Ultrasensitive electrochemical detection of miRNA coupling tetrahedral DNA modified gold nanoparticles tags and catalyzed hairpin assembly

Tuning quantum dots emission on DNA tetrahedron/silica nanosphere/graphene oxide nanointerface for ratiometric fluorescence assay of Pb2+ in multiplex samples

BACKGROUND

Assembling framework nucleic acid (FNA) nanoarchitectures and tuning luminescent quantum dots (QDs) for fluorescence assays represent a versatile strategy in analytical territory. Rationally, FNA constructs could offer a preferential orientation to efficiently recognize the target and improve detection sensitivity, meanwhile, regulating size-dependent multicolor emissions of QDs in one analytical setting for ratiometric fluorescence assay would greatly simplify operation procedures. Nonetheless, such FNA/QDs-based ratiometric fluorescence nanoprobes remain rarely explored.

RESULTS

We designed a sensitive and signal amplification-free fluorescence aptasensor for lead ions (Pb2+) that potentially cause extensive contamination to environment, cosmetic, food and pharmaceuticals. Red and green emission CdTe quantum dots (rQDs and gQDs) were facilely prepared. Moreover, silica nanosphere encapsulating rQDs served as quantitative internal reference and scaffold to anchor a predesigned FNA and DNA sandwich containing Pb2+ binding aptamer and gQD modified DNA signal reporter. On binding of Pb2+, the gQD-DNA signal reporter was set free, resulting in fluorescence quenching at graphene oxide (GO) interface. Owing to the rigid structure of FNA, the fluorescence signal reporter orderly arranged at the silica nanosphere could sensitively respond to Pb2+ stimulation. The dose-dependent fluorescence signal-off mode enabled ratiometric analysis of Pb2+ without cumbersome signal amplification. Linear relationship was established between fluorescence intensity ratio (I555/I720) and Pb2+ concentration from 10 nM to 2 μM, with detection limit of 1.7 nM (0.43 ppb), well addressing the need for Pb2+ routine monitoring. The designed nanoprobe was applied to detection of Pb2+ in soil, cosmetic, milk, drug, and serum samples, with the sensitivity comparable to conventional ICP-MS technique.

SIGNIFICANCE

Given the programmable design of FNA and efficient recognition of target, flexible tuning of QDs emission, and signal amplification-free strategy, the present fluorescence nanoprobe could be a technical criterion for other heavy metal ions detection in a straightforward manner.

Exonuclease III-propelled DNAzyme walker: an electrochemical strategy for microRNA diagnostics

MicroRNA detection is crucial for early infectious disease diagnosis and rapid cancer screening. However, conventional techniques like reverse transcription-quantitative polymerase chain reaction, requiring specialized training and intricate procedures, are less suitable for point-of-care analyses. To address this, we've developed a straightforward amplifier based on an exonuclease III (exo III)-propelled DNAzyme walker for sensitive and selective microRNA detection. This amplifier employs a specially designed hairpin probe with two exposed segments for strand recognition. Once the target microRNA is identified by the hairpin's extended single-strand DNA, exo III initiates its digestion, allowing microRNA regeneration and subsequent hairpin probe digestion cycles. This cyclical process produces a significant amount of DNAzyme, leading to a marked reduction in electrochemical signals. The biosensor exhibits a detection range from 10 fM to 100 pM and achieves a detection limit of 5 fM (3σ criterion). Importantly, by integrating an "And logic gate," our system gains the capacity for simultaneous diagnosis of multiple microRNAs, enhancing its applicability in RNA-based disease diagnostics.

Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective

DNA-modified gold nanoparticles (AuNPs) play a pivotal role in bio-nanotechnology, driving advancements in bio-sensing, bio-imaging, and drug delivery. Synthetic protocols have focused on maximizing the receptor density on particles by fine-tuning chemical conditions, particularly for DNA. Despite their significance, the understanding of hybridization kinetics on functionalized AuNPs is lacking, particularly how this kinetics depends on DNA density and to what extent it varies from particle-to-particle. This study explores the molecular mechanisms of DNA hybridization on densely coated AuNPs by employing a combination of single-molecule microscopy and coarse-grained molecular dynamics simulations providing a quantification of the molecular rate constants for single particles. Our findings demonstrate that DNA receptor density and the presence of spacer strands profoundly impact association kinetics, with short spacers enhancing association rates by up to ∼15-fold. In contrast, dissociation kinetics are largely unaffected by receptor density within the studied range. Single-particle analysis directly reveals variability in hybridization kinetics, which is analyzed in terms of intra- and inter-particle heterogeneity. A coarse-grained DNA model that quantifies hybridization kinetics on densely coated surfaces further corroborates our experimental results, additionally shedding light on how transient base pairing within the DNA coating influences kinetics. This integrated approach underscores the value of single-molecule studies and simulations for understanding DNA dynamics on densely coated nanoparticle surfaces, offering guidance for designing DNA-functionalized nanoparticles in sensor applications.

