Silica nanoparticle assisted DNA assays for optical signal amplification of conjugated polymer based fluorescent sensors

Semiconducting polymer dots as fluorescent probes for in vitro biosensing

Semiconducting polymer dots (Pdots) have emerged as novel fluorescent probes with excellent characteristics, such as ultrahigh molar extinction coefficient, easy tunable absorption and emission bands, high brightness, and excellent photostability. Combined with good biocompatibility properties, much effort has been devoted to Pdots for in vivo biological imaging and therapy applications, such as deep-tissue fluorescent imaging, photodynamic therapy, photothermal therapy, and nanocarriers of genes or chemical drugs. Many reviews have been presented in these fields. On the other hand, a large number of studies employing Pdots for in vitro biosensing applications have been reported during the past few years, and there are barely any relevant reports to summarize the progress in this area. Hence, it is necessary to review these studies to promote the comprehensive application of Pdots. Herein, we introduce the properties and functionalization of Pdots, and systematically summarize the progress in the in vitro applications of Pdots, including the detection of DNAs, microRNAs, proteins, enzymatic activity, and some biological small molecules and ions. Finally, we share our perspectives on the future direction of this field.

A centrifugation-assisted visual detection of SNP in circulating tumor DNA using gold nanoparticles coupled with isothermal amplification

Detection of single-nucleotide polymorphism (SNP) in circulating tumor DNA (ctDNA) is challenging because of the large DNA fragmentation (∼150 nt) and the strong background of normal cell free DNA (cfDNA). Here we developed a rapid centrifugation-assisted colorimetric assay using gold nanoparticles (AuNPs) coupled with isothermal amplification to detect a SNP (G to C mutation) in KRAS, p.G13D in ctDNA. Compared to conventional AuNP aggregation assays, our assay contains four unique design concepts. Firstly, a centrifugation step is introduced at the end of the reaction that significantly enhances the colorimetric readout by providing visually distinct precipitation for the SNP ctDNA. Secondly, to achieve a fast turnover rate for clinical pM demand, a “critical linker concentration” concept is introduced to the assay. Thirdly, in order to achieve an unambiguous differentiation of the SNP ctDNA from wild type cfDNA and the control sample without DNA, a “color code conversion” strategy is employed, where a complementary sequence of the linker DNA is introduced to manipulate the AuNP aggregation. Finally, ethylenediaminetetraacetic acid is used for enzyme inactivation only at room temperature while stabilizing the AuNP solution from unwanted aggregation. Our assay coupling two amplification strategies (isothermal amplification and centrifugation-assisted assembly) is capable of both quantitative and qualitative differentiation of SNP in ctDNA of ∼150 nt at a clinically relevant concentration and 67 pM limit of detection and in the presence of 99% normal cfDNA background. This assay can be used for point-of-care colon cancer diagnosis and prognosis with a fast turnover time (<2 h).

A centrifugation-assisted dual signal amplified visual detection of ctDNA SNP (∼150 nt, 1% clinic sensitivity) within 2 hours has been reported.

Surface Functionalisation of Upconversion Nanoparticles with Different Moieties for Biomedical Applications

Lanthanide ion-doped upconversion nanoparticles (UCNPs) that can convert low-energy infrared photons into high-energy visible and ultraviolet photons, are becoming highly sought-after for advanced biomedical and biophotonics applications. Their unique luminescent properties enable UCNPs to be applied for diagnosis, including biolabeling, biosensing, bioimaging, and multiple imaging modality, as well as therapeutic treatments including photothermal and photodynamic therapy, bio-reductive chemotherapy and drug delivery. For the employment of the inorganic nanomaterials into biological environments, it is critical to bridge the gap in between nanoparticles and biomolecules via surface modifications and subsequent functionalisation. This work reviews the various ways to surface modify and functionalise UCNPs so as to impart different functional molecular groups to the UCNPs surfaces for a broad range of applications in biomedical areas. We discussed commonly used base functionalities, including carboxyl, amino and thiol moieties that are typically imparted to UCNP surfaces so as to provide further functional capacity.

Zeptomole Biosensing of DNA with Flexible Selectivity Based on Acoustic Levitation of a Single Microsphere Binding Gold Nanoparticles by Hybridization

A novel scheme for DNA sensing at the zeptomole level is presented, based on the levitation of a single microsphere in a combined acoustic-gravitational (CAG) field. The levitation of a microsphere in the field is predominantly determined by its density. Capture and reporter probe DNAs are anchored on poly(methyl methacrylate) microsphere (PMMA) and gold nanoparticles (AuNPs), respectively, and a target DNA induces the binding of AuNPs on PMMA. This interparticle sandwich DNA-hybridization induces density increase in PMMA, which is detected as a shift in the levitation coordinate in the CAG field. The reporter DNAs are designed based on base-pair (bp) number selectivity, which is evaluated using direct interparticle hybridization between DNA-bound PMMA and complementary DNA-anchored AuNPs. Interestingly, the bp-number selectivity can be enlarged by lowering the reactant concentrations. Thus, the threshold bp, at which no density change is detected, can be adjusted by controlling the reactant concentrations. This strategy is extended to the sensing of HIV-2 DNA and single nucleotide polymorphism (SNP) detection of the KRAS gene by sandwich hybridization. In SNP detection, the present method selectively distinguishes wild-type DNA from mutant DNA differing by one nucleotide in the 21-nucleotide sequence by optimizing the lengths of probe DNAs and particle concentrations. This approach allows the detection of 1000 DNA molecules.

