DNA hybridization chain reaction and DNA supersandwich self-assembly for ultrasensitive detection

CaCO3 nanoparticle-encapsulated CHA circuits for sensitive fluorescence detection of miRNA in living cells

MicroRNAs (miRNAs) serve as important biomarkers for various diseases, including malignant tumors, and have broad applications in diagnosis, treatment, and prognosis. The development of real-time in situ imaging methods for monitoring miRNAs has both scientific and clinical value, and in this regard, catalytic hairpin assemblies (CHAs) can be used as precise and efficient nucleic acid circuits that facilitate hybridization without depleting targets. In this study, we developed a detection system based on CHA circuits encapsulated within CaCO3 nanoparticles, which represents a novel strategy for the detection of human pancreatic cancer. This encapsulation facilitates the pH-sensitive release of DNA probes, thereby ensuring the selective and sensitive detection of cancer-associated miRNAs. Our experimental results confirmed that the fabricated nanoparticles contributed to enhancing the stability and performance of the DNA circuits, thereby enabling precise miRNA detection and effective discrimination between cancerous and non-cancerous cells. Our findings in this study highlight the potential utility of CaCO3 nanoparticle-encapsulated CHA circuits for advancing miRNA-based cancer diagnostics and therapeutics.

Orthogonal DNA self-assembly technology enables rapid and accurate analysis of circulating tumor cells in breast cancer

BACKGROUND

As a non-invasive liquid biopsy technology, the detection of circulating tumor cells (CTCs) overcomes the limitations of traditional tissue biopsy methods, enabling continuous sample collection and long-term dynamic monitoring. However, current CTCs analysis methods typically rely on cell size to separate and identify tumor cells, which fails to effectively distinguish tumor cells from different sources. In addition, existing methods are often constrained by limited antibody species, typically detecting only 2-3 molecular phenotypes. This narrow detection scope does not fully capture the heterogeneity of CTCs at the single-cell level, thus limiting its utility in precision diagnosis and personalized treatment. To address these challenges, it is urgent to develop CTCs detection methods that can simultaneously integrate comprehensive target and cell morphology information.

RESULTS

Using breast cancer as a research model, we developed a computer-aided design-based hybridization chain reaction (CAD-HCR) by combining DNA encoding and antibody coupling technologies with orthogonal DNA self-assembly to achieve multiple detection and heterogeneity analysis of breast cancer mimic samples. This technology overcomes the limitation of antibody species in traditional CTCs detection and utilizes antibody-trigger strand coupling to convert target protein signals into DNA signals, thereby circumventing throughput limitation of existing detection methods. By utilizing the signal amplification effect of DNA self-assembly, this technology enhances sensitivity significantly, allowing for accurate single-cell level detection of CTCs.

SIGNIFICANCE

This technology provides spatial positioning and cell morphological characteristics information for CTCs analysis of breast cancer, which is expected to provide a more accurate basis for diagnosis and treatment decision-making for in-depth understanding of tumor heterogeneity and clinical applications.

Construction of an exogenously and endogenously Co-activated DNA logic amplifier for highly reliable intracellular MicroRNA imaging

DNA-based molecular amplifiers offer significant promise for molecular-level disease diagnosis and treatment, yet tailoring their activation for precise timing and localization remains a challenge. Herein, we've pioneered a dual activation strategy harnessing external light and internal ATP to create a highly controlled DNA logic amplifier (FDLA) for accurate miRNA monitoring in cancer cells. The FDLA was constructed by tethered the two functionalized catalytic hairpin assembly (CHA) hairpin modules (ATP aptamer sealed hairpin aH1 and photocleavable (PC-linker) sites modified hairpin pH2) to DNA tetrahedron (DTN). The FDLA system incorporates ATP aptamers and PC-linkers as logic control units, allowing them to respond to both exogenous UV light and endogenous ATP present within cancer cells. This response triggers the release of CHA hairpin modules, enabling amplified FRET miRNA imaging through an AND-AND gate. The DTN structure could improve the stability of FDLA and accelerate the kinetics of the strand displacement reaction. It is noteworthy that the UV and ATP co-gated DNA circuit can control the DNA bio-computing at specific time and location, offering spatial and temporal capabilities that can be harnessed for miRNA imaging. Furthermore, the miRNA-sensing FDLA amplifier demonstrates reliable imaging of intracellular miRNA with minimal background noise and false-positive signals. This highlights the feasibility of utilizing both exogenous and endogenous regulatory strategies to achieve spatial and temporal control of DNA molecular circuits within living cancer cells. Such advancements hold immense potential for unraveling the correlation between miRNA and associated diseases.

