Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction

Prospects and challenges of dynamic DNA nanostructures in biomedical applications

The physicochemical nature of DNA allows the assembly of highly predictable structures via several fabrication strategies, which have been applied to make breakthroughs in various fields. Moreover, DNA nanostructures are regarded as materials with excellent editability and biocompatibility for biomedical applications. The ongoing maintenance and release of new DNA structure design tools ease the work and make large and arbitrary DNA structures feasible for different applications. However, the nature of DNA nanostructures endows them with several stimulus-responsive mechanisms capable of responding to biomolecules, such as nucleic acids and proteins, as well as biophysical environmental parameters, such as temperature and pH. Via these mechanisms, stimulus-responsive dynamic DNA nanostructures have been applied in several biomedical settings, including basic research, active drug delivery, biosensor development, and tissue engineering. These applications have shown the versatility of dynamic DNA nanostructures, with unignorable merits that exceed those of their traditional counterparts, such as polymers and metal particles. However, there are stability, yield, exogenous DNA, and ethical considerations regarding their clinical translation. In this review, we first introduce the recent efforts and discoveries in DNA nanotechnology, highlighting the uses of dynamic DNA nanostructures in biomedical applications. Then, several dynamic DNA nanostructures are presented, and their typical biomedical applications, including their use as DNA aptamers, ion concentration/pH-sensitive DNA molecules, DNA nanostructures capable of strand displacement reactions, and protein-based dynamic DNA nanostructures, are discussed. Finally, the challenges regarding the biomedical applications of dynamic DNA nanostructures are discussed.

PCR-Free Colorimetric DNA Hybridization Detection Using a 3D DNA Nanostructured Reporter Probe

A "sandwich-like" biosensor was developed on the basis of the magnetic bead platform for sensitive detection of breast cancer 1 (BRCA1) DNA. In the present study, a tetrahedron-structured reporter probe (TSRP) was designed, in which 3 vertices of the tetrahedron were labeled with digoxin (Dig), and the other one was labeled with a detection probe. TSRP here provided accurate enzyme loading and well-organized spatial arrangement for optimized signal amplification. The detection limit of this biosensor was as low as 10 fM, which is at least 4 orders of magnitude lower than that of the single DNA probe (100 pM), and the signal gain was 2 times higher than the analysis using three one-dimensional (1D) reporter probes. We could distinguish DNA sequences with only 1 base mismatch, and the performance of our TSRP biosensor was proven to be equally good in both PCR products and real fetal calf serum (FCS) sample as in buffer. We believe this work provided a novel avenue for the development of signal amplification strategies.

A magnetic nanoparticle-labeled immunoassay with europium and samarium for simultaneous quantification of serum pepsinogen I and II

OBJECTIVE

To develop a novel immunoassay for the simultaneous determination of serum pepsinogen I (PG I) and pepsinogen II (PG II) by combining established methods of time-resolved fluoroimmunoassay (TRFIA) and magnetic nanoparticles separation.

MATERIALS AND METHODS

This new immunoassay method was characterised by immobilising primary antibodies on the surface of magnetic particles and labelled with stable fluorescent chelates of europium and samarium.

RESULTS

Using magnetic nanoparticles, the TRFIA immunoassay exhibited broad dynamic assay ranges for PG I with detection limit of 0.33 ng/mL, while for PG II with detection limit of 0.38 ng/mL. Cross-reactivity between PGs I and II were <15. The intra- and inter-assay coefficient variations of the method were <3%, and the recoveries were in the range of 97-103% for serum samples. Bland-Altman analysis of 124 serum samples showed good consistency with a commercial TRFIA kit. For PG I, the mean (95% confidence interval) difference was 0.97 (-14.3-12.3) ng/mL, whilst for PG II the difference was 0.6 (-4.4-3.2) ng/mL.

CONCLUSIONS

Our data suggest that the method is feasible and could be developed into a platform for the routine clinical determination of PG I and PG II levels in human serum.

Fluorescent/phosphorescent dual-emissive conjugated polymer dots for hypoxia bioimaging

Fluorescent/phosphorescent dual-emissive conjugated polymer dots were designed and synthesized, ere used for tumor hypoxia sensing via ratiometric imaging and photoluminescence lifetime imaging.

