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

New conjugated poly(pyridinium salt) derivative: AIE characteristics, the interaction with DNA and selective fluorescence enhancement induced by dsDNA

Fluorescence turn-on DNA sensor with excellent sensitivity and selectivity is developed based on a new conjugated poly(pyridinium salt) with AIE characteristics. The probe is also successfully utilized to follow the DNA cleavage process by DNase I.

Cationic conjugated polymer/fluoresceinamine-hyaluronan complex for sensitive fluorescence detection of CD44 and tumor-targeted cell imaging

Simple, rapid, and sensitive detection of CD44 is of paramount importance since it plays pivotal roles in tumor initiation, growth and metastasis. Herein, we describe a novel method for sensitive, visual and facile fluorescence detection of CD44 and CD44-mediated cancer cell imaging, using a probe based on cationic conjugated polymer (CCP)-PFEP and fluoresceinamine-hyaluronan (FA-HA). HA is an anionic natural glycosaminoglycan that can specifically bind to the overexpressed CD44 on various kinds of cancer cells. PFEP and FA-HA formed a complex through electronic interactions, resulting in a highly efficient fluorescence resonance energy transfer (FRET) from PFEP to FA-HA; moreover, the efficiencies of FRET correlated with the concentrations of CD44 because the specific binding of HA-CD44 would separate FA-HA away from PFEP. This method did not require laborious and expensive dual-labeling or protein-labeling needed in previously reported detection methods of CD44. Just mix the sample and test solution containing the PFEP/FA-HA complex, and the results allowed naked-eye detection by observing fluorescent color of solutions with the assistance of a UV lamp. Most importantly, the use of a conjugated polymer with excellent amplification property as well as the specific binding of HA-CD44 endowed this method with high sensitivity and specificity, making it applicable for reliable quantitative detection of CD44. Furthermore, the PFEP/FA-HA complex formed nanoparticles in aqueous solution, and the nanoparticles can be selectively taken up by MCF-7 cells (cancer cell) through the HA-CD44 interaction, thereby giving rise to a dual-color tumor-targeted imaging probe with good photostability. The development of this fluorescent probe showed promising potential to make a reliable and routine method available for early diagnosis of cancer.

Influence of three anionic gemini surfactants with different chain lengths on the optical properties of a cationic polyfluorene

The effects of three sulfonate gemini surfactants with different hydrophobic chain lengths (8, 10, and 12 carbon atoms) on the optical properties of a fluorene-based conjugated cationic polymer poly{[9,9-bis(6'-N,N,N-trimethylammonium)hexyl]-fluorene-phenylene} bromide (PFP) dissolved in DMSO-water solutions (4% v/v) or water were investigated, respectively. When surfactants with PFP dissolved in DMSO-water solutions (4% v/v) are incubated, a decrease in photoluminescence (PL) intensity and a red shift of emission maxima are obtained at low surfactant concentrations. Intriguingly, two different Stern-Volmer constants (KSV1 and KSV2) are obtained and analyzed in detail for the first time. Further increase in the surfactant concentration enhanced PL intensity, and distinct blue shifts of both absorption and emission maxima are observed. Importantly, the turning point between the emission quenching and enhancement is closely related to the hydrophobic chain length: the longer the chain length, the earlier the turning point appears. Simulation studies provide strong evidence to explain these phenomena. Surface tension measurements show more insight on the interactions between PFP and surfactant. On the contrary, no emission quenching is obtained at low surfactant concentrations for PFP dissolved in water.

New water soluble terphenylene diethynylene fluorophores

Inspired by our earlier works on sensors from dendritic phenyleneethynylenes, two new star-shaped water-soluble fluorophores containing terphenylene diethynylene units and anionic carboxylate peripheries are successfully synthesized. The convergent synthesis relies on Sonogashira cross-coupling reactions between tris-(4-ethynylphenyl)amine and the iodophenyleneethynylene branches. All of the compounds are characterized by (1)H, (13)C NMR, and mass spectrometry. In aqueous solution, the less polar fluorophore 1 shows lower quantum yield than 2 (18 vs 33%) as a result of hydrophobic induced aggregation. One of these anionic water-soluble fluorophores exhibits a selective fluorescence quenching by Fe(3+) ion in phosphate buffer pH 8.