Hybridization Chain Reaction-Based Electrochemical Biosensors by Integrating the Advantages of Homogeneous Reaction and Heterogeneous Detection

The conventional hybridization chain reaction (HCR)-based electrochemical biosensors usually require the immobilization of probes on the electrode surface. This will limit the applications of biosensors due to the shortcomings of complex immobilization processes and low HCR efficiency. In this work, we proposed astrategy for the design of HCR-based electrochemical biosensors by integrating the advantages of homogeneous reaction and heterogeneous detection. Specifically, the targets triggered the autonomous cross-opening and hybridization oftwobiotin-labeled hairpin probes to form long-nicked dsDNA polymers. The HCR products with many biotin tags were then captured by a streptavidin-covered electrode, thus allowing for the attachment of streptavidin-conjugated signal reporters through streptavidin-biotin interactions. By employing DNA and microRNA-21 as the model targets and glucose oxidase as the signal reporter, the analytical performances of the HCR-based electrochemical biosensors were investigated. The detection limits of this method were found to be 0.6 fM and 1 fM for DNA and microRNA-21, respectively. The proposed strategy exhibited good reliability for target analysis in serum and cellular lysates. The strategy can be used to develop various HCR-based biosensors for a wide range of applications because sequence-specific oligonucleotides exhibit high binding affinity to a series of targets. In light of the high stability and commercial availability of streptavidin-modified materials, the strategy can be used for the design of different biosensors by changing the signal reporter and/or the sequence of hairpin probes.

An activatable DNA nanodevice for correlated imaging of apoptosis-related dual proteins

Apoptosis plays an important role in the life cycle of multicellular organisms. The development of techniques for sensitive monitoring of apoptosis-related key molecules can be used to assess not only disease progression but also its therapeutic interventions. However, there is still a lack of an imaging probe amenable for simultaneously detecting multiple biomarkers during drug-induced apoptosis. Herein, a novel activatable DNA nanodevice was designed to image apoptosis-related dual proteins in real time. The turn-on and specific recognition properties of our probe allow the spatially selective detection of apoptotic-related marker cytochrome c and apurinic/apyrimidinic endonuclease 1 in living cells. We demonstrated that the DNA nanodevice has the ability to monitor apoptosis and evaluate the efficacy of apoptosis-related drugs, which potentially can be used as a tool to evaluate the molecular mechanism of apoptosis regulation or to screen apoptotic drugs.

Coupling nucleic acid circuitry with the CRISPR-Cas12a system for universal and signal-on detection

We report a universal and signal-on HCR based detection platform via innovatively coupling the CRISPR-Cas12a system with HCR. By using this CRISPR-HCR pathway, we can detect different targets by only changing the crRNA. The CRISPR-HCR platform coupling with an upstream amplifier can achieve a practical sensitivity as low as ∼aM of ASFV gene in serum.

