Aptamer-tethered self-assembled FRET-flares for microRNA imaging in living cancer cells

Accurate and sensitive dual-response fluorescence detection of microRNAs based on an upconversion nanoamplicon with red emission

Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer. In recent years, researchers have found a close relationship between microRNAs (miRNAs) and OSCC. In addition, miRNAs are highly stable in tissues and circulation, and are also considered potential biomarkers for cancer detection and prognosis. Among a variety of tools for miRNAs with low abundance, single red-emitting UCNP-based biosensors have attracted special interest due to their unique properties, including deep organizational penetration, weak radiation damage, and low autofluorescence. Additionally, the measurement of low-abundance analytes via enzyme-free signal amplification is also an effective means. Herein, by taking advantage of red-emitting UCNPs and an enzyme-toehold-mediated strand displacement cascade, a dual-signal amplification biosensor was constructed. The recycled miRNA can be regarded as a catalyst for the assembly of multiple H1/H2 duplexes, which promoted the response signal of augmented analyte expression. Moreover, the proposed biosensors improved the measurement accuracy via a dual-signal response to obviously avert false-positive signals. The proposed method was applied to measure miRNA-222 (a model analyte) in serum samples, and the results were similar to those of polymerase chain reaction (PCR), with spiked recoveries ranging from 91.2% to 101.7%. The proposed assay has the merits of high sensitivity, strong recognition, and low background, indicating broad potential for the measurement of diverse analytes in biological samples.

Docking-aided rational tailoring of a fluorescence- and affinity-enhancing aptamer for a label-free ratiometric malachite green point-of-care aptasensor

Although nucleic acid aptasensors are increasingly applied in the detection of environmentally hazardous biomolecules, several formidable challenges remain with this technique because of their vulnerability, high cost and suboptimal sensitivity. Here, a docking-aided rational tailoring (DART) strategy was established at three levels and in two dimensions for the refinement of malachite green (MG) DNA aptamers. Guided by in silico molecular docking, coarse and fine tailoring were conducted at three levels each, to significantly enhance fluorescence activation intensity and binding affinity in two dimensions. Empowered by the results of the rational tailoring, a mechanistic view of the MG DNA aptamer-target interaction was thoroughly analyzed via four types of interactions. To meet the demand for point-of-care testing (POCT), a label-free and ratiometric fluorescent aptasensor was developed leveraging the tailored MG aptamer, based on the binding site competition-equilibrium effect via the introduction of a reference dye. This sensitive, specific, low-cost and rapid aptasensor subsequently demonstrated outstanding detection performance, achieving an ideal signal response range of 5 nmol·L^-1 - 6 μmol·L^-1 and a low limit of detection (LOD) of 1.49 nmol·L^-1. The DART strategy and systematic exploration of the MG DNA luminescent aptamers herein will provide a valuable reference in the field of aptamer tailoring, biosensing and bioimaging. The proposed label-free ratiometric aptasensor also provides a highly generalizable strategy for hazardous biomolecular detection.

Multivalent self-assembled nano string lights for tumor-targeted delivery and accelerated biomarker imaging in living cells and in vivo

Multivalent self-assembled nano string lights for tumor-targeted delivery with high efficiency and accelerated biomarker imaging in living cells and in vivo.

Hairpin-functionalized DNA tetrahedra for miRNA imaging in living cells via self-assembly to form dendrimers

A DNA tetrahedron-based intramolecular catalytic hairpin self-assembly platform that uses fluorescence signals to image miRNAs in live cells for accurate tumor cell identification.

