Two-wheel drive-based DNA nanomachine and its sensing potential for highly sensitive analysis of cancer-related gene

Nanomolecular machines: Pioneering precision medicine for neoplastic diseases through advanced diagnosis and treatment

Tumors pose a major threat to human health, accounting for nearly one-sixth of global deaths annually. The primary treatments include surgery, radiotherapy, chemotherapy, and immunotherapy, each associated with significant side effects. This has driven the search for new therapies with fewer side effects and greater specificity. Nanotechnology has emerged as a promising field in this regard, particularly nanomolecular machines at the nanoscale. Nanomolecular machines are typically constructed from biological macromolecules like proteins, DNA, and RNA. These machines can be programmed to perform specialized tasks with precise instructions. Recent research highlights their potential in tumor diagnostics-identifying susceptibility genes, detecting viruses, and pinpointing tumor markers. Nanomolecular machines also offer advancements in tumor therapy. They can reduce traditional treatment side effects by delivering chemotherapy drugs and enhancing immunotherapy, and they support innovative treatments like sonodynamic and phototherapy. Additionally, they can starve tumors by blocking blood vessels, and eliminate tumors by disrupting cell membranes or lysosomes. This review categorizes and explains the latest achievements in molecular machine research, explores their models, and practical clinical uses in tumor diagnosis and treatment. It aims to broaden the research perspective and accelerate the clinical adoption of these technologies.

Fluorescence biosensing of the leukemia gene by combining Target-Programmed controllable signal inspiring engineering

Clinical diagnosis urgently requires ultrasensitive, accurate and rapid monitoring of low-abundance biomarkers. A biosensing strategy capable of detecting target genes at the femtomolar scale was designed in this work. In the biosensing strategy, the target can induce the specially designed hairpin probe H1 to self-fold and form a 3' blunt-ended structure. When there are the hybrid double-stranded P1-T1, ligase, polymerase and nickase, the target gene was recycled, and at the same time the system produces a lot of T1 and T2. T1 and T2 can simultaneously trigger HCR, causing the modified fluorophore FAM on the DNA strand to move away from the quencher group BHQ. The amplified fluorescent signal can be captured by a fluorescence instrument. It is exciting for us that three signal amplifications are involved to achieve femtomolar detection of target genes, namely target recycling, dual-triggered HCR of T1 and T2, and HCR. In addition, it still has good detection ability in actual samples simulated by serum. We expect that the sensing strategy proposed in this paper offers great potential for biomarker detection of leukemia for early clinical diagnosis.

Photo-gated and self-powered three-dimensional DNA motors with boosted biostability for exceptionally precise and efficient tracing of intracellular survivin mRNA

Benefiting from the outstanding signal amplification effect and the admirable construction flexibility, the currently proposed DNA motors (particularly DNA walkers) based biosensing concepts have provided a forceful fluorescence imaging tool for intracellular detection. Even so, this promising sensing means is not only subject to poor controllability and prone to produce false signals but also requires exogenous powering forces owing to the common employment of DNAzyme. In response to these challenges, we are herein motivated to present some meaningful solving strategies. For one thing, the surfaces of gold nanoparticles are conducted with a photo-gated walking behavior by introducing a photocleave mode, under which the light-switchable DNA walkers are capable of being selectively activated via an external ultraviolet source to faultlessly prevent the sensing frame from being pre-initiated during cellular uptake and intracellular delivery. For another, the intracellular biothiols are consumed by MnO₂ nanosheets to effectively avoid the competitions to Au-S bonds to eliminate potential false outputs and also self-supply sufficient cofactors (Mn²⁺) to actualize a self-powered operation pattern as well as facilitate the endocytosis process. Following these breakthroughs, a favorable analysis performance towards a model tumor biomarker (survivin mRNA) is endowed with the newly raised biosensor, whose sensitivity is low to pM level with a sound specificity for identifying single base mismatching. Moreover, the significantly improved autonomous three-dimensional DNA walkers can be used to determine and dynamically trace the targets in live cancer cells with an exceptional precise and efficient manner, commendably impelling the sensing ability of DNA motors in biological specimens.