Conjugated amplifying polymers for optical sensing applications

Thanks to their unique optical and electrochemical properties, conjugated polymers have attracted considerable attention over the last two decades and resulted in numerous technological innovations. In particular, their implementation in sensing schemes and devices was widely investigated and produced a multitude of sensory systems and transduction mechanisms. Conjugated polymers possess numerous attractive features that make them particularly suitable for a broad variety of sensing tasks. They display sensory signal amplification (compared to their small-molecule counterparts) and their structures can easily be tailored to adjust solubility, absorption/emission wavelengths, energy offsets for excited state electron transfer, and/or for use in solution or in the solid state. This versatility has made conjugated polymers a fluorescence sensory platform of choice in the recent years. In this review, we highlight a variety of conjugated polymer-based sensory mechanisms together with selected examples from the recent literature.

Incorporating graphene oxide and gold nanoclusters: a synergistic catalyst with surprisingly high peroxidase-like activity over a broad pH range and its application for cancer cell detection

A synergistic graphene oxide-gold nanocluster (GO-AuNC) hybrid has been constructed as an enzyme mimic that is able to show high catalytic activity over a broad pH range, especially at neutral pH. Importantly, the target-functionalized hybrid has been applied as a robust nanoprobe for selective, quantitative, and fast colorimetric detection of cancer cells.

Detection and differential diagnosis of colon cancer by a cumulative analysis of promoter methylation

Alterations in the methylation of promoters of cancer-related genes are promising biomarkers for the early detection of disease. Compared with single methylation alteration, assessing combined methylation alterations can provide higher association with specific cancer. Here we use cationic conjugated polymer-based fluorescence resonance energy transfer to quantitatively analyse DNA methylation levels of seven colon cancer-related genes in a Chinese population. Through a stepwise discriminant analysis and cumulative detection of methylation alterations, we acquire high accuracy and sensitivity for colon cancer detection (86.3 and 86.7%) and for differential diagnosis (97.5 and 94%). Moreover, we identify a correlation between the CpG island methylator phenotype and clinically important parameters in patients with colon cancer. The cumulative analysis of promoter methylation alterations by the cationic conjugated polymer-based fluorescence resonance energy transfer may be useful for the screening and differential diagnosis of patients with colon cancer, and for performing clinical correlation analyses.

Thiazole-containing conjugated polymer as a visual and fluorometric sensor for iodide and mercury

A neutral conjugated polymer poly-p-phenylene (PPP) derivative, poly(1,4-bis-(8-(4-phenylthiazole-2-thiol)-octyloxy)-benzene) (PPT), was prepared using a simple and economical method of oxidative polymerization reaction. This newly synthesized polymer PPT was characterized by means of Fourier transform infrared spectroscopy (FT-IR), (1)H nuclear magnetic resonance ((1)H NMR), ultraviolet-visible (UV-Vis), and fluorescence spectroscopy. PPT displays fluorescence "turn-off/turn-on" characteristics and colorimetric responses to I(-) and Hg(2+). The UV-Vis and fluorescence spectra of the PPT showed a significant shift in λmax via the addition of iodides and mercury. A colorless PPT solution turns to deep yellow in the presence of iodide salts, which subsequently becomes colorless again on addition of Hg(2+) salts that could be easily detected visually by the naked eye. The Stern-Volmer constant (Ksv) value obtained for the detection of iodide is 0.13 × 10(5) M(-1), confirming very high sensitivity of this polymer for iodide salts. The detection limit of Hg(2+) salt using the PPT polymer was found to be 2.1 nM in water. The detection of both iodide and mercury was also possible in solid state by using a membrane film prepared by mixing 1% PPT in polystyrene. This membrane changes color in the presence of iodide as well as mercury salts. These results confirm that the PPT polymer can be applied for the colorimetric as well as fluorometric sensing of I(-) and Hg(2+) ions in a competent environment in solution, as well as in the solid state, using a membrane film rapidly.