Development and characterization of a DNA aptamer for MLL-AF9 expressing acute myeloid leukemia cells using whole cell-SELEX

Current classes of cancer therapeutics have negative side effects stemming from off-target cytotoxicity. One way to avoid this would be to use a drug delivery system decorated with targeting moieties, such as an aptamer, if a targeted aptamer is available. In this study, aptamers were selected against acute myeloid leukemia (AML) cells expressing the MLL-AF9 oncogene through systematic evolution of ligands by exponential enrichment (SELEX). Twelve rounds of SELEX, including two counter selections against fibroblast cells, were completed. Aptamer pools were sequenced, and three candidate sequences were identified. These sequences consisted of two 23-base primer regions flanking a 30-base central domain. Binding studies were performed using flow cytometry, and the lead sequence had a binding constant of 37.5 + / - 2.5 nM to AML cells, while displaying no binding to fibroblast or umbilical cord blood cells at 200 nM. A truncation study of the lead sequence was done using nine shortened sequences, and showed the 5' primer was not important for binding. The lead sequence was tested against seven AML patient cultures, and five cultures showed binding at 200 nM. In summary, a DNA aptamer specific to AML cells was developed and characterized for future drug-aptamer conjugates.

The systemic characterization of aptamer cocktail for bacterial detection studied by graphene oxide-based fluorescence resonance energy transfer aptasensor

Aptamers have gained significant attention as the molecular recognition element to replace antibodies in sensor development and target delivery. Nevertheless, it is noteworthy that unlike the wide application of polyvalent antibodies, existing researches on the combined use of heterologous aptamers with similar recognition affinity and specificity for target detection were sporadic. Herein, first, the wide existence of polyaptamer for bacteria was revealed through the summary of existing literature. Furthermore, based on the establishment of a sensitive aptamer cocktail/graphene oxide fluorescence resonance energy transfer polyaptasensor with a detection limit as low as 10 CFU/ml, the systemic characterization of aptamer cocktails in bacterial detection was carried out by taking E. coli, Vi. parahemolyticus, S. typhimurium, and C. sakazakii as the assay targets. It was turned out that the polyaptasensors for C. sakazakii and S. typhimurium owned prevalence in the broader concentration range of target bacteria. While the polyaptasensors for E. coli and V. parahemolyticus outperformed monoaptasensor mainly in the lower concentration of target bacteria. The linear relationships between fluorescence recovery and the concentration of bacteria were also discussed. The different characteristics of the bacterial cellular membrane, including the binding affinity and the robustness to variation, are analyzed to be the main reason for the diverse detection performance of aptasensors. The study here enhances a sensor detection strategy with super sensitivity. More importantly, this systemic study on the aptamer cocktail in reference to antibodies will advance the in-depth understanding and rational design of aptamer based biological recognition, detection, and targeting.

Ultrasensitive Detection of Amyloid β Oligomers Based on the "DD-A" FRET Binary Probes and Quadrivalent Cruciform DNA Nanostructure-Mediated Cascaded Amplifier

The reported donor donor-acceptor ("DD-A") fluorescence resonance energy transfer (FRET) was typically achieved through random collisions and interactions of DNA molecules in the bulk solution, which has inevitable defects, including weak biological stability, slow reaction kinetics, and low hybridization efficiency. In order to overcome these deficiencies, this work developed a quadrivalent cruciform DNA nanostructure (qCDN)-mediated cascaded catalyzed hairpin assembly (CHA) amplifier for the fluorescence detection of amyloid β oligomer species (AβOs). First, four H1 and four H2 hairpins were assembled on one qCDN to obtain qCDNH1 and qCDNH2, respectively. In the presence of AβOs, strand C was released from the P1-C hybrid hairpin and then alternately opened qCDNH1 and qCDNH2 to trigger the qCDN-mediated CHA. As a result, double donors in H1 and one acceptor in H2 were mutually closed, and the porous DNA nanonet with a high loading of "DD-A" FRET binary probes was formed. The FRET efficiency was approximately 78%, and the initial reaction rate was 25-fold faster than the conventional CHA. The detection limit of AβOs was as low as 0.69 pM. The combination of the "DD-A" FRET binary probes and qCDN-mediated cascaded amplifier exhibited great promise for detecting biomarkers with trace levels.

