Multifunctional Plasmonic Core-Satellites Nanoprobe for Cancer Diagnosis and Therapy Based on a Cascade Reaction Induced by MicroRNA

DNA tetrahedral molecular sieve for size-selective fluorescence sensing of miRNA 21 in living cells

In situ monitoring of intracellular microRNAs (miRNAs) often encounters the challenges of surrounding complexity, coexistence of precursor miRNAs (pre-miRNAs) and the degradation of biological enzyme in living cells. Here, we designed a novel probe encapsulated DNA tetrahedral molecular sieve (DTMS) to realize the size-selective detection of intracellular miRNA 21 that can avoid the interference of pre-miRNAs. In such strategy, quencher (BHQ-1) labeled probe DNA (S6-BHQ 1) was introduced into the inner cavity of fluorophore (FAM) labeled DNA tetrahedral scaffolds (DTS) to prepare DTMS, making the FAM and BHQ-1 closely proximate, and resulting the sensor in a "signal-off" state. In the presence of miRNA 21, strand displacement reaction happened to form more stable DNA double-stranded structure, accompanied by the release of S6-BHQ 1 from the inner cavity of DTMS, making the sensor in a "signal-on" state. The DTMS based sensing platform can then realized the size-selective detection of miRNA 21 with a detection limit of 3.6 pM. Relying on the mechanical rigidity of DTS and the encapsulation of DNA probe using DTMS, such proposed method achieved preferable reproducibility and storage stability. Moreover, this sensing system exhibited good performance for monitoring the change of intracellular miRNA 21 level during the treatment with miRNA-related drugs, demonstrating great potential for biological studies and accurate disease diagnosis.

Dark-field imaging and fluorescence dual-mode detection of microRNA-21 in living cells by core-satellite plasmonic nanoprobes

The in situ precise quantification and simultaneous imaging of low abundance microRNAs (miRNAs) within living cells is critical for cancer diagnosis, yet it remains a significant challenge. Leveraging the excellent sensitivity and spatiotemporal resolution of dark-field microscopy (DFM) and fluorescence imaging, we have successfully devised a novel detection approach using dual-signal reporter probes (DSRPs). These probes allow for highly sensitive detection of miRNA-21 in living cells via toehold-mediated strand displacement cascades. The DSRPs were constructed by Au nanoparticles and Ag nanoclusters core-satellite nanostructures. After the recognition of miRNA-21, the strand displacement cascades were triggered, inducing the disassembly of the Au/Ag core-satellite nanostructure with apparent scattering intensity decrease and peak wavelength shifts. Additionally, the fluorescence of Ag clusters could be recovered and further enhanced when in close proximity to specific guanine-rich strands. The dual-signal response capability enables the accurate detection of miRNA-21 from 1 fM to 1 nM, with a limit of detection reached 0.75 fM. DFM and fluorescent imaging of living cells efficiently confirms the applicable detection of miRNA-21 in complex detection media. The biosensor based on DSRPs represents a promising nanoplatform for visual monitoring and imaging of biomolecules in living cells, even at the single particle level.

Self-Powered Biosensor Based on DNA Walkers for Ultrasensitive MicroRNA Detection

A novel self-powered biosensor is fabricated for ultrasensitive microRNA-21 (miRNA-21) detection, which includes an enzymatic biofuel cell (EBFC), DNA walkers, a digital multimeter (DMM), and a capacitor. As a novel strategy for signal amplification, DNA walkers are designed in the cathode, while the capacitor stores electrochemical energy from the EBFC to further boost the instantaneous current displayed by the DMM. When miRNA-21 is present, the DNA walkers are provoked to walk from as-opened hairpin structures to other hairpin structures, generating double-strand DNA structures, which stimulate [Ru(NH3)6]3+ to be adsorbed on the cathode surface by electrostatic interaction. Afterward, [Ru(NH3)6]3+ is reduced to [Ru(NH3)6]2+, and the open circuit voltage (EOCV) is significantly increased. Depending on the approach of signal amplification from DNA walkers, this biosensor displays an ultrasensitive assay toward miRNA-21 in the range of 0.5 to 104 fM, with a detection limit of 0.15 fM. In addition, this self-powered biosensor displays high selectivity for miRNA-21 assay in human serum samples.