A kind of fluorescent/phosphorescent dual-emissive conjugated polyelectrolyte has been prepared by introducing phosphorescent platinum(ii) porphyrin (O₂-sensitive) into a fluorene-based conjugated polyelectrolyte (O₂-insensitive), which can form ultrasmall conjugated polymer dots (FP-Pdots) in the phosphate buffer solution (PBS) via self-assembly caused by their amphiphilic structures with hydrophobic backbones and hydrophilic side chains. These FP-Pdots can exhibit an excellent ratiometric luminescence response to O₂ content with high reliability and full reversibility for measuring oxygen levels, and the excellent intracellular ratiometric O₂ sensing properties of the FP-Pdots nanoprobe have also been confirmed by the evident change in the I_red/I_blue ratio values in living cells cultured at different O₂ concentrations. To confirm the reliability of the O₂ sensing measurements of the FP-Pdots nanoprobe, O₂ quenching experiments based on lifetime measurements of phosphorescence from Pt(ii) porphyrin moieties have also been carried out. Utilizing the sensitivity of the long phosphorescence lifetime from Pt(ii) porphyrins to oxygen, the FP-Pdots have been successfully applied in time-resolved luminescence imaging of intracellular O₂ levels, including photoluminescence lifetime imaging and time-gated luminescence imaging, which will evidently improve the sensing sensitivity and reliability. Finally, in vivo oxygen sensing experiments were successfully performed by luminescence imaging of tumor hypoxia in nude mice.

Sequence-selective binding of oligonucleotides to superparamagnetic cobalt ferrite nanoparticles: a new way to fabricate functional nanoconjugates

The interaction between homo-oligonucleotides and unmodified superparamagnetic cobalt ferrite nanoparticles has been investigated.

Labeling-free fluorescent detection of DNA hybridization through FRET from pyrene excimer to DNA intercalator SYBR green I

A novel labeling-free fluorescence complex probe has been developed for DNA hybridization detection based on fluorescence resonance energy transfer (FRET) mechanism from pyrene excimer of pyrene-functionalized poly [2-(N, N-dimethylamino) ethyl methacrylate] (PFP) to SYBR Green I (SG, a specific intercalator of double-stranded DNA) in a cost-effective, rapid and simple manner. The complex probe consists of the positively charged PFP, SG and negatively charged single-stranded DNA (ssDNA). Upon adding a complementary strand to the complex probe solution, double-stranded DNA (dsDNA) was formed, followed by the intercalation of SG into dsDNA. The pyrene excimer emission was overlapped with the absorption of SG very well and the electrostatic interactions between PFP and dsDNA kept them in close proximity, enabling efficient FRET from pyrene excimer to SG. The fluorescence of SG in the duplex DNA resulting from FRET can be successfully applied to detect DNA hybridization with high sensitivity for a very low detection limit of 10nM and excellent selectivity for detection of single base pair mismatch.

A graphene-based platform for fluorescent detection of SNPs

A novel fluorescent single nucleotide polymorphism (SNP) assay was developed by using Graphene Oxide (GO), which provides a fast, sensitive and simple method for SNP detection. The strategy was based on the single base extension reaction and different absorption capacity of fluorescein labeled dGTP (dGTP-Fl) and double-stranded DNA (dsDNA) to GO. dGTP-Fl is incorporated into the probe by extension reaction for the mutant target but not for the wild target, which leads to recovered fluorescence for the mutant target because of weak interaction between dsDNA and GO and weak fluorescence for the wild target because of the quenched fluorescence of dGTP-Fl by GO. The method shows a linear range for the mutant-type target from 3 nM to 50 nM and 3 nM is the detection limit. It was noted that as low as 10% mutant-type target could be detected in the presence of the wild-type target, in which the concentration is 9 times higher than that of the mutant-type target.

Monodispersed magnetic polystyrene beads with excellent colloidal stability and strong magnetic response

Monodispersed polystyrene beads incorporated with Fe(3) O(4) nanoparticles are prepared via dispersion polymerization. The resultant magnetic beads present well-defined composite structures, excellent colloidal stability, and strong magnetic response. The formation mechanism for the monodispersed composite beads, incorporated with preformed Fe(3) O(4) nanocrystals, was investigated. The potential applications of the monodispersed magnetic beads in bacteria capturing were demonstrated. After being coated with anti-Salmonella CSA-1 antibody, the magnetic beads show capturing efficiencies of >99.4% in isolating Salmonella sp.