Aptamer Self-Assembly-Functionalized Nanochannels for Sensitive and Precise Detection of Chloramphenicol

Sensitive and precise determination of chloramphenicol (CAP) is of great significance for human health due to its high risk in trace amounts. Solid-state artificial nanochannels are expected to be highly promising sensing devices owing to single-molecule sensitivity, target-specific selectivity, and portability. Herein, we report an aptamer self-assembly-functionalized artificial nanochannel-based sensor for highly sensitive and precise determination of CAP. Aptamer self-assembly (AAs) served as the specific recognition component and were in situ grown on the surface of stable anodic aluminum oxide (AAO) nanochannels to develop an AAs@AAO nanochannel-based sensor. Selective interaction with CAP led to the disassembly of AAs and sensitive current change of AAs@AAO nanochannels, allowing sensitive and precise sensing of CAP in complex food samples. The developed AAs@AAO nanochannel-based sensor showed a wide linear range from 0.32 to 1600 pg. mL^-1, low limit of detection (LOD) of 0.1 pg. mL^-1, high precision with relative standard deviation of 2.9%, and quantitative recoveries of 93.4-102.2% for CAP in milk, milk powder, and honey samples. This work proposes a versatile nanochannel-based platform for facile, sensitive, and precise sensing of hazardous residues in food samples.

Complex Nucleic Acid Hybridization Reactions inside Capillary-Driven Microfluidic Chips

Nucleic acid hybridization reactions play an important role in many (bio)chemical fields, for example, for the development of portable point-of-care diagnostics, and often such applications require nucleic acid-based reaction systems that ideally run without enzymes under isothermal conditions. The use of novel capillary-driven microfluidic chips to perform two isothermal nucleic acid hybridization reactions, the simple opening of molecular beacon structures and the complex reaction cascade of a clamped-hybridization chain reaction (C-HCR), is reported here. For this purpose, reagents are arranged in a self-coalescence module (SCM) of a passive silicon microfluidic chip using inkjet spotting. The SCM occupies a footprint of ≈7 mm² of a ≈0.4 × 2 cm² microfluidic chip. By means of fluorophore-labeled DNA probes, the hybridization reactions can be analyzed in just ≈2 min and using only ≈3 µL of the sample. Furthermore, the SCM chip offers a variety of reagent delivery options, allowing, for example, the influence of the initiator concentration on the kinetics of C-HCR to be investigated systematically with minimal sample and time requirements. These results suggest that self-powered microfluidic chips equipped with a SCM provide a powerful platform for performing and investigating complex reaction systems.

Employing an Intercalated Redox Reporter in Electrochemical Aptamer-Based Biosensors to Enable Calibration-Free Molecular Measurements in Undiluted Serum

Electrochemical aptamer-based (E-AB) biosensors suffer from sensor-to-sensor signal variations due to the variation of the total number and the heterogeneity of probes immobilized on the electrode surface, with the former attracting more attention. As such, a calibration process to correct for such variations is required for this type of sensor, causing inconvenience and inaccessibility in harsh sensing environments such as blood samples, which has dramatically limited the widespread clinical use of biosensors. In response, here, we have adopted E-AB sensors to achieve calibration-free measurements of small biological/drug molecules. Specifically, we employ one probe-attached redox reporter and a second intercalated redox reporter to generate two signals, achieving good sensor-to-sensor reproducibility and thus obviating the need for calibration. We first demonstrated the capability of E-AB sensors for the accurate measurement of kanamycin, tobramycin, and adenosine triphosphate (ATP) in phosphate-buffered saline (PBS) buffer, achieving concentration ranges of approximately 4.7 × 10³-, 2.0 × 10³-, and 12.7-fold, respectively. Then, we applied this calibration-free approach to the measurement of these three target molecules directly in undiluted serum, achieving a concentration precision of a few micromolars.

Self-Assembly of Ultrathin Nanocrystals to Multidimensional Superstructures

The self-assembly of ultrathin nanocrystals (UTNCs) into well-organized multidimensional superstructures is one of the key topics in material chemistry and physics. Highly ordered nanocrystal assemblies also known as superstructures or synthetic structures have remained a focus for researchers over the past few years due to synergy in their properties as compared to their components. Here, we aim to present the recent progress being made in this field with highlights of our research group endeavors in the engineering of self-assembled complex multidimensional superstructures of various inorganic materials, including polyoxometalates. The driving forces for the assembly process and its kinetics along with the potential applications associated with these unique ordered and spatially complex superstructures are also discussed.

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.