Machine Learning Color Feature Analysis of a High Throughput Nanoparticle Conjugate Sensing Assay

Plasmonic nanoparticles are finding applications within the single molecule sensing field in a "dimer" format, where interaction of the target with hairpin DNA causes a decrease in the interparticle distance, leading to a localized surface plasmon resonance shift. While this shift may be detected using spectroscopy, achieving statistical relevance requires the measurement of thousands of nanoparticle dimers and the timescales required for spectroscopic analysis are incompatible with point-of-care devices. However, using dark-field imaging of the dimer structures, simultaneous digital analysis of the plasmonic resonance shift after target interaction of thousands of dimer structures may be achieved in minutes. The main challenge of this digital analysis on the single-molecule scale was the occurrence of false signals caused by non-specifically bound clusters of nanoparticles. This effect may be reduced by digitally separating dimers from other nanoconjugate types. Variation in image intensity was observed to have a discernible impact on the color analysis of the nanoconjugate constructs and thus the accuracy of the digital separation. Color spaces wherein intensity may be uncoupled from the color information (hue, saturation, and value (HSV) and luminance, a* vector, and b* vector (LAB) were contrasted to a color space which cannot uncouple intensity (RGB) to train a classifier algorithm. Each classifier algorithm was validated to determine which color space produced the most accurate digital separation of the nanoconjugate types. The LAB-based learning classifier demonstrated the highest accuracy for digitally separating nanoparticles. Using this classifier, nanoparticle conjugates were monitored for their plasmonic color shift after interaction with a synthetic RNA target, resulting in a platform with a highly accurate yes/no response with a true positive rate of 88% and a true negative rate of 100%. The sensor response of tested single stranded RNA (ssRNA) samples was well above control responses for target concentrations in the range of 10 aM-1 pM.

Gold Nanoparticles as a Biosensor for Cancer Biomarker Determination

Molecular biology applications based on gold nanotechnology have revolutionary impacts, especially in diagnosing and treating molecular and cellular levels. The combination of plasmonic resonance, biochemistry, and optoelectronic engineering has increased the detection of molecules and the possibility of atoms. These advantages have brought medical research to the cellular level for application potential. Many research groups are working towards this. The superior analytical properties of gold nanoparticles can not only be used as an effective drug screening instrument for gene sequencing in new drug development but also as an essential tool for detecting physiological functions, such as blood glucose, antigen-antibody analysis, etc. The review introduces the principles of biomedical sensing systems, the principles of nanomaterial analysis applied to biomedicine at home and abroad, and the chemical surface modification of various gold nanoparticles.

Single-Particle Optical Imaging for Ultrasensitive Bioanalysis

The quantitative detection of critical biomolecules and in particular low-abundance biomarkers in biofluids is crucial for early-stage diagnosis and management but remains a challenge largely owing to the insufficient sensitivity of existing ensemble-sensing methods. The single-particle imaging technique has emerged as an important tool to analyze ultralow-abundance biomolecules by engineering and exploiting the distinct physical and chemical property of individual luminescent particles. In this review, we focus and survey the latest advances in single-particle optical imaging (OSPI) for ultrasensitive bioanalysis pertaining to basic biological studies and clinical applications. We first introduce state-of-the-art OSPI techniques, including fluorescence, surface-enhanced Raman scattering, electrochemiluminescence, and dark-field scattering, with emphasis on the contributions of various metal and nonmetal nano-labels to the improvement of the signal-to-noise ratio. During the discussion of individual techniques, we also highlight their applications in spatial-temporal measurement of key biomarkers such as proteins, nucleic acids and extracellular vesicles with single-entity sensitivity. To that end, we discuss the current challenges and prospective trends of single-particle optical-imaging-based bioanalysis.

