A facile DNA/RNA nanoflower for sensitive imaging of telomerase RNA in living cells based on "zipper lock-and-key" strategy

Aptamer-controlled stimuli-responsive drug release

Aptamers have been widely researched and applied in nanomedicine due to their programmable, activatable, and switchable properties. However, there are few reviews on aptamer-controlled stimuli-responsive drug delivery. This article highlights the mechanisms and advantages of aptamers in the construction of stimuli-responsive drug delivery systems. We summarize the assembly/reconfiguration mechanisms of aptamers in controlled release systems. The assembly and drug release strategies of drug delivery systems are illustrated. Specifically, we focus on the binding mechanisms to the target and the factors that induce/inhibit the binding to the stimuli, such as strand, pH, light, and temperature. The applications of aptamer-based stimuli-responsive drug release are elaborated. The challenges are discussed, and the future directions are proposed.

Aptamer-Loop DNA Nanoflower Recognition and Multicolor Fluorescent Carbon Quantum Dots Labeling System for Multitarget Living Cell Imaging

Visualization of multiple targets in living cells is important for understanding complex biological processes, but it still faces difficulties, such as complex operation, difficulty in multiplexing, and expensive equipment. Here, we developed a nanoplatform integrating a nucleic acid aptamer and DNA nanotechnology for living cell imaging. Aptamer-based recognition probes (RPs) were synthesized through rolling circle amplification, which were further self-assembled into DNA nanoflowers encapsulated by an aptamer loop. The signal probes (SPs) were obtained by conjugation of multicolor emission carbon quantum dots with oligonucleotides complementary to RPs. Through base pairing, RPs and SPs were hybridized to generate aptamer sgc8-, AS1411-, and Apt-based imaging systems. They were used for individual/simultaneous imaging of cellular membrane protein PTK7, nucleolin, and adenosine triphosphate (ATP) molecules. Fluorescence imaging and intensity analysis showed that the living cell imaging system can not only specifically recognize and efficiently bind their respective targets but also provide a 5-10-fold signal amplification. Cell-cycle-dependent distribution of nucleolin and concentration-dependent fluorescence intensity of ATP demonstrated the utility of the system for tracking changes in cellular status. Overall, this system shows the potential to be a simple, low-cost, highly selective, and sensitive living cell imaging platform.

Multifunctional rolling circle transcription-based nanomaterials for advanced drug delivery

As the up-and-comer in the development of RNA nanotechnology, RNA nanomaterials based on functionalized rolling circle transcription (RCT) have become promising carriers for drug production and delivery. This is due to RCT technology can self-produce polyvalent tandem nucleic acid prodrugs for intervention in intracellular gene expression and protein production. RNA component strands participating in de novo assembly enable RCT-based nanomaterials to exhibit good mechanical properties, biostability, and biocompatibility as delivery carriers. The biostability makes it to suitable for thermodynamically/kinetically favorable assembly, enzyme resistance and efficient expression in vivo. Controllable RCT system combined with polymers enables customizable and adjustable size, shape, structure, and stoichiometry of RNA building materials, which provide groundwork for the delivery of advanced drugs. Here, we review the assembly strategies and the dynamic regulation of RCT-based nanomaterials, summarize its functional properties referring to the bottom-up design philosophy, and describe its advancements in tumor gene therapy, synergistic chemotherapy, and immunotherapy. Last, we elaborate on the unique and practical value of RCT-based nanomaterials, namely "self-production and self-sale", and their potential challenges in nanotechnology, material science and biomedicine.

CRISPR/Cas-Based Techniques for Live-Cell Imaging and Bioanalysis

CRISPR/Cas systems have found widespread applications in gene editing due to their high accuracy, high programmability, ease of use, and affordability. Benefiting from the cleavage properties (trans- or cis-) of Cas enzymes, the scope of CRISPR/Cas systems has expanded beyond gene editing and they have been utilized in various fields, particularly in live-cell imaging and bioanalysis. In this review, we summarize some fundamental working mechanisms and concepts of the CRISPR/Cas systems, describe the recent advances and design principles of CRISPR/Cas mediated techniques employed in live-cell imaging and bioanalysis, highlight the main applications in the imaging and biosensing of a wide range of molecular targets, and discuss the challenges and prospects of CRISPR/Cas systems in live-cell imaging and biosensing. By illustrating the imaging and bio-sensing processes, we hope this review will guide the best use of the CRISPR/Cas in imaging and quantifying biological and clinical elements and inspire new ideas for better tool design in live-cell imaging and bioanalysis.