Periodically programmed building and collapse of DNA networks enables an ultrahigh signal amplification effect for ultrasensitive nucleic acids analysis

ANALYSIS

of molecular species is needed for applications in diagnosis of infections and genetic diseases. Herein, we demonstrate a target DNA-responsive ultrahigh fluorescence signal-on DNA amplification system via periodically programmed building and collapse of DNA networks. In this system, a pair of oligonucleotides of padlock probe (PP) and palindromic hairpin probe (PHP) are utilized. The presence of target DNA firstly hybridizes with PP, allowing the occurrence of rolling circle amplification (RCA) to produce RCA products with tandem repeats in abundance to bind and unfold numbers of PHPs. The conformational change of PHPs enables the building of DNA networks via the intermolecular palindrome pairing, but then makes the DNA networks collapsed via the palindrome-induced strand displacement polymerization. The displaced RCA products are dynamically reused to undergo periodically programmed multiple rounds of DNA network building and collapse. Depend on the bidirectional DNA assembly and disassembly, a strikingly amplified fluorescence can be collected to ultrasensitive and specific detection of target DNA. The practicability has been demonstrated by evaluating target-spiked human serum, saliva, and urine samples with acceptable recoveries and reproducibility. Therefore, this newly explored method opens a promising avenue for the detection of nucleic acids with low abundance in biochemical analysis and diseases diagnosis.

A simple, one-pot and ultrasensitive DNA sensor via Exo III-Assisted target recycling and 3D DNA walker cascade amplification

Rapid, sensitive, and user-friendly nucleic acid detection is of growing importance in early clinical diagnosis. Here, we construct a simple, one-pot and ultrasensitive DNA sensor via exonuclease III (Exo III)-assisted target recycling amplification (ERA) combined with 3D DNA walker cascade amplification. In the presence of single-stranded DNA target, the ERA process is activated to generate numerous walker strands (WS). Thereafter, Exo III-powered WSs autonomously move along magnetic bead (MB)-based 3D track to release numerous AgNCs into the supernatant as an amplified signal output. This biosensor had a low detection limit of 18 fM and an analytical range of 40 fM to 1 pM. Furthermore, the practical application potential of this biosensor was also confirmed by the spiking experiments of p53 into human serum and urine samples.

Dual catalytic DNA circuit-induced gold nanoparticle aggregation: An enzyme-free and colorimetric strategy for amplified detection of nucleic acids

An enzyme-free dual catalytic DNA circuit for amplified detection of nucleic acids has been developed. The system functions based on a cyclic self-assembly of two auxiliary hairpins (H1 and H2) and three biotinylated hairpin oligonucleotides (H3, H4 and H5), in the format of two molecular circuits. In the upstream circuit, a target initiator (I) besides H1 and H2 hairpins constructs H1-H2 duplexes that trigger the operation of a subsequent circuit. In the downstream circuit, the H1-H2 duplex initiates cascaded self-assembly reactions, produces triplex H3-H4-H5, as sensing system, and releases the H1-H2 duplex as the catalyst for the self-assembly of additional hairpins. The H3-H4-H5 triplex acts as the scaffolds for assembling and orienting the streptavidin-functionalized gold nanoparticles (SA-AuNPs) into a lattice-like arrangement that generates a DNA-SA-AuNP cross-linked network, resulting in a dramatic pale red-to-blue color change. By ingeniously engaging two catalytic circuits with feedback amplification capabilities, the system can detect the target nucleic acid with an LOD value of 5 femtomolar and unambiguously discriminate spurious targets (i.e. targets containing substitution, insertion, and deletion nucleotides) without instrumentation. Simple and convenient operation of the assay makes the DNA circuit appropriate for point-of-care monitoring in resource-constrained settings.

A functionalized dumbbell probe-based cascading exponential amplification DNA machine enables amplified probing of microRNAs

A functionalized dumbbell probe (FDP) based amplification method, termed as a cascading exponential amplification DNA machine (CEA-DNA machine), has been developed to autonomously accumulate single G-quadruplexes (SGQs) and twin-G-quadruplexes (TGQs) for robust fluorescence signal-on probing of miRNA-21.