Gold Nanoconjugates for miRNA Modulation in Cancer Therapy: From miRNA Silencing to miRNA Mimics

Cancer is a major healthcare burden and cause of death worldwide, with an estimated 19.3 million new cancer cases and 10 million cancer deaths globally only in 2020. While several anticancer therapeutics are available to date, many of these still show low treatment efficacy and high off-target effects and adverse reactions. This prompts a serious need to develop novel therapies that can decrease the side effects and increase treatment efficacy. MicroRNAs (miRNAs) can have a role in tumor development and progression, making them important targets for the improvement of anticancer therapies. In this context, gold nanoparticles have been widely studied for different clinical applications due to their biocompatibility and possibility of customization, and gold nanoconjugates targeting miRNAs are being developed for cancer diagnosis and treatment. Here we summarize the research developed so far and how it can contribute to cancer treatment, discuss how it can be improved, and present the current challenges and future perspectives on their design and application.

Intelligent Programmable DNA Nanomachines for the Spatially Controllable Imaging of Intracellular MicroRNA

The high programmability of DNA molecules makes them particularly suitable for constructing artificial molecular machines to perform sophisticated functions by simulating complex living systems. However, intelligent DNA nanomachines which can perform precise tasks logically in complex environments still remain challenging. Herein, we develop a general strategy to design a pH-responsive programmable DNA (PRPD) nanomachine to perform multilayer DNA cascades, enabling precise sensing and calculation of intracellular biomolecules. The PRPD nanomachine is built on a four-stranded DNAzyme walker precursor with a DNA switch on the surface of an Au nanoparticle, which is capable of precisely responding to pH variations in living cells by sequence tuning. This multilayer DNA cascade networks have been applicated in spatially controlled imaging of intracellular microRNA, which efficiently avoided the DNA nanomachine activated by nonspecific extracellular molecules and achieved apparent signal amplification. Our strategy enables the sensing-computing-output functional integration of DNA nanomachines, facilitating the application of programmable and complex nanomachines in nanoengineering, chemistry, and biomedicine.

A Novel Ratiometric Electrochemical Biosensor Using Only One Signal Tag for Highly Reliable and Ultrasensitive Detection of miRNA-21

Herein, a novel ratiometric electrochemical biosensor with methylene blue (MB) as the only one signal tag was proposed for highly reliable and ultrasensitive detection of microRNA-21 (miRNA-21) under the assistance of an intelligent target-induced dual signal amplification (T-DSA). First, a small amount of target miRNA-21 could produce abundant mimic targets DNA S1 and Zn²⁺ through target-induced recycle and acid dissolution, respectively. Then, S1 triggered rolling circle amplification (RCA) to generate functional DNA nanospheres (DSP) encoded by DNAzyme and substrate sequence for loading numerous signal tag MB with a remarkable electrochemical signal (signal on), and the Zn²⁺ cofactor mediated the nonviolent DNAzyme-catalyzed cleavage of DSP to sharply release MB with obviously reduced electrochemical responses (signal off). Impressively, our strategy could controllably load and release the only signal tag MB through the well-designed DSP to effectively avoid the false positive responses caused by the non-ideal upright state of DNA probes connected to electrodes in traditional distance-dependent signal adjustment ratiometric strategies with two different signal tags. Meanwhile, with the aid of innovative T-DSA recycle and RCA-produced functional DSP, the detection sensitivity of this sensing platform was significantly improved. As a result, the proposed biosensor successfully realized highly reliable and ultrasensitive detection of miRNA-21 with a detection limit down to 26.7 aM, which shows exceptional promise in biological analysis and medical diagnosis.

Crosstalk Among circRNA/lncRNA, miRNA, and mRNA in Osteoarthritis

Osteoarthritis (OA) is a joint disease that is pervasive in life, and the incidence and mortality of OA are increasing, causing many adverse effects on people's life. Therefore, it is very vital to identify new biomarkers and therapeutic targets in the clinical diagnosis and treatment of OA. ncRNA is a nonprotein-coding RNA that does not translate into proteins but participates in protein translation. At the RNA level, it can perform biological functions. Many studies have found that miRNA, lncRNA, and circRNA are closely related to the course of OA and play important regulatory roles in transcription, post-transcription, and post-translation, which can be used as biological targets for the prevention, diagnosis, and treatment of OA. In this review, we summarized and described the various roles of different types of miRNA, lncRNA, and circRNA in OA, the roles of different lncRNA/circRNA-miRNA-mRNA axis in OA, and the possible prospects of these ncRNAs in clinical application.

