Ultrasensitive Dual-Signal Detection of Telomerase and MiR-21 Based on Boolean Logic Operations

Nuclear-Targeted Material Enabled Intranuclear MicroRNA Imaging for Tracking Gene Editing Process

Gene editing technology based on clustered regularly interspaced short palindromic repeats/associated protein (CRISPR/Cas) systems serves as an efficient tool in cancer therapy. Tracking the gene editing process can help identify the progress of cancer treatment. However, existing techniques for monitoring the gene editing process rely on lysed cells, which can not reflect the dynamic changes of nucleic acid in living cells. It urgently needs in situ and real-time imaging technologies to track the gene editing process at a living single-cell level more effectively and precisely. Here, we reported a highly efficient nuclear-targeted material, phenylboronic acid modified linear PEI (LPBA), for loading gene editing plasmids and fluorescent probes to track gene editing processes of microRNA. Based on LPBA, we achieved efficient intranuclear microRNA imaging at the living cell level, reaching 32.4-fold higher than the linear PEI (LPEI) delivery system, which facilitated further sensitive monitoring of the gene editing process both in living cells and in vivo. Meanwhile, this efficient gene-editing and real-time detection technique could be extended to screening effective gene-editing plasmids. Such LPBA-based imaging technology extended the imaging area of microRNA and offered new insight in the field of gene editing and nucleic acid detection.

Dynamic Nanostructure-Based DNA Logic Gates for Cancer Diagnosis and Therapy

DNA logic gates with dynamic nanostructures have made a profound impact on cancer diagnosis and treatment. Through programming the dynamic structure changes of DNA nanodevices, precise molecular recognition with signal amplification and smart therapeutic strategies have been reported. This enhances the specificity and sensitivity of cancer theranostics, and improves diagnosis precision and treatment outcomes. This review explores the basic components of dynamic DNA nanostructures and corresponding DNA logic gates, as well as their applications for cancer diagnosis and therapies. The dynamic DNA nanostructures would contribute to cancer early detection and personalized treatment.

An approach for state differentiation in nucleic acid circuits: Application to diagnostic DNA computing

BACKGROUND

Differentiating between different states in nucleic acid circuits is crucial for various biological applications. One approach, there is a requirement for complicated sequential summation, which can be excessive for practical purposes. By selectively labeling biologically significant states, this study tackles the issue and presents a more cost-effective and streamlined solution. The challenge is to efficiently distinguish between different states in a nucleic acid circuit.

RESULTS

An innovative method is introduced in this study to distinguish between states in a nucleic acid circuit, emphasizing the biologically relevant ones. The circuit comprises four DNA logic gates and two detection modules, one for determining fetal gender and the other for diagnosing X-linked genetic disorders. The primary module generates a G-quadruplex DNAzyme when activated by specific biomarkers, which leads to a distinct colorimetric signal. The secondary module responds to hemophilia and choroideremia biomarkers, generating one or two DNAzymes. The absence of female fetus indicators results in no DNAzyme or color change. The circuit can differentiate various fetal states by producing one to four active DNAzymes in response to male fetus biomarkers. A single-color solution for state differentiation is provided by this approach, which promises significant advancements in DNA computing and diagnostic applications.

SIGNIFICANCE

The innovative approach used in this study to distinguish states in nucleic acid circuits holds great significance. By selectively labeling biologically relevant states, circuit design is simplified and complexity is reduced. This advancement enables cost-effective and efficient diagnostic applications and contributes to DNA computing, providing a valuable solution to a fundamental problem.

Aptameric Fluorescent Biosensors for Liver Cancer Diagnosis

Liver cancer is a prevalent global health concern with a poor 5-year survival rate upon diagnosis. Current diagnostic techniques using the combination of ultrasound, CT scans, MRI, and biopsy have the limitation of detecting detectable liver cancer when the tumor has already progressed to a certain size, often leading to late-stage diagnoses and grim clinical treatment outcomes. To this end, there has been tremendous interest in developing highly sensitive and selective biosensors to analyze related cancer biomarkers in the early stage diagnosis and prescribe appropriate treatment options. Among the various approaches, aptamers are an ideal recognition element as they can specifically bind to target molecules with high affinity. Furthermore, using aptamers, in conjunction with fluorescent moieties, enables the development of highly sensitive biosensors by taking full advantage of structural and functional flexibility. This review will provide a summary and detailed discussion on recent aptamer-based fluorescence biosensors for liver cancer diagnosis. Specifically, the review focuses on two promising detection strategies: (i) Förster resonance energy transfer (FRET) and (ii) metal-enhanced fluorescence for detecting and characterizing protein and miRNA cancer biomarkers.

