Swelling of Serum-Stable DNA Nanoparticles upon Target-Induced Conformational Rearrangement of Sensing Probes for the Signal-On Detection of Cancer-Related Genes

Intelligent Reconfiguration-Promoted Cellular Internalization of Core-Shell DNA Nanoprobe Equipped with Successive Dual Stimuli-Responsive Protective Satellites for Amplification Fluorescence Imaging of Tumor Cells

Although DNA probes have attracted increasing interest for precise tumor cell identification by imaging intracellular biomarkers, the requirement of commercial transfection reagents, limited targeting ligands, and/or non-biocompatible inorganic nanostructures has hampered the clinic translation. To circumvent these shortcomings, a reconfigurable ES-NC (Na+-dependent DNAzyme (E)-based substrate (S) cleavage core/shell DNA nanocluster (NC)) entirely from DNA strands is assembled for precise imaging of cancerous cells in a successive dual-stimuli-responsive manner. This nanoprobe is composed of a strung DNA tetrahedral satellites-based protective (DTP) shell, parallelly aligned target-responsive sensing (PTS) interlayer, and hydrophobic cholesterol-packed innermost layer (HCI core). Tetrahedral axial rotation-activated reconfiguration of DTP shell promotes the exposure of interior hydrophobic moieties, enabling cholesterol-mediated cellular internalization without auxiliary elements. Within cells, over-expressed glutathione triggers the disassembly of the DTP protective shell (first stimulus), facilitating target-stimulated signal transduction/amplification process (second stimuli). Target miRNA-21 is detected down to 10.6 fM without interference from coexisting miRNAs. Compared with transfection reagent-mediated counterpart, ES-NC displays a higher imaging ability, resists nuclease degradation, and has no detectable damage to healthy cells. The blind test demonstrates that the ES-NC is suitable for the identification of cancerous cells from healthy cells, indicating a promising tool for early diagnosis and prediction of cancer.

Three-dimensional DNA biomimetic networks (B-3D Net)-based ratiometric fluorescence platform for cancer-related gene biosensing

Efficient detection of cancer-related nucleic acids is pivotal for early cancer diagnosis. This study introduces a target induced three-dimensional DNA biomimetic networks (B-3D Net)-based ratiometric fluorescence platform using manganese dioxide nanosheets (MnO2 NS)/o-phenylenediamine in combination with hybridization chain reaction to detect cancer-related genes (p53 gene). The incorporation of multiple signals within the B-3D networks can significantly enhance catalytic activity and amplify the output signals, enabling a high sensitivity. Compared with traditional ratio fluorescence platforms, there is no demand to synthesize fluorescent nanoprobes due to the in-situ formation of fluorescence species, which is simple and cost-effective. The corresponding assay demonstrated exceptional sensitivity (with a detection limit as low as 2 fM), selectivity, reproducibility, and accuracy, which mitigates disturbances caused by instrument errors, an inaccurate probe count, and the microenvironment. Furthermore, the ease and straightforwardness of discerning changes in fluorescent brightness and colour by the naked eye are evident. Using the relevant software, a linear relationship between fluorescent images using a smartphone and target concentration was obtained. Hence, the novel ratiometric sensing system will demonstrate new opportunities on determination of target DNA samples in complex biological environments.

A label-free activatable biosensor for in situ detection of exosomal microRNAs based on DNA-AgNCs and hairpin type nucleic acid probes

Exosomal microRNA (miRNA) is a potential biomarker for cancer diagnosis, metastasis, and treatment. In situ detection of exosomal miRNA is an attractive option due to its simplicity and high accuracy. However, in situ exosomal miRNA detection has encountered challenges because of the low target abundance of targets and limited probe permeability. Herein, a label-free and activatable biosensor was developed for in situ exosomal miRNA assays by utilizing hairpin-shaped nucleic acid probes and DNA-hosted silver nanoclusters (DNA-AgNCs). The probe is directly internalized into the exosomes, and then hybridized with the target miRNA-21. Subsequently, the DNA-AgNCs are pulled closer to the G-rich sequence, ultimately leading to in situ red fluorescence activation. The biosensor not only can detect exosomal miRNA-21 but also distinguish cancer cells from normal cells. Under optimal reaction conditions, the detection limit (LOD) of exosomal miRNA-21 is 1.53 × 107 particles per mL. Furthermore, DNA-AgNCs are used as label-free signal elements for in situ detection of exosomal miRNAs for the first time, expanding the application of nanomaterials in this field. This strategy does not require tedious RNA extraction steps and expensive instruments, and may develop into a non-invasive diagnostic tool for ovarian cancer.