Ladder-Like DNA Nanostructure-Mediated Cascade Catalytic Nanomachine for Construction of Ultrasensitive Biosensors

Herein, a novel two-dimensional ladder-like DNA nanostructure (LDN)-mediated cascade catalytic nanomachine (LDN-CCN) with a higher catalytic efficiency beyond those of a conventional one-dimensional hybrid chain reaction (HCR) nanostructure-mediated CCN was constructed and applied to design an electrochemical biosensing platform with first-rank performance for ultrasensitive detection of target miRNA-21. First, output DNA S1' and S2' were produced through the DNAzyme recycle amplification when the target miRNA-21 existed. Then, the controllable LDN-CCN was constructed on S1-S2 modified electrodes by the subsequent reaction triggered by S1' and S2' with H1-AuNPs, H2, H3-AuNPs, and H4 with the assistance of K⁺ and hemin, in which the hemin/G-quadruplexes could produce a prominent electrochemical signal response to the substrate glucose. The best performance of cascade catalysis was acquired when the distance of Au nanoparticles (glucose oxidase-like activity) modified on H1 and H3 and hemin/G-quadruplexes (peroxidase-like activity) formed by the sticky ends of H2 and H4 was roughly 9 nm (27 bp) in LDN-CCN. The constructed electrochemical platform realized the sensitive detection of target miRNA-21 with the linear range from 100 aM to 10 nM and with a detection limit as low as 48.5 aM, which provided novel insights to explore the new functional DNA nanostructure and well-performing mimic enzyme cascade catalytic platforms for applications in biological fields and early diagnosis of diseases.

DNA Tetrahedron-Based MNAzyme for Sensitive Detection of microRNA with Elemental Tagging

Heterogeneous immunoassay based on magnetic separation is commonly used in inductively coupled plasma-mass spectrometry (ICP-MS)-based biomedical analysis with elemental labeling. However, the functionalized magnetic beads (MBs) often suffer from non-specific adsorption and random distribution of the functional probes. To overcome these problems, DNA tetrahedron (DT)-functionalized MBs were designed and further conjugated with substrate modified Au NPs (Sub-AuNP). Based on the prepared MB-DT-AuNP probes, an MB-DT based multicomponent nucleic acid enzyme (MNAzyme) system involving Au NPs as the elemental tags was proposed for highly sensitive quantification of miRNA-155 by ICP-MS. Target miRNA would trigger the assembly of MNAzyme, and Sub-AuNP would be cleaved from the MB-DT-AuNP probe, resulting in a cyclic amplification. Single-stranded DNA-functionalized MB (MB-ssDNA)-AuNP probes were prepared as well. Comparatively, the amount of Au NPs grafted onto MB-ssDNA-AuNP probes was higher than that grafted onto MB-DT-AuNP probes. Meanwhile, a higher signal-to-noise ratio was obtained by using MB-DT-AuNP probes over MB-ssDNA-AuNP probes in the MNAzyme system. Under the optimal experimental conditions, the limit of detection for target miRNA obtained by using MB-DT-AuNP probes was 1.15 pmol L^-1, improved by 23 times over that obtained by the use of MB-ssDNA-AuNP probes. The proposed MB-DT-MNAzyme-ICP-MS method was applied to the analysis of miRNA-155 in serum samples, and recoveries of 86.7-94.6% were obtained. This method is featured with high sensitivity, good specificity, and simple operation, showing a great application potential in biomedical analysis.

Programmable DNAzyme Computing for Specific In Vivo Imaging: Intracellular Stimulus-Unlocked Target Sensing and Signal Amplification

Molecular probe that enables in vivo imaging is the cornerstone of accurate disease diagnosis, prognostic estimation, and therapies. Although several nucleic acid-based probes have been reported for tumor detection, it is still a challenge to develop programmable methodology for accurately identifying tumors in vivo. Herein, a reconfigurable DNA hybridization-based reaction was constructed to assemble DNAzyme computing that contains an intracellular miRNA-unlocked entropy-driven catalysis module and an endogenous metal ion-responsive DNAzyme module for specific in vivo imaging. By reasonable design, the programmable DNAzyme computing can not only successfully distinguish tumor cells from normal cells but also enable tumor imaging in living mice. Due to its excellent operation with high specificity and sensitivity, this design may be broadly applied in the biological study and personalized medicine.