A plasmonic MNAzyme signal amplification strategy for quantification of miRNA-4739 breast cancer biomarker

A major challenge in the 21st century is the development of point-of-care diagnostic tools capable to detect and quantify disease biomarkers in a straightforward, affordable, sensitive, and specific manner. The remarkable plasmonic properties of gold nanoparticles (AuNPs) have promoted their use for development of simple methodologies for nucleic acid detection in combination with a variety of oligonucleotides amplification techniques. Here, assemblies of AuNPs with Multicomponent Nucleic Acid enzymes (MNAzymes) has been successfully used in the design of a highly sensitive and simple bioassay for rapid spectroscopic detection and quantification of miRNA-4739 in blood samples. The miRNA selected is a doxorubicin chemoresistant biomarker in breast cancer which overexpression promotes the proliferation, progression, and survival of cancer cells. In this work, two alternatives experimental designs, based on use of MNAzymes and AuNPs, have been optimized and applied for sensitive miRNA-4739 quantification: one based on a traditional direct measurement of wavelength shift and a second non-conventional simple approach based on isolation and measurement of free nanoparticles absorbance. Improvement in sensitivity and, higher measurement accuracy and precision were achieved with the second approach. The developed bioassay provides a detection limit as low as 7 pmolL-1 for miRNA-4739 quantification and performed satisfactory selectivity and well practical applicability by analysis of the miRNA-4739 in blood, demonstrating that the proposed strategy is a promising and suitable spectroscopic method for breast cancer diagnosis thought liquid biopsy of circulating tumoral cells.

The Current Progress of Tetrahedral DNA Nanostructure for Antibacterial Application and Bone Tissue Regeneration

Recently, programmable assembly technologies have enabled the application of DNA in the creation of new nanomaterials with unprecedented functionality. One of the most common DNA nanostructures is the tetrahedral DNA nanostructure (TDN), which has attracted great interest worldwide due to its high stability, simple assembly procedure, high predictability, perfect programmability, and excellent biocompatibility. The unique spatial structure of TDN allows it to penetrate cell membranes in abundance and regulate cellular biological properties as a natural genetic material. Previous studies have demonstrated that TDNs can regulate various cellular biological properties, including promoting cells proliferation, migration and differentiation, inhibiting cells apoptosis, as well as possessing anti-inflammation and immunomodulatory capabilities. Furthermore, functional molecules can be easily modified at the vertices of DNA tetrahedron, DNA double helix structure, DNA tetrahedral arms or DNA tetrahedral cage structure, enabling TDN to be used as a nanocarrier for a variety of biological applications, including targeted therapies, molecular diagnosis, biosensing, antibacterial treatment, antitumor strategies, and tissue regeneration. In this review, we mainly focus on the current progress of TDN-based nanomaterials for antimicrobial applications, bone and cartilage tissue repair and regeneration. The synthesis and characterization of TDN, as well as the biological merits are introduced. In addition, the challenges and prospects of TDN-based nanomaterials are also discussed.

A catalytic hairpin assembly-based Förster resonance energy transfer sensor for ratiometric detection of ochratoxin A in food samples

Ochratoxin A (OTA) poses severe risks to the environment and human health, making the development of an accurate and sensitive analytical method for OTA detection essential. In this study, a catalytic hairpin assembly (CHA)-based Förster resonance energy transfer (FRET) aptasensor was developed to detect OTA using carbon quantum dots (CDs) and 6-carboxy-fluorescein (FAM) as dual signal readout. In the presence of OTA, the aptamer specifically interacted with OTA to release the helper DNA (HP), which could open the hairpin structure of FAM-labeled hairpin DNA 1 (H₁-FAM) modified on the surface of gold nanoparticles (AuNPs). CHA between H₁-FAM and hairpin H₂ labeled with CDs (H₂-CDs) can release HP for the next cycle, resulting in the occurrence of FRET with CDs as the energy donor and FAM as the energy acceptor. According to the ratio of F_CDs/F_FAM, the proposed aptasensor showed a wide linear range from 5.0 pg/mL to 3.0 ng/mL and a low detection limit of 1.5 pg/mL for OTA detection. Moreover, satisfactory results were obtained for OTA detection in rice, suggesting the potential application of this sensor in food safety analysis.

DNA-functionalized gold nanoparticles: Modification, characterization, and biomedical applications

With the development of technologies based on gold nanoparticles (AuNPs), bare AuNPs cannot meet the increasing requirements of biomedical applications. Modifications with different functional ligands are usually needed. DNA is not only the main genetic material, but also a good biological material, which has excellent biocompatibility, facile design, and accurate identification. DNA is a perfect ligand candidate for AuNPs, which can make up for the shortcoming of bare AuNPs. DNA-modified AuNPs (DNA-AuNPs) have exciting features and bright prospects in many fields, which have been intensively investigated in the past decade. In this review, we summarize the various approaches for the immobilization of DNA strands on the surface of AuNPs. Representative studies for biomedical applications based on DNA-AuNPs are also discussed. Finally, we present the challenges and future directions.