Simple and sensitive method for detecting point mutations of epidermal growth factor receptor using cationic conjugated polymers

The L858R mutation of epidermal growth factor receptor (EGFR) in nonsmall cell lung cancer is associated with the increased sensitivity to EGFR tyrosine kinase inhibitors. In this paper, a simple and sensitive method for identification of L858R mutation in cell lines and tumor tissues was developed using cationic conjugated polymer-based fluorescence resonance energy transfer technology (CCP-based FRET). The new detection system can detect even as low as 4-8% mutation of the total DNA. Through the detection results for 48 DNA samples from tumor tissues, a sensitivity of 95.24% (20/21) and a specificity of 96.30% (26/27) were demonstrated. Further, the application of this method in clinical molecular diagnosis was validated by detecting T790 M in EGFR of 35 patients. In comparison with DNA sequencing and real-time PCR methods, our new protocol simplifies procedures by eliminating the need for primer labeling, cumbersome workups and sophisticated instruments and improves sensitivity by amplifying fluorescence signals. Our CCP-based FRET technology is particularly attractive because of its higher sensitivity, cost-effective, and simple characteristics. Particularly, this new method could confirm the suspected positive samples arisen by DNA sequencing and real-time PCR methods. Thus, the CCP-based FRET technology opens up an avenue for clinical therapy by guiding medication to lung cancer patients responsive to anti-EGFR therapy.

Enhanced two-photon singlet oxygen generation by photosensitizer-doped conjugated polymer nanoparticles

We have prepared photosensitizer-doped conjugated polymer nanoparticles by using a reprecipitation method. The conjugated polymer, poly[9,9-dibromohexylfluorene-2,7-ylenethylene-alt-1,4-(2,5-dimethoxy)phenylene] (PFEMO), was used as the host matrix to disperse tetraphenylporphyrin (TPP). These TPP-doped PFEMO nanoparticles are stable and have a uniform size of ∼50 nm. Efficient intraparticle energy transfer from PFEMO to TPP has been observed. The TPP emission of the nanoparticles was found to be enhanced by 21-fold by PFEMO under two-photon excitation. Enhanced two-photon excitation singlet oxygen generation efficiency in the TPP-doped PFEMO nanoparticles has been demonstrated. Our results suggest that these photosensitizer-doped conjugated polymer nanoparticles can act as novel photosensitizing agents for two-photon photodynamic therapy and related applications.

Amplified fluorescent recognition of g-quadruplex folding with a cationic conjugated polymer and DNA intercalator

The single stranded DNA (ssDNA) with G-rich sequence can fold into G-quadruplex via intramolecular hydrogen-bonding interaction in the presence of ligand. This structure conversion can be specifically detected by a fluorescence method based on different interaction between SYBR Green I (SG) and various DNA structures. SG is proved to intercalate into G-quadruplex and results in high fluorescence intensity, which can be further amplified by 6-fold through fluorescence resonance energy transfer (FRET) from a water-soluble cationic conjugated polymer (CCP) to SG due to the high affinity of positively charged CCP to negatively charged rigid G-quadruplex, whereas it is not performed for ssDNA in the absence of K(+). As a result, the ssDNA/SG/CCP complex can be used to detect potassium ions with improved selectivity in a label-free and cost-effective manner.

Biocompatible magnetofluorescent probes: luminescent silicon quantum dots coupled with superparamagnetic iron(III) oxide

Luminescent silicon quantum dots (SiQDs) are gaining momentum in bioimaging applications, based on their unique combination of optical properties and biocompatibility. Here, we report the development of a multimodal probe that combines the optical properties of silicon quantum dots with the superparamagnetic properties of iron oxide nanoparticles to create biocompatible magnetofluorescent nanoprobes. Multiple nanoparticles of each type are coencapsulated within the hydrophobic core of biocompatible phospholipid-polyethyleneglycol (DSPE-PEG) micelles. The size distribution and composition of the magnetofluorescent nanoprobes were characterized by transmission electron microscopy (TEM) and energy-dispersive X-ray spectroscopy (EDS). Enhanced cellular uptake of these probes in the presence of a magnetic field was demonstrated in vitro. Their luminescence stability in a prostate cancer tumor model microenvironment was demonstrated in vivo. This paves the way for multimodal silicon quantum-dot-based nanoplatforms for a variety of imaging and delivery applications.

Rigid hydrophilic structures for improved properties of conjugated polymers and nitrotyrosine sensing in water

The efficient synthesis of a hydrophilic monomer bearing a three-dimensional noncompliant array of hydroxyl groups is described that prevents water-driven excimer features of hydrophobic poly(p-phenylene ethynylene) backbones. Sensitivity of the polymer to 3-nitrotyrosine is also discussed.