Orderly Assembled, Self-Powered FRET Flares for MicroRNA Imaging in Live Cells

Signal amplification provides unparalleled opportunities for visualizing low-abundance targets in living cells. However, self-powered signal amplification has not been achieved because of the lack of "fuel" in living cells. Thus, the aim of this work was to develop an integrated amplification platform for the detection of intracellular miRNA by itself. This system, termed self-powered FRET flares (SPF), was first established by self-assembly to form a DNA nanostructure, and then the FRET flares and fuel DNA as the driving force were precisely and orderly loaded on it, which was able to power target recycle and realize signal amplification without any auxiliary additives under the trigger of intracellular miRNA-21. In addition, it employed AS1411 aptamer to target specific cancer cells and facilitated cell internalization of assembly DNA nanostructures. As a proof of concept, we demonstrated that SPF enabled rapid response to miRNA-21 and improvement of the detection sensitivity compared to previously proposed FRET flares without amplification. This strategy is promising for advancing integrated and self-powered nanomachines to execute diverse tasks, facilitating their biological and medical application.

Aptamer-Based Detection of Circulating Targets for Precision Medicine

The past decade has witnessed ongoing progress in precision medicine to improve human health. As an emerging diagnostic technique, liquid biopsy can provide real-time, comprehensive, dynamic physiological and pathological information in a noninvasive manner, opening a new window for precision medicine. Liquid biopsy depends on the sensitive and reliable detection of circulating targets (e.g., cells, extracellular vesicles, proteins, microRNAs) from body fluids, the performance of which is largely governed by recognition ligands. Aptamers are single-stranded functional oligonucleotides, capable of folding into unique tertiary structures to bind to their targets with superior specificity and affinity. Their mature evolution procedure, facile modification, and affinity regulation, as well as versatile structural design and engineering, make aptamers ideal recognition ligands for liquid biopsy. In this review, we present a broad overview of aptamer-based liquid biopsy techniques for precision medicine. We begin with recent advances in aptamer selection, followed by a summary of state-of-the-art strategies for multivalent aptamer assembly and aptamer interface modification. We will further describe aptamer-based micro-/nanoisolation platforms, aptamer-enabled release methods, and aptamer-assisted signal amplification and detection strategies. Finally, we present our perspectives regarding the opportunities and challenges of aptamer-based liquid biopsy for precision medicine.

Nucleolin-Targeted DNA Nanotube for Precise Cancer Therapy through Förster Resonance Energy Transfer-Indicated Telomerase Responsiveness

Precise drug delivery holds great promise in cancer treatment but still faces challenges in controllable drug release in tumor cells specifically. Herein, a nucleolin-targeted and telomerase-responsive DNA nanotube for drug release was developed. First, a DNA nanosheet with four capture strands on its surface was prepared, which could bind and load ricin A chain (RTA). The RTA-loaded nanosheet was further converted into a DNA nanotube with a high Förster resonance energy transfer (FRET) efficiency in the presence of a Cy3-modified DNA fastener by hybridizing with the Cy5-modified DNA and another DNA-containing telomerase primer sequence along the long sides. Moreover, the aptamer of nucleolin was assembled on the DNA nanotube by combining with the hybrid chain at the terminal. The aptamer-functionalized and RTA-loaded DNA nanotube displayed enhanced tumor permeability and precise drug release in response to the telomerase in tumor cells, following the change of the FRET signal and RTA-induced cell death. Moreover, the DNA nanotube was applied successfully in vivo, and there was an obvious inhibition of tumor growth on xenograft-bearing mice following systemic administration, indicating that the constructed DNA nanotube represents a promising platform for precise RTA delivery in target cancer therapy.

Plasmonic gold nanostructures for biosensing and bioimaging

As one kind of noble metal nanostructures, the plasmonic gold nanostructures possess unique optical properties as well as good biocompatibility, satisfactory stability, and multiplex functionality. These distinctive advantages make the plasmonic gold nanostructures an ideal medium in developing methods for biosensing and bioimaging. In this review, the optical properties of the plasmonic gold nanostructures were firstly introduced, and then biosensing in vitro based on localized surface plasmon resonance, Rayleigh scattering, surface-enhanced fluorescence, and Raman scattering were summarized. Subsequently, application of the plasmonic gold nanostructures for in vivo bioimaging based on scattering, photothermal, and photoacoustic techniques  has been also briefly covered. At last, conclusions of the selected examples are presented and an outlook of this research topic is given.