalized on the basis of electrostatics and form the basis for a colorimetric assay to identify specific sequences and single nucleotide polymorphisms on polymerase chain reaction (PCR)-amplified DNA. The assay is label-free, requires no covalent modification of the DNA or Au-np surfaces, and takes on the sensitivity of PCR. Most important, binding of target and probe takes place in solution where hybridization occurs in less than 1 min. As an example, we test PCR-amplified genomic DNA from clinical samples for single nucleotide polymorphisms (SNPs) associated with a fatal arrhythmia known as long QT syndrome.

Selective and Sensitive Fluorescent Sensors for Metal Ions Based on Manipulation of Side-Chain Compositions of Poly(p-phenyleneethynylene)s

The syntheses and metal-responsive properties of poly(p-phenyleenethynylene)s with grafted new pseudo-crown-ether groups are reported. These polymers exhibit high sensitivities to alkali ions because of their collective optical properties, which are very sensitive to ion-induced conformational changes. The quenching of polymer fluorescence caused by the conformational changes is proportional to the ion concentration. The selectivity of the sensing materials toward Li(+) ions is significantly enhanced by controlling the size of the binding site via manipulation of the polymer side-chain compositions. The polymers are very stable for their six-month solid-state storage at room temperature.

DNA Sequence Detection Using Selective Fluorescence Quenching of Tagged Oligonucleotide Probes by Gold Nanoparticles

Simple, fast, economical, and sensitive detection of specific DNA sequences is crucial to pathogen detection and biomedical research. We have designed a novel fluorescent assay for DNA hybridization based on the electrostatic properties of DNA. We exploit the ability to create conditions where single-stranded DNA adsorbs on negatively charged gold nanoparticles while double-stranded DNA does not. Dye-tagged probe sequences have their fluorescence efficiently quenched when they are mixed with gold nanoparticles unless they hybridize with components of the analyte. Subfemtomole amounts of untagged target are detected in minutes using commercially available materials. Target sequences in complex mixtures of DNA and single-base mismatches in DNA sequences are easily detected.

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.

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.

Fluorescein Provides a Resonance Gate for FRET from Conjugated Polymers to DNA Intercalated Dyes

Fluorescence spectra show that excitation of the cationic water-soluble conjugated polymer poly[(1,4-phenylene)-2,7-[9,9-bis(6'-N,N,N-trimethylammonium)-hexyl]fluorene diiodide] (1) results in inefficient fluorescence resonance energy transfer (FRET) to ethidium bromide (EB) intercalated within double-stranded DNA (dsDNA). When fluorescein (Fl) is attached to one terminus of the dsDNA, there is efficient FRET from 1 through Fl to EB. The cascading energy-transfer process was examined mechanistically via fluorescence decay kinetics and fluorescence anisotropy measurements. These experiments show that the proximity and conformational freedom of Fl provide a FRET gate to dyes intercalated within DNA which are optically amplified by the properties of the conjugated polymer. The overall process provides a substantial improvement over previous homogeneous conjugated polymer based DNA sensors, namely, in the form of improved selectivity.

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.

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.

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.