DNA-Functionalized Dye-Loaded Polymeric Nanoparticles: Ultrabright FRET Platform for Amplified Detection of Nucleic Acids

Going beyond the limits of optical biosensing motivates exploration of signal amplification strategies that convert a single molecular recognition event into a response equivalent to hundreds of fluorescent dyes. In this respect, Førster Resonance Energy Transfer (FRET) with bright fluorescent nanoparticles (NPs) is an attractive direction, but it is limited by poor efficiency of NPs as FRET donors, because their size is typically much larger than the Førster radius (∼5 nm). Here, we established FRET-based nanoparticle probes that overcome this fundamental limitation by exploiting a phenomenon of giant light harvesting with thousands of strongly coupled dyes in a polymer matrix. These nanoprobes are based on 40 nm dye-loaded poly(methyl methacrylate- co-methacrylic acid) (PMMA-MA) NPs, so-called light-harvesting nanoantennas, which are functionalized at their surface with oligonucleotides. To achieve this functionalization, we developed an original methodology: PMMA-MA was modified with azide/carboxylate bifunctional group that enabled assembly of small polymeric NPs and their further Cu-free click coupling with oligonucleotides. The obtained functionalized nanoantenna behaves as giant energy donor, where hybridization of target nucleic acid (encoding survivin cancer marker) with ∼23 grafted oligonucleotides/Cy5-acceptors switches on/off FRET from ∼3200 rhodamine-donors of the nanoantenna, leading to 75-fold signal amplification. In solution and on surfaces at single-particle level, the nanoprobe provides sequence-specific two-color ratiometric response to nucleic acids with limit of detection reaching 0.25 pM. It displays unprecedented brightness for a FRET biosensor: it outperforms analogous FRET-based molecular probe by >2000-fold and QDot-605 by ∼100-fold. The developed concept of amplified sensing will increase orders of magnitude sensitivity of fluorescent probes for biomolecular targets.

High-Resolution and Universal Visualization of Latent Fingerprints Based on Aptamer-Functionalized Core-Shell Nanoparticles with Embedded SERS Reporters

Although fingerprints have been widely used in forensic investigations, low resolution and poor universality are still the main obstacles for the development of fingerprint visualization. In this paper, a facile and universal imaging protocol for latent fingerprints (LFPs) was developed by combining sandwiched SERS probes with the highly sensitive and selective recognition of aptamers. The embedded SERS probes (Au/pNTP/SiO2) successfully avoid the environment interference, ascertaining the stability and reproducibility of Raman signals, and simultaneously improve the efficiency of the fingerprint identification. This approach is operationally simple without complicated pre- or post-treatments. Moreover, the fingerprint images display the high resolution in which third-level details can be clearly identified. This is a general approach and can be used to detect various types of fingerprints, including sebaceous, eccrine, fresh LFPs, and aged LFPs on different substrates (such as smooth, scratching, semiporous, and porous surfaces).

The utilization of post-synthetic modification in opto-electronic polymers: an effective complementary approach but not a competitive one to the traditional direct polymerization process

By presenting some typical examples, the recent progress of opto-electronic polymers is reviewed, which were only accessible from the post-synthetic modification strategy.

Highly sensitive optical biosensor for thrombin based on structure switching aptamer-luminescent silica nanoparticles

We describe here the construction of a sensitive and selective optical sensor system for the detection of human α-thrombin. The surface functionalized luminescent [Ru(dpsphen)(3)](4-) (dpsphen-4,7-diphenyl-1,10-phenanthroline disulfonate) ion doped silica nanoparticles (SiNPs) with a size ~70 nm have been prepared. The DABCYL (2-(4-dimethylaminophenyl)diazenyl-benzoic acid) quencher labeled thrombin binding aptamer is conjugated to the surface of SiNPs using BS(3) (bis(sulfosuccinimidyl) suberate) as a cross-linker, resulting in the conformational change of aptamer to form G-quadruplex structure upon the addition of thrombin. The binding event is translated into a change in the luminescence intensity of Ru(II) complex via FRET mechanism, due to the close proximity of DABCYL quencher with SiNPs. The selective detection of thrombin using the SiNPs-aptamer system up to 4 nM is confirmed by comparing its sensitivity towards other proteins. This work demonstrates the application of simple aptamer-SiNPs conjugate as a highly sensitive system for the detection of thrombin and also it is highly sensitive towards thrombin in the presence of other proteins and complex medium such as BSA.