Entropy-Driven Three-Dimensional DNA Nanofireworks for Simultaneous Real-Time Imaging of Telomerase and MicroRNA in Living Cells

Real-time monitoring of different types of intracellular tumor-related biomarkers is of key importance for the identification of tumor cells. However, it is hampered by the low abundance of biomarkers, inefficient free diffusion of reactants, and complex cytoplasmic milieu. Herein, we present a stable and general method for in situ imaging of microRNA-21 and telomerase utilizing simple highly integrated dual tetrahedral DNA nanostructures (TDNs) that can naturally enter cells, which could initiate to form the three-dimensional (3D) higher-order DNA superstructures (DNA nanofireworks, DNFs) through a reliable target-triggered entropy-driven strand displacement reaction in living cells for remarkable signal amplification. Importantly, the excellent biostability, biocompatibility, and sensitivity of this approach benefited from (i) the precise multidirectional arrangement of probes with a pure DNA structure and (ii) the local target concentration enhanced by the spatially confined microdomain inside the DNFs. This strategy provides a pivotal molecular toolbox for broad applications such as biomedical imaging and early precise cancer diagnosis.

Self-assembly of DNA-hyperbranched aggregates catalyzed by a dual-targets recognition probe for miRNAs SERS detection in single cells

MicroRNAs (miRNAs) are very important for the early diagnosis and prognosis of tumors. In this work, we achieved the simultaneous detection of microRNA-155 (miR-155) and microRNA-21 (miR-21) with a dual target recognition probe (DRP) based on the nonlinear hybridization chain reaction (HCR). The multi-branched DNA products, three-dimensional multi-hotspot DNA dendrimers (3DmhD) were used in the amplification of the target miRNAs signal. The DRP is constructed with a core of gold nanocages (AuNCs), modified by nucleic acid probes and labeled with Raman signaling molecules ROX and Cy3. Experiments demonstrated that DRP could activate the multi-branched DNA reaction and generate 3DmhD in the presence of miR-155 and miR-21, which can achieve effective amplification of miR-21 and miR-155. When Surface Enhanced Raman Scattering (SERS) analysis was performed on 3DmhD, the multi-hot spot effect of 3DmhD significantly enhanced the signals of ROX and Cy3, allowing ultra-sensitive detection of miR-21 and miR-155 in vitro. To our delight, DRP also exhibited sensitive specificity and significant signal amplification for intracellular miRNAs. These results revealed that DRP has the potential to screen tumor cells by analyzing the expression levels of intracellular miRNAs.

Kinetics-accelerated one-step detection of MicroRNA through spatially localized reactions based on DNA tile self-assembly

The localization of isothermal amplification systems has elicited extensive attention due to the enhanced reaction kinetics when detecting ultra-trace small-molecule nucleic acids. Therefore, the seek for an appropriate localization cargo of spatially confined reactions is urgent. Herein, we have developed a novel approach to localize the catalytic hairpin assembly (CHA) system into the DNA tile self-assembly nanostructure. Thanks to the precise programming and robust probe loading capacity, this strategy achieved a 2.3 × 10⁵-fold higher local reaction concentration than a classical CHA system with enhanced reaction kinetics in theory. From the experimental results, this strategy could reach the reaction plateau faster and get access to a magnified effect of 1.57-6.99 times higher in the linear range of microRNA (miRNA) than the simple CHA system. Meanwhile, this strategy satisfied the demand for the one-step detection of miRNA in cell lysates at room temperature with good sensitivity and specificity. These features indicated its excellent potential for ultra-trace molecule detection in clinical diagnosis and provided new insights into the field of bioassays based on DNA tile self-assembly nanotechnology.

A light-operated dual-mode method for neuroblastoma diagnosis based on a Tb-MOF: from biometabolite detection to logic devices

Tb-DBA can not only serve as a light-operated dual-mechanism driven platform to detect VMA (an early pathological feature of neuroblastoma), but can also produce a different fluorescence response to epinephrine (EP, the metabolic precursor of VMA).

DNA-Based Nanoprobes for Simultaneous Detection of Telomerase and Correlated Biomolecules

Telomerase (TE), a ribonucleoprotein reverse transcriptase, is enzymatically activated in most tumor cells and is responsible for promoting tumor progression and malignancy by enabling replicative immortality of cancer cells. TE has become an important hallmark for cancer diagnosis and a potential therapy target. Therefore, accurate and in site detection of TE activity, especially the simultaneous imaging of TE activity and its correlated biomolecules, is highly essential to medical diagnostics and therapeutics. DNA-based nanoprobes, with their effective cell penetration capability and programmability, are the most advantageous for detection of intracellular TE activity. This concept article introduces the recent strategies for in situ sensing and imaging of TE activity, with a focus on simultaneous detection of TE and related biomolecules, and provides challenges and perspectives for the development of new strategies for such correlated imaging.