A novel label-free capillary electrophoresis LED-induced fluorescence platform based on catalytic hairpin assembly for sensitive detection of multiple circulating tumor DNA

Circulating tumor DNA (ctDNA) is a highly promising biomarker for the early diagnosis and treatment of gastric cancer (GC). However, there is still a lack of effective and practical ctDNA detection methods. In this work, a simple and economical capillary non-gel sieving electrophoresis-LED induced fluorescence detection (NGCE-LEDIF) platform coupled with catalytic hairpin assembly (CHA) as the signal amplification strategy is proposed for quantitative detection of PIK3CA E542K and TP53 (two types of ctDNA associated with GC). We have reasonably designed two pairs of programmable oligonucleotide hairpin probes for PIK3CA E542K and TP53. Using a one-pot reaction, the presence of ctDNA triggers the cyclic amplification of CHA, forming numerous thermodynamically stable H1/H2 double-strands. The H1/H2 double-stranded DNA catalyzed by PIK3CA E542K and TP53 can be easily separated by NGCE due to their different lengths, enabling simultaneous detection of both ctDNAs. Under optimal experimental conditions, the detection limits of this strategy for detecting GC-related biomarkers PIK3CA E542K and TP53 are 20.35 pM and 19.61 pM, respectively, and can achieve 730-fold signal amplification. This strategy has a good recovery in the serum matrix. The results of this study show that this strategy has significant advantages such as high selectivity, a simple process, no special instruments and equipment, no need for fluorescence modification of hairpin probes in advance, high automation, low cost, and minimal sample consumption. This provides a powerful method for the detection of trace cancer biomarkers in the serum matrix with good application prospects.

Spatial confinement-based Figure-of-Eight nanoknots accelerated simultaneous detection and imaging of intracellular microRNAs

Developing highly efficient and reliable methods for simultaneous imaging of microRNAs in living cells is often appealed to understanding their synergistic functions and guiding the diagnosis and treatment of human diseases, such as cancers. In this work, we rationally engineered a four-arm shaped nanoprobe that can be stimuli-responsively tied into a Figure-of-Eight nanoknot via spatial confinement-based dual-catalytic hairpin assembly (SPACIAL-CHA) reaction and applied for accelerated simultaneous detection and imaging of different miRNAs in living cells. The four-arm nanoprobe was facilely assembled from a cross-shaped DNA scaffold and two pairs of CHA hairpin probes (²¹HP-a and ²¹HP-b for miR-21, while ¹⁵⁵HP-a and ¹⁵⁵HP-b for miR-155) via the "one-pot" annealing method. The DNA scaffold structurally provided a well-known spatial-confinement effect to improve the localized concentration of CHA probes and shorten their physical distance, resulting in an enhanced intramolecular collision probability and accelerating the enzyme-free reaction. The miRNA-mediated strand displacement reactions can rapidly tie numerous four-arm nanoprobes into Figure-of-Eight nanoknots, yielding remarkably dual-channel fluorescence proportional to the different miRNA expression levels. Moreover, benefiting from the nuclease-resistant DNA structure based on the unique arched DNA protrusions makes the system ideal for operating in complicated intracellular environments. We have demonstrated that the four-arm-shaped nanoprobe is superior to the common catalytic hairpin assembly (COM-CHA) in stability, reaction speed, and amplification sensitivity in vitro and living cells. Final applications in cell imaging have also revealed the capacity of the proposed system for reliable identification of cancer cells (e.g., HeLa and MCF-7) from normal cells. The four-arm nanoprobe shows great potential in molecular biology and biomedical imaging with the above advantages.

Design and application of DNA nanostructures for organelle-targeted delivery of anticancer drugs

INTRODUCTION

DNA nanostructures targeting organelles are of great significance for the early diagnosis and precise therapy of human cancers. This review is expected to promote the development of DNA nanostructure-based cancer treatment with organelle-level precision in the future.

AREAS COVERED

In this review, we introduce the different principles for targeting organelles, summarize the progresses in the development of organelle-targeting DNA nanostructures, highlight their advantages and applications in disease treatment, and discuss current challenges and future prospects.

EXPERT OPINION

Accurate targeting is a basic problem for effective cancer treatment. However, current DNA nanostructures cannot meet the actual needs. Targeting specific organelles is expected to further improve the therapeutic effect and overcome tumor cell resistance, thereby holding great practical significance for tumor treatment in the clinic. With the deepening of the research on the molecular mechanism of disease development, especially on tumorigenesis and tumor progression, and increasing understanding of the behavior of biological materials in living cells, more versatile DNA nanostructures will be constructed to target subcellular organelles for drug delivery, essentially promoting the early diagnosis of cancers, classification, precise therapy and the estimation of prognosis in the future.