The development of a silica nanoparticle-based label-free DNA biosensor

A silica nanoparticle-based DNA biosensor capable of detecting Bacillus anthracis bacteria through the use of unlabelled ss-oligonucleotides has been developed. The biosensor makes use of the optical changes that accompany a nanoparticle-immobilized cationic conjugated polymer (polythiophene) interacting with single-stranded vs. hybridized oligonucleotides, where a fluorescence signal appears only when hybridized DNA is present (i.e. only when the ss-oligonucleotide interacting with the polymer has hybridized with its complement). In order to enhance the sensitivity of the biosensor, two different nanoparticle architectures were developed and used to elucidate how the presence of neighboring fluorophores on the nanoparticle surface affects Förster-resonant energy transfer (FRET) between the polythiophene/oligonucleotide complex (FRET donor) and the fluorophores (FRET acceptors). We demonstrate that the silica nanoparticle-based FRET platform lowers the limit of detection at least 10-fold in comparison to the polythiophene itself, and allows the detection of ∼2 × 10(-12) moles of ss-oligonucleotide in a 100 μL sample with a standard fluorimeter (i.e. has a limit of detection of ∼2 nM ssDNA). Such nanoparticle-based biosensor platforms are beneficial because of the robustness and stability inherent to their covalent assembly and they provide a valuable new tool that may allow for the sensitive, label-free detection (the target DNA that produces the fluorescence signal is unlabelled) without the use of polymerase chain reaction.

Label-free biosensing based on multilayer fluorescent nanocomposites and a cationic polymeric transducer

This study describes the preparation and characterization of a DNA sensing architecture combining the molecular recognition capabilities of a cationic conjugated polymer transducer with highly fluorescent core-shell nanoparticles (NPs). The very structure of the probe-labeled NPs and the polymer-induced formation of NP aggregates maximize the proximity between the polymer donor and acceptor NPs that is required for optimal resonant energy transfer. Each hybridization event is signaled by a potentially large number of excited reporters following the efficient plasmon-enhanced energy transfer between target-activated polymer transducer and fluorophores located in the self-assembled core-shell aggregates, resulting in direct molecular detection of target nucleic acids at femtomolar concentrations.

Anionic conjugated polymer with aptamer-functionalized silica nanoparticle for label-free naked-eye detection of lysozyme in protein mixtures

An assay triggered by recognition-induced charge switching is developed for protein detection and quantification. Aptamer-functionalized silica nanoparticles (NPs) have been synthesized to capture lysozyme, resulting in an alternation of the surface charge from negative to partially positive. The binding event is then translated and monitored by the fluorescence signal of a highly fluorescent anionic poly(fluorene-alt-vinylene) (PFVSO(3)), which "stains" on protein/aptamer-NP complexes via electrostatic interaction. Blue-greenish fluorescence of PFVSO(3) is observed in the presence of lysozyme by the naked eye, while no fluorescence is obtained for NPs upon treatment with a mixture of foreign proteins. A linear relationship between NP fluorescence and lysozyme is observed in the concentration range of 0-22.5 microg/mL, which gives a limit of detection as approximately 0.36 microg/mL. This work demonstrates a convenient label-free conjugated polyelectrolyte (CPE)-based protein detection with high specificity and sensitivity, which has potential applications in medical diagnosis.

Fluorescent detection of ATP based on signaling DNA aptamer attached silica nanoparticles

Novel methods for rapid, sensitive and low-cost biomolecule detection have attracted particular interest because of their wide use in medical diagnostics, food inspection and biomedical research applications. In this work, we report a simple and efficient silica nanoparticle (NP)-based fluorescent assay for ATP detection. It takes advantage of the washing and separation properties of NPs and the structure-switch property of DNA aptamers, resulting in fluorescence change of the supernatant in the presence of targets. A linear response for ATP detection was observed from 0 to 6 mM with a detection limit of ∼34 µM. This detection strategy could be generalized to other aptamer-based detection systems.

Optimizing the cationic conjugated polymer-sensitized fluorescent signal of dye labeled oligonucleotide for biosensor applications

Methods for real time, highly selective and sensitive polynucleotide detection are of vast scientific and economic importance. Fluorescence resonance energy transfer (FRET)-based assays which take advantage of the collective response of water-soluble conjugated polymers (CPs) and the self-assembly characteristic of aqueous polyelectrolytes have been widely used for the detection of DNA, RNA, protein and small molecules. The detection sensitivity of CP-based biosensor is dependent on the signal amplification of dye emission upon excitation of CP relative to that upon direct excitation of the dye. Using cationic polyfluorene derivatives and chromophore (fluorescein or Texas Red) labeled single-stranded DNA molecules (ssDNA-C*) as donor/acceptor pairs, we show that in addition to the spectral overlap, orientation and distance between the donor and the acceptor, the energy levels and fluorescence quenching of the donor/acceptor within the polymer/DNA-C* complexes are also important factors that affect the signal output of dye emission.