An all-in-one homogeneous DNA walking nanomachine and its application for intracellular analysis of miRNA

DNA walker is a powerful type of DNA nanomachine that can produce amplified signals during the "burnt-bridge"-like walking process. Despite their successful application in extracellular bioanalysis, the heterogeneity of the existing DNA walkers makes it difficult to guarantee the consistency of the results during the analysis of different cells.

Methods: Here, an all-in-one homogeneous DNA walking nanomachine is reported that can be delivered into living cells for intracellular bioanalysis of miRNA without auxiliary materials.

Results: This DNA walking nanomachine is constructed of gold nanoparticles on which two types of interrelated DNA tracks are assembled. The target miRNA, cancer-related miR-21, can be captured by one of the tracks (track 1) and then walk to the other track (track 2), releasing the hybrid of track 1 and track 2 from the nanoparticle to produce a signal. The walking process can proceed in a cyclic 1-2-1-2 manner and thereby produce amplified signals. Thus, sensitive imaging of the miRNA in situ can be achieved.

Conclusion: Benefiting from the homogeneity of the detection system, the method can be applied for intracellular analysis without interference induced by the fluctuations of stimuli or accessorial contents.

A Polyamidoamine Dendrimer-Based Electrochemical Immunosensor for Label-Free Determination of Epithelial Cell Adhesion Molecule- Expressing Cancer Cells

A new electrochemical immunosensor for cancer cell detection based on a specific interaction between the metastasis-related antigen of epithelial cell adhesion molecule (EpCAM) on the cell membrane and its monoclonal antibody (Anti-EpCAM) immobilized on a gold electrode has been developed. The amino-terminated polyamidoamine dendrimer (G6 PAMAM) was first covalently attached to the 3-mercaptopropionic acid (MPA)-functionalized gold electrode to obtain a thin film, and then completely carboxylated by succinic anhydride (SA). Next, the Anti-EpCAM was covalently bound with the G6 PAMAM to obtain a stable recognition layer. In the presence of the EpCAM expressing hepatocellular carcinomas cell line of HepG2, the specific immune recognition (Anti-EpCAM/EpCAM) led to an obvious change of the electron transfer ability. The properties of the layer-by-layer assembly process was examined by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The final determination of HepG2 cells was performed in the presence of the reversible [Fe(CN)₆]^3−/4− redox couple using impedance technique. Based on the advantages of PAMAM nanomaterial and immune reaction, a linear response to HepG2 cells ranging from 1 × 10⁴ to 1 × 10⁶ cells mL⁻¹ with a calculated detection limit of 2.1 × 10³ cells mL⁻¹ was obtained. We expect this method can provide a potential tool for cancer cell monitoring and protein expression analysis.

A DNA minimachine for selective and sensitive detection of DNA

Synthetic molecular machines have been explored to manipulate matter at the molecular level.

Smart engineering of a dual-DNA machine with a high signal-to-noise ratio for one-pot robust and sensitive miRNA signaling

A target triggered dual-DNA machine composed of RCA and SDA was developed for robust and one-pot determination of miRNA.

Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging

Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.

Comparisons between Graphene Oxide and Graphdiyne Oxide in Physicochemistry Biology and Cytotoxicity

Graphdiyne (GDY) and graphene are regarded as two promising two-dimensional carbon-based materials, which have unique planar structure and novel electronic properties. Differences between the two carbon allotropes in their physicochemistry biology and cytotoxicity have never been explored. Here, we chemically functionalized the surface of the two carbon allotropes using similar oxidation processes and compared their physicochemistry, biology, and mutagenesis. Graphene oxide (GO) and GDY oxide (GDYO) showed similarities in their size, morphology, and physical spectral characteristics, excepting the differences in sp- and sp²-hybridizations and Fourier transform infrared spectroscopy. GDYO was well soluble in various media. In contrast, GO was only soluble in H₂O, but kinetically aggregated in 0.9% NaCl, phosphate buffered saline, and cell media within 24 h incubation when its concentrations increased. GO nanoparticles adhered and aggregated to the surface of a human hepatocyte membrane, resulting in cell membrane ruffle, methuosis, and apoptosis. Adhesion of GO to cells caused cell stress and induced reactive oxygen species. In contrast, GDYO did not adhere to the cell membrane to produce the related consequences. Both GDYO and GO showed in vivo mutagenesis potential but no erythrocyte-killing effect, and both were antioxidant and bioequivalent at binding to single-stranded DNA and doxorubicin, thus causing fluorescence quenching. The present study significantly enriches our existing knowledge of GO/alkene and GDYO/alkyne chemistry.

