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.

Optical coherence and theoretical study of the excitation dynamics of a highly symmetric cyclophane-linked oligophenylenevinylene dimer.

Optoelectronic properties of a polyphenylenevinylene-based oligomer and its paracylophane-linked dimer are studied using a variety of experimental and theoretical techniques. Despite the symmetrical structure and redshifted absorption of the dimer versus the monomer, an exciton picture is not the most appropriate. Electronic structure calculations establish changes in charge density upon optical excitation and show localized excitations that cannot be accounted for by a simple Frenkel exciton model. Visible frequency pump-probe anisotropy measurements suggest that the dimer should be considered as a three-level system with a fast, approximately 130 fs, internal conversion from the higher to lower energy excited electronic state. Signatures of nuclear relaxation processes are compared for electric field-resolved transient grating and two-dimensional photon echo spectra. These measurements reveal that nuclear relaxation occurs on similar time scales for the monomer and dimer. The connection between the spectral phase of four-wave mixing signals and the time dependent width of a nuclear wave packet is discussed. Semiempirical electronic structure and metropolis Monte Carlo calculations show that the dominant line broadening mechanisms for the monomer and dimer are associated with inter-ring torsional coordinates. Together, the theoretical calculations and electric field-resolved four-wave mixing experiments suggest that while the structure of dimer is more rigid than that of monomer, the difference in their rigidities is not sufficient to slow down excited state relaxation of dimer with respect to the monomer.

Theoretical study of the effects of solvent environment on photophysical properties and electronic structure of paracyclophane chromophores.

We use first-principles quantum-chemical approaches to study absorption and emission properties of recently synthesized distyrylbenzene (DSB) derivative chromophores and their dimers (two DSB molecules linked through a [2.2]paracyclophane moiety). Several solvent models are applied to model experimentally observed shifts and radiative lifetimes in Stokes nonpolar organic solvents (toluene) and water. The molecular environment is simulated using the implicit solvation models, as well as explicit water molecules and counterions. Calculations show that neither implicit nor explicit solvent models are sufficient to reproduce experimental observations. The contact pair between the chromophore and counterion, on the other hand, is able to reproduce the experimental data when a partial screening effect of the solvent is taken into account. Based on our simulations we suggest two mechanisms for the excited-state lifetime increase in aqueous solutions. These findings may have a number of implications for organic light-emitting devices, electronic functionalities of soluble polymers and molecular fluorescent labels, and their possible applications as biosensors and charge/energy conduits in nanoassemblies.

Synthesis of cationic water-soluble light-harvesting dendrimers.

Four generations of phenylenefluorene (1F)- and phenylenebis(fluorene) (2F)-terminated polyamidoamine (PAMAM) dendrimers were synthesized by coupling activated esters with commercially available PAMAM precursors. Treatment of Boc-terminated pendant groups on the optically active units with 3 M HCl in dioxane yields cationic water-soluble dendrimers. Fluorescence resonance energy transfer (FRET) experiments with the cationic dendrimers as the donor and double stranded DNA containing a fluorescein label as the acceptor reveal cooperative optical behavior.

Solvatochromism of distyrylbenzene pairs bound together by [2.2]paracyclophane: evidence for a polarizable "through-space" delocalized state.

A series of compounds were designed and synthesized to examine how through-space and through-bond electron delocalization respond to solvent effects. The general strategy involves the study of "dimers" of the distyrylbenzene chromophore held in close proximity by the [2.2]paracyclophane core and a systematic dissection of the chromophore into components with through-space and through-bond electronic delocalization. Steady state and time-resolved fluorescence spectroscopy in a range of solvents reveals a red-shift in emission and an increase in the intrinsic fluorescence lifetime for the emitting state in polar solvents when donor substituents are absent. We propose that through-space delocalization across the [2.2]paracyclophane core is more polarizable in the excited state, relative to the through-bond (distyrylbenzene based) excited state. When strong donors are attached to the distyrylbenzene chromophore, the charge transfer character of the distyrylbenzene-based excited state dominates fluorescence properties.

Water-soluble [2.2]paracyclophane chromophores with large two-photon action cross sections.

A series of alpha,omega-donor-substituted distyrylbenzene dimers held together by the [2.2]paracyclophane core were designed, synthesized, and characterized. Different substituents were chosen to modulate the strength of the donor nitrogen groups and to allow the molecules to be either neutral and soluble in nonpolar organic solvents or charged and water-soluble. The specific neutral structures are (in order of decreasing donor strength) 4,7,12,15-tetra[N,N-bis(6' '-chlorohexyl)-4'-aminostyryl]-[2.2]paracyclophane (1N), 4,7,12,15-tetra[(N-(6' '-chlorohexyl)carbazol-3'-yl)vinyl]-[2.2]paracyclophane (2N), and 4,7,12,15-tetra[N,N-bis(4' '-(6' ''-chlorohexyl)phenyl)-4'-aminostyryl]-[2.2]paracyclophane (3N). The charged species are 4,7,12,15-tetra[N,N-bis(6' '-(N,N,N-trimethylammonium)hexyl)-4'-aminostyryl]-[2.2]paracyclophane octaiodide (1C), 4,7,12,15-tetra[(N-(6' '-(N,N,N-trimethylammonium)hexyl)carbazol-3'-yl)vinyl]-[2.2]paracyclophane octaiodide (2C), and 4,7,12,15-tetra[N,N-bis(4' '-(6' ''-(N,N,N-trimethylammonium)hexyl)phenyl)-4'-aminostyryl]-[2.2]paracyclophane octaiodide (3C). Two-photon excitation spectra, measured using the two-photon induced fluorescence technique, show in toluene the following trend for the two-photon cross sections (delta): 3N > 2N > 1N. In water the delta values follow the same order, 3C approximately 2C > 1C, but are smaller (approximately one-third). Significantly, the fluorescence quantum yield (eta) in water decreases much more for 1, relative to 2 and 3. The two-photon action cross sections (deltaeta) of 2C and 3C are 294 GM and 359 GM, respectively. These values are among the highest reported thus far. These results show that, to maximize the deltaeta in this class of chromophores, one needs to fine-tune the magnitude of the charge transfer character of the excited state, to minimize fluorescence quenching in polar media.

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.

Diastereomer assignment of an olefin-linked bis-paracyclophane by ion mobility mass spectrometry.

trans-1,2-Bis([2.2]paracyclophanyl)ethene (1) exists as a pair of diastereomers whose conformations, and thus effective collision cross sections, are quite different. The two forms can be obtained by different transition metal-catalyzed reactions. To assign meso and racemic structures, a novel method is reported in which experimental gas-phase ion mobility data are compared with theoretical structures obtained from molecular mechanics calculations.

Through-space delocalized water-soluble paracyclophane bichromophores: new fluorescent optical reporters.

Conjugated polymers and oligomers can serve as highly responsive fluorescent reporters for biosensor applications. However, their optical properties in aqueous media are highly dependent upon environmental conditions. The structure of the paracyclophane framework provides a platform for designing optical reporters that show little sensitivity to surfactants, and thus is well-suited for fluorescent assays. The permanent intramolecular delocalization through the paracyclophane core dominates intermolecular perturbations in spontaneously formed aggregates.

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.

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.