Application of cationic conjugated polymers in microarrays using label-free DNA targets.

A fluorescence-based microarray technique that does not require target DNA labeling is detailed. This 'label-free' approach utilizes a cationic, water-soluble conjugated polymer PFBT (poly[9,9'-bis(6''-(N,N,N-trimethylammonium)hexyl)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide]), and neutral PNA (peptide nucleic acid) hybridization probes. DNA hybridization to immobilized PNA spots results in a change in the net charge at that particular surface. Electrostatic interactions between the cationic polymer and negatively charged DNA bind the polymer to the hybrid DNA/PNA complex. By exciting the conjugated polymer at 488 nm on a commercial microarray scanner, the presence of the target is directly indicated by the fluorescence emission of the polymer. This feature eliminates the necessity of target labeling required in traditional microarray protocols. There are five steps involved in the procedure before scanning or imaging the array: (i) slide hydration, (ii) target hybridization, (iii) post-hybridization washing, (iv) polymer application and (v) polymer washing. Each step takes 20 min to 1 h. The overall protocol requires approximately 2-3 h.

PNA/dsDNA complexes: site specific binding and dsDNA biosensor applications.

The ability of peptide nucleic acids (PNA) to form specific higher-order (i.e., three- and four-stranded) complexes with DNA makes it an ideal structural probe for designing strand-specific dsDNA biosensors. Higher-order complexes are formed between a dye-labeled charge-neutral PNA probe and complementary dsDNA. Addition of a light-harvesting cationic conjugated polymer (CCP) yields supramolecular structures held together by electrostatic forces that incorporate the CCP and the dye-labeled PNA/DNA complexes. Optimization of optical properties allows for excitation of the CCP and subsequent fluorescence resonance energy transfer (FRET) to the PNA-bound dye. In the case of noncomplementary dsDNA, complexation between the probe and target does not occur, and dye emission is weak. The binding between PNA and noncomplementary and complementary dsDNA was examined by several methods. Gel electrophoresis confirms specificity of binding and the formation of higher-order complexes. Nano-electrospray mass spectrometry gives insight into the stoichiometric composition, including PNA/DNA, PNA(2)/DNA, PNA/DNA(2), and PNA(2)/DNA(2) complexes. Finally, structural characteristics and binding-site specificity were examined using ion mobility mass spectrometry in conjunction with molecular dynamics. These results give possible conformations for each of the higher-order complexes formed and show exclusive binding of PNA to the complementary stretch of DNA for all PNA/DNA complexes. Overall, the capability and specificity of binding indicates that the CCP/PNA assay is a feasible detection method for dsDNA and eliminates the need for thermal denaturing steps typically required for DNA hybridization probe assays.

SNP detection using peptide nucleic acid probes and conjugated polymers: applications in neurodegenerative disease identification.

A strategy employing a combination of peptide nucleic acid (PNA) probes, an optically amplifying conjugated polymer (CP), and S1 nuclease enzyme is capable of detecting SNPs in a simple, rapid, and sensitive manner. The recognition is accomplished by sequence-specific hybridization between the uncharged, fluorescein-labeled PNA probe and the DNA sequence of interest. After subsequent treatment with S1 nuclease, the cationic water soluble CP electrostatically associates with the remaining anionic PNA/DNA complex, leading to sensitized emission of the labeled PNA probe via FRET from the CP. The generation of fluorescent signal is controlled by strand-specific electrostatic interactions and is governed by the complementarity of the probe/target pair. To assess the method, we compared the ability of the sensor system to detect normal, wild-type human DNA sequences, and those sequences containing a single base mutation. Specifically, we examined a PNA probe complementary to a region of the gene encoding the microtubule associated protein tau. The probe sequence covers a known point mutation implicated in a dominant neurodegenerative dementia known as frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17), which has clinical and molecular similarities to Alzheimer's disease. By using an appropriate PNA probe, the conjugated polymer poly[(9,9-bis(6'-N,N,N-trimethylammoniumhexylbromide)fluorene)-co-phenylene] and S1 nuclease, unambiguous FRET signaling is achieved for the wild-type DNA and not the mutant sequence harboring the SNP. Distance relationships in the CP/PNA assay are also discussed to highlight constraints and demonstrate improvements within the system.

Perturbation of fluorescence by nonspecific interactions between anionic poly(phenylenevinylene)s and proteins: implications for biosensors.

The use of anionic water-soluble conjugated polymers (CPs) for sensing the presence of avidin by use of a biotin-modified fluorescence quencher was studied. The molecules involved in the study included poly[2-methoxy-5-(3'-propyloxysulfonate)-1,4-phenylenevinylene] with either lithium (Li+-MPS-PPV) or sodium (Na(+)-MPS-PPV) countercations, the well-defined oligomer pentasodium 1,4-bis(4'(2",4"-bis(butoxysulfonate)-styryl)-styryl)2-butoxysulfonate-5-methoxybenzene (5R5-), the quenchers N-methyl-4,4'-pyridylpyridinium iodide (mMV+) and [N-(biotinoyl)-N'-(acetyl 4,4'-pyridylpyridinium iodide)] ethylenediamine (BPP+), which contains a molecular recognition fragment (biotin) attached to a unit that accepts an electron from a CP excited state, and the proteins avidin, tau, BSA, and pepsin A. Fluorescence quenching experiments were examined in a variety of conditions. Experiments carried out in water and in ammonium carbonate buffer (which ensures avidin/biotin complexation) reveal that nonspecific interactions between the CP and the proteins cause substantial perturbations on the CP fluorescence. The overall findings are not consistent with a simple mechanism whereby avidin complexation of BPP+ leads to encapsulation of the quencher molecule and recovery of Li+-MPS-PPV fluorescence. Instead, we propose that binding of BPP+ to avidin results in the quenching unit attaching to a positively charged macromolecule. Electrostatic attraction to the negatively charged conjugated polymer results in closer proximity to the quencher. Therefore, more enhanced fluorescence quenching is observed.

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.

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.

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.

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

A sensor is provided that detects single-stranded deoxyribonucleic acid (ssDNA) with a specific base sequence. The ssDNA sequence sensor comprises an aqueous solution containing a cationic water-soluble conjugated polymer [in this case, poly(9,9-bis(6'-N,N,N-trimethylammonium)-hexyl)-fluorene phenylene), 1] with a ssDNA labeled with a dye (in this case, fluorescein). The emission of light from the sensor solution with the wavelength characteristic of the probe oligonucleotide indicates the presence of ssDNA with a specific base sequence complementary to that of the probe ssDNA-fluorescein. Maximum energy transfer from 1 to the signaling chromophore occurs when the ratio of polymer chains to DNA strands is approximately 1:1. Energy transfer from 1 results in a fluorescein emission that is more intense than that observed by direct excitation of the chromophore. Furthermore, the decrease in energy transfer upon addition of electrolyte indicates that electrostatic forces dominate the interactions between 1 and DNA.

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.

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.