Construction of rolling circle amplification products-based pure nucleic acid nanostructures for biomedical applications

Nucleic acid nanomaterials with good biocompatibility, biodegradability, and programmability have important applications in biomedical field. Nucleic acid nanomaterials are usually combined with some inorganic nanomaterials to improve their biological stability. However, undefined toxic side effects of composite nanocarriers hamper their application in vivo. As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. RCA products with different functional parts can be customized by changing the sequence of the circular template, thereby generating complex multifunctional DNA nanostructures, such as DNA nanowire, nanoflower, origami, nanotube, nanoribbon, etc. More importantly, RCA products as nonnicked building blocks can enhance the biostability of DNA nanostructures, especially in vivo. These RCA products-based nucleic acid nanostructures can be used as scaffolds or nanocarriers to interact or load with metal nanoparticles, proteins, lipids, cationic polymers, therapeutic nucleic acids or drugs, etc. This paper reviews the assembly strategies of RCA based DNA nanostructures with different shape and their applications in biosensing, bioimaging and biomedicine. Finally, the development prospects of the nucleic acid nanomaterials in clinical diagnosis and treatment of diseases are described. STATEMENT OF SIGNIFICANCE: As a nanotool capable of avoiding potential biotoxicity, nanostructures composed entirely of DNA oligonucleotides have been rapidly developed in the field of biomedicine in recent years. Rolling circle amplification (RCA) is an isothermal enzymatic nucleic acid amplification technology for large-scale production of periodic DNA/RNA with pre-designed desirable structures and functions. This paper reviews the construction of various shapes of pure nucleic acid nanomaterials based on RCA products and their applications in biosensing, bioimaging and biomedicine. This will promote the development of biocompatible DNA nanovehicles and their further application in living systems, including bioimaging, molecular detection, disease diagnosis and drug delivery, finally producing a significant impact in the field of nanotechnology and nanomedicine.

Triple signal amplification strategy for ultrasensitive in situ imaging of intracellular telomerase RNA

Abnormal upregulation of telomerase RNA (TR) is a hallmark event at various stages of tumor progression, providing a universal marker for early diagnosis of cancer. Here, we have developed a triple signal amplification strategy for in situ visualization of TR in living cells, which sequentially incorporated the target-initiated strand displacement circuit, multidirectional rolling circle amplification (RCA), and Mg²⁺ DNAzyme-mediated amplification. All oligonucleotide probes and cofactors were transfected into cells in one go, and then escaped from lysosomes successfully. Owing to the specific base pairing, the amplification cascades could only be triggered by TR and performed as programmed, resulting in a satisfactory signal-to-background ratio. Especially, the netlike DNA structure generated by RCA encapsulated high concentrations of DNAzyme and substrates (FQS) in a local region, thereby improving the reaction efficiency and kinetics of the third amplification cycle. Under optimal conditions, the proposed method exhibited ultrasensitive detection of TR mimic with a detection limit at pM level. Most importantly, after transfection with the proposed sensing platform, tumor cells can be easily distinguished from normal cells based on TR abundance-related fluorescence signal, providing a new insight into initial cancer screening.

Novel DNA nanoflower biosensing technologies towards next-generation molecular diagnostics

DNA nanoflowers (DNFs) are topological flower-like nanostructures based on ultralong-strand DNA and inorganic metal-ion frameworks. Because of their programmability, biocompatibility, and controllable assembly size for specific responses to molecular recognition stimuli, DNFs are powerful biosensing tools for detecting biomolecules. Here, we review the current state of DNF-based biosensing strategies for in vivo and in vitro detection, with a view of how the field has evolved towards molecular diagnostics. We also provide a detailed classification of DNF-based biosensing strategies and propose their future utility. Particularly as transduction elements, DNFs can accelerate biosensing engineering by signal amplification. Finally, we discuss the key challenges and further prospects of DNF-based biosensing technologies in developing applications of a broader scope.