Synthesis of phenyleneethynylene-doped poly(pphenylenebutadiynylene) s for live cell imaging

We developed a new synthetic approach to high molecular weight poly(p-phenylenebutadiynylene) s (PPBs) by increasing backbone flexibility. The introduction of a small amount of flexible units along the backbone improved both the physical and photophysical properties of the polymers. These materials were successfully fabricated into conjugated polymer nanoparticles (CPNs) and used for fluorescent live cell imaging for the first time.

New water-soluble cationic poly(p-phenylenevinylene) derivative: the interaction with DNA and selective fluorescence enhancement induced by ssDNA

A new cationic cyano-substituted poly(p-phenylenevinylene) (N-CNPPV) is synthesized by Knoevenagel condensation. The water-soluble polymer shows different emission spectra in different solvents and displays unique fluorescent behaviors in the mixed solvents of water and THF. The new polymer can form a complex with ssDNA by adopting a more planar conformation, exhibiting red shift of emission wavelength and enhancement of fluorescence intensity. By investigating the fluorescent response of N-CNPPV to various surfactants, we demonstrate that the hydrophobic interaction and electrostatic interaction result in the selective response of N-CNPPV to ssDNA. This is the first report on selective fluorescence enhancement of conjugated polyelectrolyte induced by ssDNA.

Real-time fluorescent image analysis of DNA spot hybridization kinetics to assess microarray spot heterogeneity

Current microarray assay technology predominately uses fluorescence as a detectable signal end point. This study assessed real-time in situ surface hybridization capture kinetics for single printed DNA microspots on solid array surfaces using fluorescence. The influence of the DNA target and probe cyanine dye position on oligo-DNA duplex formation behavior was compared in solution versus surface-hybridized single DNA printed spots using fluorescence resonance energy transfer (FRET) analysis. Fluorophore Cy3/Cy5 fluorescence intensities were analyzed both through the printed hybridized DNA spot thickness and radially across single-spot surfaces. Confocal single-spot imaging shows that real-time in situ hybridization kinetics with constant target concentrations changes as a function of the printed probe density. Target-specific imaging in single spots exhibits a heterogeneous printed probe radial density that influences hybridization spatially and temporally via radial hemispherical diffusion of dye-labeled target from the outside edge of the spot to the interior. FRET of the surface-captured target occurs irrespective of the probe/target fluorophore position, resulting from excess printed probe density and spot thickness. Both heterogeneous probe density distributions in printed spots and the fluorophore position on short DNA oligomers influence duplex formation kinetics, hybridization efficiencies, and overall fluorescence intensity end points in surface-capture formats. This analysis is important to understanding, controlling, and quantifying the array assay signal essential to reliable application of the surface-capture format.

Target-triggered polymerization for biosensing

Because of the potential applications of biosensors in clinical diagnosis, biomedical research, environmental analysis, and food quality control, researchers are very interested in developing sensitive, selective, rapid, reliable, and low-cost versions of these devices. A classic biosensor directly transduces ligand-target binding events into a measurable physical readout. Because of the limited detection sensitivity and selectivity in earlier biosensors, researchers have developed a number of sensing/signal amplification strategies. Through the use of nanostructured or long chain polymeric materials to increase the upload of signal tags for amplification of the signal readout associated with the ligand-target binding events, researchers have achieved high sensitivity and exceptional selectivity. Very recently, target-triggered polymerization-assisted signal amplification strategies have been exploited as a new biosensing mechanism with many attractive features. This strategy couples a small initiator molecule to the DNA/protein detection probe prior to DNA hybridization or DNA/protein and protein/protein binding events. After ligand-target binding, the in-situ polymerization reaction is triggered. As a result, tens to hundreds of small monomer signal reporter molecules assemble into long chain polymers at the location where the initiator molecule was attached. The resulting polymer materials changed the optical and electrochemical properties at this location, which make the signal easily distinguishable from the background. The assay time ranged from minutes to hours and was determined by the degree of amplification needed. In this Account, we summarize a series of electrochemical and optical biosensors that employ target-triggered polymerization. We focus on the use of atom transfer radical polymerization (ATRP), as well as activator generated electron transfer for atom transfer radical polymerization (AGET ATRP) for in-situ formation of polymer materials for optically or electrochemically transducing DNA hybridization and protein-target binding. ATRP and AGET ATRP can tolerate a wide range of functional monomers. They also allow for the preparation of well-controlled polymers with narrow molecular weight distribution, which was predetermined by the concentration ratio of the consumed monomer to the introduced initiator. Because the reaction initiator can be attached to a variety of detection probes through well-established cross-linking reactions, this technique could be expanded as a universal strategy for the sensitive detection of DNA and proteins. We see enormous potential for this new sensing technology in the development of portable DNA/protein sensors for point-of-need applications.