Aptamers and New Bioreceptors for the Electrochemical Detection of Biomarkers Expressed in Hepatocellular Carcinoma

Hepatocellular carcinoma is a malignancy associated with high mortality and increasing incidence. Early detection of this disease could help increase survival and overall patient benefit. Non-invasive strategies for the diagnosis of this medical condition are of utmost importance. In this scope, the detection of hepatocellular carcinoma biomarkers could provide a useful diagnostic tool. Aptamers represent as short, single-stranded DNAs or RNAs that can specifically bind selected analytes, and also as pseudo-biorecognition elements that can be employed for electrode functionalization. Also, other types of DNA sequences can be used for the construction of DNA-based biosensors applied for the quantification of hepatocellular carcinoma biomarkers. Herein, we will be analyzing recent examples of aptasensors and DNA biosensors for the detection of hepatocellular carcinoma biomarkers like micro-RNAs, long non-coding RNAs, exosomes, circulating tumor cells and proteins. The literature data is discussed comparatively in a critical manner highlighting the advantages of using electrochemical biosensors in diagnosis, as well as the use of nanomaterials and biocomponents in the functionalization of electrodes for improved sensitivity and selectivity.

DNA nanolantern-mediated catalytic hairpin assembly nanoamplifiers for simultaneous detection of multiple microRNAs

Simultaneous detection of multiple microRNAs (miRNAs) with high sensitivity can give accurate and reliable information for clinical applications. By uniformly anchoring hairpin probes on the surface of DNA nanolantern, a three-dimensional DNA nanostructure contains abundant and adjustable modification sites, highly integrated DNA nanoprobes were designed and developed as catalytic hairpin assembly (CHA)-based signal amplifiers for enzyme-free signal amplification detection of target miRNAs. The nanolantern-based CHA (NLC) amplifiers, which were facilely prepared via a simple "one-pot" annealing method, showed enhanced biostability, improved cell internalization efficiency, accelerated CHA reaction kinetics, and increased signal amplification capability compared to the single-stranded DNA hairpin probes used in traditional CHA reaction. By co-assembling multiple hairpin probes on a DNA nanolantern surface, as-prepared NLC amplifiers were demonstrated to work well for highly sensitive and specific imaging, expression level fluctuation analysis of two miRNAs in living cells, and miRNAs-guided tumor imaging in living mice. The proposed DNA nanolantern-based nanoamplifier strategy might provide a feasible way to promote the cellular and in vivo applications of nucleic acid probes.

A novel electrochemical sensor based on process-formed laccase-like catalyst to degrade polyhydroquinone for tumor marker

Methods to improve the sensitivity of electrochemical sensors based on catalytic reactions generally require adscititious or pre-modified catalysts, which make the sensitive detection of sensors extremely challenging. This is because the activity of the catalyst is susceptible to the storage and modification process, such as aggregation during storage or loss of active sites during multi-step modification, which impairs the performance of the sensor. To solve this thorny issue, a novel electrochemical sensor based on a process-formed laccase-like catalyst was constructed for sensitive detection of tumor markers. Cu²⁺-polydopamine (CuPDA) combined with antibody (Ab₂) were employed as copper-containing immunoprobe, which released Cu(Ⅱ) ions under acidic stimulation. Cu(Ⅱ) ions coordinate with the self-assembly cationic diphenylalanine-glutaraldehyde nanospheres (CDPGA) to form a laccase-like catalyst, which had stronger catalytic activity than laccase. The freshly formed catalyst was immediately used to degrade the polyhydroquinone-reduced graphene oxide (PHQ-rGO) composite, resulting in a significant reduction in the current signal. The PHQ-rGO composite plays dual roles of signal substance and substrate on the sensing interface. The proposed electrochemical sensor demonstrated wide linearity for the determination of a model analyte, human epididymis protein 4 (HE4), from 1 pg mL^-1 to 100 ng mL^-1, and the detection limit was as low as 0.302 pg mL^-1 (S/N = 3), which had good consistency with that of electrochemiluminescence method. This process-formed catalyst approach will have potential reference significance for the construction of other sensors.

Recent advances in catalytic hairpin assembly signal amplification-based sensing strategies for microRNA detection

Accumulative evidences have indicated that abnormal expression of microRNAs (miRNAs) is closely associated with many health disorders, making them be regarded as potentialbiomarkers for early clinical diagnosis. Therefore, it is extremely necessary to develop a highly sensitive, specific and reliable approach for miRNA analysis. Catalytic hairpin assembly (CHA) signal amplification is an enzyme-free toehold-mediated strand displacement method, exhibiting significant potential in improving the sensitivity of miRNA detection strategies. In this review, we first describe the potential of miRNAs as disease biomarkers and therapeutics, and summarize the latest advances in CHA signal amplification-based sensing strategies for miRNA monitoring. We describe the characteristics and mechanism of CHA signal amplification and classify the CHA-based miRNA sensing strategies into several categories based on the "signal conversion substance", including fluorophores, enzymes, nanomaterials, and nucleotide sequences. Sensing performance, limit of detection, merits and disadvantages of these miRNA sensing strategies are discussed. Moreover, the current challenges and prospects are also presented.