Cationic conjugated polymers for optical detection of DNA methylation, lesions, and single nucleotide polymorphisms

Simple, rapid, and sensitive technologies to detect nucleic acid modifications have important applications in genetic analysis, clinical diagnosis, and molecular biology. Because genetic modifications such as single nucleotide polymorphisms (SNP), DNA methylation, and other lesions can serve as hallmarks of human disease, interest in such methods has increased in recent years. This Account describes a new strategy for the optical detection of these DNA targets using cationic conjugated polymers (CCPs). Because of their unique signal amplification properties, researchers have extensively investigated conjugated polymers as optical transducers in highly sensitive biosensors. Recently, we have shown that cationic polyfluorene can detect SNPs within the DNA of clinical samples. When we incorporated deoxyguanosine triphosphate (dGTP-Fl) into the DNA chain at an SNP site where the target/probe pair is complementary, we observed higher fluorescence resonance energy transfer (FRET) efficiency between cationic polyfluorene and fluorescein label on the dGTP. By monitoring the change in emission intensity of cationic polyfluorene or fluorescein, we identified the homozygous or heterozygous SNP. The high sensitivity of this assay results from the 10-fold enhancement of fluorescein emission intensity by the FRET from polyfluorene. This method can detect allele frequencies (the proportion of all copies of a gene that is made up of a particular gene variant) as low as 2%. Using this novel method, we clearly discriminated among the SNP genotypes of 76 individuals of Chinese ancestry. Improving on this initial system, we designed a method for multicolor and one-tube SNP genotyping assays based on cationic polyfluorene using fluorescein-labeled deoxyuridine triphosphate (dUTP-Fl) and Cy3-labeled deoxycytidine triphosphate (dCTP-Cy3) in extension reactions. We also developed a one-step method for direct detection of SNP genotypes from genomic DNA by combining allele-specific PCR with CCPs. In 2008, we developed a new method for DNA methylation detection based on single base extension reaction and CCPs. Treatment of DNA with bisulfite followed by PCR amplification converts unmethylated DNA into a C/T polymorphism, which allows us to characterize the methylation status of the target DNA. Furthermore, we used CCPs to detect DNA lesions caused by ultraviolet light irradiation for the first time. By monitoring the color change of cationic polythiophene before and after DNA cleavage, we also detected oxidative damage to DNA by hydroxyl radical. These CCP-based new assays avoid primer labeling, cumbersome workups, and sophisticated instruments, leading to simpler procedures and improved sensitivity. We expect that these features could lead to major advances in human disease diagnostics and genomic study in the near future.

A new light-harvesting conjugated polyelectrolyte microgel for DNA and enzyme detections

A new fluorescent microgel containing the CP moiety (PFP-NIPAm) was prepared with the size within 100 nm. Covalent linking of the conjugated polyelectrolyte moiety into the microgel prevents leakage of the fluorophore while keeping its fluorescence property. The new fluorescent microgel can be used as an optical platform to detect DNA and enzyme. More importantly, because the electrostatic attraction dominates the interactions between cationic PFP-NIPAm microgel and negatively charged target, washing with high ionic strength aqueous solution can block their interactions and displace the target from the PFP-NIPAm microgel. Thus, PFP-NIPAm can be readily reusable for detection. Another unique feature is that the PFP-NIPAm microgel extends the detection media from homogeneous solution to solid phase, which shows great potential for biodetection in the real world using conjugated polymers. Furthermore, the detection can be carried out under UV light, and no expensive detection instrumentation is needed. In principle, such an assay system could be expanded to a high-throughput assay.

Fluorescence logic-signal-based multiplex detection of nucleases with the assembly of a cationic conjugated polymer and branched DNA

An energy-transfer cascade is generated from a cationic conjugated polymer (PFP) and negatively charged, Y-shaped DNA labeled with three dyes at its termini (fluorescein (Fl), Tex Red, and Cy5). Multistep fluorescence resonance energy transfer regulates the fluorescence intensities of PFP and the dyes. Different types of logic gates can be operated by observing the emission wavelengths of different dyes with multiplex nucleases as inputs.

Label-free DNA sequence detection with enhanced sensitivity and selectivity using cationic conjugated polymers and PicoGreen

In this Letter, we demonstrate that PicoGreen can be used in combination with cationic conjugated polymers to develop label-free DNA sensors with enhanced detection efficiency and further improved selectivity. The high selectivity enables detection of single nucleotide mismatch even at room temperature. This method uses all commercially available materials. It is low cost, is simple to use, and works in a "mix-and-detect" manner. The detection sensitivity could be improved by a factor of 19 times through resonance energy transfer using poly[(9,9-di(3,3'-N,N'-trimethyl-ammonium)propylfluorenyl-2,7-diyl)-alt-co-(1,4-phenylene)] diiodide salt (PFP) as a light harvesting complex, to take advantage of its collective optical response and optical amplification effects. The further improved selectivity is ascribed to the stronger binding interaction between PicoGreen with dsDNA compared to that between PicoGreen and ssDNA, which results in selective repelling of PicoGreen away from the DNA strands.