Brain-Penetration and Neuron-Targeting DNA Nanoflowers Co-Delivering miR-124 and Rutin for Synergistic Therapy of Alzheimer's Disease

Alzheimer disease (AD) is the leading cause of dementia that affects millions of old people. Despite significant advances in the understanding of AD pathobiology, no disease modifying treatment is available. MicroRNA-124 (miR-124) is the most abundant miRNA in the normal brain with great potency to ameliorate AD-like pathology, while it is deficient in AD brain. Herein, the authors develop a DNA nanoflowers (DFs)-based delivery system to realize exogenous supplementation of miR-124 for AD therapy. The DFs with well-controlled size and morphology are prepared, and a miR-124 chimera is attached via hybridization. The DFs are further modified with RVG29 peptide to simultaneously realize brain-blood barrier (BBB) penetration and neuron targeting. Meanwhile, Rutin, a small molecular ancillary drug, is co-loaded into the DFs structure via its intercalation into the double stranded DNA region. Interestingly, Rutin could synergize miR-124 to suppress the expression of both BACE1 and APP, thus achieving a robust inhibition of amyloid β generation. The nanosystem could pro-long miR-124 circulation in vivo, promote its BBB penetration and neuron targeting, resulting in a significant increase of miR-124 in the hippocampus of APP/PS1 mice and robust therapeutic efficacy in vivo. Such a bio-derived therapeutic system shows promise as a biocompatible nanomedicine for AD therapy.

Flexible photoelectrochemical biosensor for ultrasensitive microRNA detection based on concatenated multiplex signal amplification

Precise microRNA (miRNA) analysis is significant importance for early disease diagnosis. Herein, a novel flexible photoelectrochemical (PEC) biosensor for miRNA determination was developed by employing CdS NPs-modified carbon cloth (CC) on polyimide (PI) film as photoelectric material to provide the PEC responses and an efficient four-stage reaction system as the target recognition and signal amplification unit to improve the analytical performance. In this PEC biosensor, the presence of target miR-21 would trigger the catalytic hairpin assembly (CHA) and the following hybridization chain reaction (HCR) to produce a long dsDNA labeled with numerous biotins, which would further capture a large amount of alkaline phosphatase (ALP) for catalyzing the generation of ascorbic acid (AA). As an efficient electron donor, AA could be oxidized by the photoelectrode, which would initiate a redox cycling amplification process to regenerate AA, resulting in the enhancement of the photocurrent response. Benefitting from the synergistic nucleic acid-based, enzyme catalytic, and chemical signal amplification strategies, the proposed biosensing strategy enabled ultrasensitive miRNA determination. As expected, the PEC biosensor performed satisfactory analytical performances with a linear range of 1 fM to 1 nM and the detection limit down to 0.41 fM. Furthermore, the PEC biosensing strategy exhibited recommendable selectivity, stability, flexibility, and practical applicability. Therefore, this sensing platform provides promising potential for application in bioassay and early diagnosis of disease.

Detecting Pb2+by a 'turn-on' fluorescence sensor based on DNA functionalized magnetic nanocomposites

Sensitive and selective detection of the lead ion (Pb2+) plays an important role in terms of both human health and environmental protection, as the heavy metal is fairly ubiquitous and highly toxic. The highly stable fluorescence biosensor is composed of Fe3O4@TiO2core-shell nanocomposites, functionalized with a carboxyl fluorescein labeled DNA. The morphology, physical and chemical properties of the sensing nanomaterials were studied by transmission electron microscopy, FT-IR spectroscopy (FT-IR), x-ray powder diffraction and vibrating sample magnetometer. UV-visible and fluorescence spectroscopy were used to characterize the fluorescein functionalized magnetic nanoparticles. The performance of Pb2+detection displayed an excellent linearity (R2 = 0.995) in the range of 10-10to 5 × 10-9ppm with a detection limit of 10-10ppm, based on the optimization of the fabrication process and aptamers' specification. The fluorescence biosensor has an accurate response, excellent recoveries and high adsorbent capacities. It was successfully applied for the determination of Pb2+in contaminated water and serum samples; the detection of limit in both media were 10-10ppm. These features ensure the potential use of aptamer functionalized magnetic nanocomposites as a new class of non-toxic biocompatible sensors for biological and environmental applications.