Immunomagnetic antibody plus aptamer pseudo-DNA nanocatenane followed by rolling circle amplication for highly-sensitive CTC detection

Biosensing and detecting the rare circulating tumor cells (CTCs) in complex blood samples are a great challenge but necessary for cancer metastasis prevention. Here we show a novel highly-sensitive biosensing system for detecting CTCs in whole blood. The system is composed of Her2-coated immunomagnetic beads and an anti-EpCAM aptamer assembled pseudo-DNA nanocatenane (PDN) for dual targeting and separating CTCs, in conjunction with the rolling circle amplification (RCA) and molecular beacon (MB) system for CTCs signal amplification. The Her-2-coated beads separated CTCs from blood after their elution from a magnetic column. The unique PDN, which is a tailor-designed self-assembly of three circular DNAs that are inter-locked with independent and non-interfered templates for periodic RCA process, binds EpCAM-rich CTCs. In the presence of the RCA primer, phi29 DNA polymerase and MB, the system collaboratively generated the amplified fluorescent signals for highly-sensitive detection of CTCs. Through this system, we achieved the limit of detection less than 10 CTCs/mL blood, and quantified the number of CTCs in patient blood, which is proportional to the patient cancer status. Our technique is highly-sensitive, practicable and convenient enough for clinical detection of breast CTCs.

Stepwise nanoassembly of a single hairpin probe and its biosensing

Herein, we describe a novel trigger-induced DNA nanoassembly method using only one loop-stem shaped hairpin probe (HP) that consists of three different functional regions as a single building unit. The Region I is designed complementary to the trigger, while the Region II and Region III are projected to complementary with each other. When hybridized with the trigger, a toehold mediated strand displacement (TMSD) occurred on the strand of Region I, leading to the release of Region III for further hybridization with the Region II on another HP molecule and in turn inducing a stepwise growth of HP with the aid of polymerase. Unlike the conventional assembly approaches that rely on the sophisticated sequence design and complex operation, the single-HP nanoassembly is easy and fast. Moreover, because many HPs are opened during the assembly process, we exemplified the nanoassembly strategy by re-designing a new labeled hairpin probe to analyze the Kras oncogene with a high sensitivity and specificity. The present study demonstrated a novel promising DNA nanoassembly strategy for biological applications.

Artificial molecular and nanostructures for advanced nanomachinery

Artificial nanomachines can be broadly defined as manmade molecular and nanosystems that are capable of performing useful tasks, very often, by means of doing mechanical work at the nanoscale. Recent advances in nanoscience allow these tiny machines to be designed and made with unprecedented sophistication and complexity, showing promise in novel applications, including molecular assemblers, self-propelling nanocarriers and in vivo molecular computation. This Feature Article overviews and compares major types of nanoscale machines, including molecular machines, self-assembled nanomachines and hybrid inorganic nanomachines, to reveal common structural features and operating principles across different length scales and material systems. We will focus on systems with feature size between 1 and 100 nm, where classical laws of physics meet those of quantum mechanics, giving rise to a spectrum of exotic physiochemical properties. Concepts of nanomachines will be illustrated by selected seminal work along with state-of-the-art progress, including our own contribution, across the fields. The Article will conclude with a brief outlook of this exciting research area.

Long-stem shaped multifunctional molecular beacon for highly sensitive nucleic acids determination via intramolecular and intermolecular interactions based strand displacement amplification

LS-MMB based intra-SDA and inter-SDA for amplified gene signaling.