An exonuclease III and graphene oxide-aided assay for DNA detection

We have developed a novel DNA assay based on exonuclease III (ExoIII)-induced target recycling and the fluorescence quenching ability of graphene oxide (GO). This assay consists of a linear DNA probe labeled with a fluorophore in the middle. Introduction of target sequence induces the exonuclease III catalyzed probe digestion and generation of single nucleotides. After each cycle of digestion, the target is recycled to realize the amplification. Finally, graphene oxide is added to quench the remaining probes and the signal from the resulting fluorophore labeled single nucleotides is detected. With this approach, a sub-picomolar detection limit can be achieved within 40 min at 37°C. The method was successfully applied to multicolor DNA detection and the analysis of telomerase activity in extracts from cancer cells.

Interface engineering catalytic graphene for smart colorimetric biosensing

Herein a hybrid catalyst consisting of "naked" Au-NPs in situ grown on graphene sheets is engineered, which exhibits a synergetic effect in mimicking peroxidase at its interface, although free Au-NPs or graphene alone has very little activity. What is more, one of the unique features of our synergetic catalyst is that its interface can be reversibly switched from "inactive" to "active" upon treatment with different ssDNA species in solution, thus providing a powerful and versatile basis for designing graphene/DNA-based label-free colorimetric biosensors. Compared with other signal transduction modes in traditional graphene/aptamer-based systems, our novel signaling strategy not only avoids any labeling or modification procedures but also reduces the background signal due to the "off-on" switching mode during the sensing. Furthermore, this facile and general approach can be applicable to the other extended graphene/aptamer-based systems for colorimetric detection of a wide range of analytes. We envision that the tunable graphene-based smart interface could find potential applications in the development of biocatalysis, bioassays, and smart material devices in the future.

Cationic conjugated polyelectrolytes-triggered conformational change of molecular beacon aptamer for highly sensitive and selective potassium ion detection

We demonstrate highly sensitive and selective potassium ion detection against excess sodium ions in water, by modulating the interaction between the G-quadruplex-forming molecular beacon aptamer (MBA) and cationic conjugated polyelectrolyte (CPE). The K(+)-specific aptamer sequence in MBA is used as the molecular recognition element, and the high binding specificity of MBA for potassium ions offers selectivity against a range of metal ions. The hairpin-type MBA labeled with a fluorophore and quencher at both termini undergoes a conformational change (by complexation with CPEs) to either an open-chain form or a G-quadruplex in the absence or presence of K(+) ions. Conformational changes of MBA as well as fluorescence (of the fluorophore in MBA) quenching or amplification via fluorescence resonance energy transfer from CPEs provide clear signal turn-off and -on in the presence or absence of K(+). The detection limit of the K(+) assays is determined to be ~1.5 nM in the presence of 100 mM Na(+) ions, which is ~3 orders of magnitude lower than those reported previously. The successful detection of 5'-adenosine triphosphate (ATP) with the MBA containing an ATP-specific aptamer sequence is also demonstrated using the same sensor scheme. The scheme reported herein is applicable to the detection of other kinds of G-rich aptamer-binding chemicals and biomolecules.