Intracellular enzyme-powered DNA circuit with a tunable amplifier for miRNA imaging

We describe an intracellular enzyme-powered DNA circuit probe with a tunable amplifier for sensitive and selective detection of miRNA. This approach has been successfully applied for in situ miRNA-21 fluorescence imaging in live cells. Also, we used chemicals to elevate the APE1 expression level rendering a tunable amplification strength for more flexible imaging applications.

MNAzyme probes mediated DNA logic platform for microRNAs logic detection and cancer cell identification

Here, a MNAzyme probes mediated DNA logic platform was developed for microRNAs (miRNAs) logic detection and cancer cells identification. A series of MNAzyme probes containing the cleavage active center were designed. Four types of logic gates were constructed, including YES, AND, XOR and NOR gate. These logic gates used miRNAs that were high expression in cancer cells as logic inputs and used MNAzyme cleavage amplification reaction to output signals. For the construction of intracellular logic gates, MnO₂ nanosheets were used as carriers and cofactor providers. When MnO₂ nanoprobes entered the cells through endocytosis, the intracellular glutathione degraded the MnO₂ nanosheets to release the cofactor Mn²⁺ and MNAzyme probes. The MNAzyme probes bound to the miRNAs and catalyze the MNAzyme cleavage amplification reaction, producing enhanced fluorescent signal with "true" output. The logic detection of miRNAs was achieved by integrating information from the AND, XOR and NOR logic gates. Moreover, through the construction of intracellular YES and AND logic gates, the cancer cells identification, especially the identification of same type of cancer cells with different phenotypes was achieved. These experimental results showed that this platform held great promise in accurate diagnosis and treatment of cancer.

A DNA Based Biosensor Amplified With ZIF-8/Ionic Liquid Composite for Determination of Mitoxantrone Anticancer Drug: An Experimental/Docking Investigation

An ultrasensitive DNA electrochemical biosensor based on the carbon paste electrode (CPE) amplified with ZIF-8 and 1-butyl-3-methylimidazolium methanesulfonate (BMIMS) was fabricated in this research. The DNA/BMIMS/ZIF-8/CPE was used for the selective determination of a mitoxantrone anticancer drug in aqueous solution, resulting in a good catalytic effect and a powerful ability for determining mitoxantrone. Also, the interaction of the mitoxantrone anticancer drug with guanine bases of ds-DNA was used as a powerful strategy in the suggested biosensor, which was confirmed with docking investigation. Docking study of mitoxantrone into the ds-DNA sequence showed the intercalative binding mode of mitoxantrone into the nitrogenous-based pairs of ds-DNA. The effective factors such as ds-DNA concentration, temperature, buffer types, and incubation time were also optimized for the fabricated mitoxantrone biosensor. The results showed that, under optimum conditions (T = 25°C; incubation time=12 min; pH= 4.8 acetate buffer solution and [DNA] = 50 mg/L), the DNA/BMIMS/ZIF-8/CPE could be used in mitoxantrone assay in a concentration ranging from 8.0 nM to 110 μM with a detection limit of 3.0 nM. In addition, recovery data between 99.18 and 102.08% were obtained for the determination of mitoxantrone in the injection samples using DNA/ZIF-8/BMIMF/CPE as powerful biosensors.

Autocatalytic DNAzyme assembly for amplified intracellular imaging

The autocatalytic HCR-DNAzyme platform was constructed as a versatile amplification platform for intracellular microRNA imaging by integrating hybridization chain reaction (HCR) circuit with DNAzyme biocatalysis. The HCR-assembled multifunctional DNAzyme nanowires produce new HCR triggers and numerous transducer DNAzyme amplifier, and thus shows great promise in earlier cancer diagnosis.