Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers

Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.

In Situ Coupling of Catalytic Centers into Artificial Substrate Mesochannels as Super-Active Metalloenzyme Mimics

Highly evolved substrate channels in natural enzymes facilitate the rapid capture of substrates and direct transfer of intermediates between cascaded catalytic units, thus rationalizing their efficient catalysis. In this study, a nanoscale ordered mesoporous Ce-based metal-organic framework (OMUiO-66(Ce)) is designed as an artificial substrate channel, where MnO₂ is coupled to Ce-O clusters as a super-active catalase (CAT). An in situ soft template reduction strategy is developed to deposit well-dispersed and exposed MnO₂ in the mesochannels of OMUiO-66(Ce). Several synthesis parameters are optimized to minimize the particle size to ≈150 nm for efficient intracellular endocytosis. The mesochannels provide interaction guidance that not only rapidly drove H₂ O₂ substrates to CAT-like catalytic centers, but also seamlessly transfer H₂ O₂ intermediates between superoxide dismutase-like and CAT-like biocatalytic cascades. As a result, the biomimetic system exhibits high efficiency, low dosage, and long-lasting intracellular antioxidant function. Under disease-related oxidative stress, the artificial substrate channels promote the rate of the reactions catalyzed by MnO₂ , which exceeds that of the reactions catalyzed by natural CAT. Based on this observation, a set of design rules for substrate channels are proposed to guide the rational design of super-active biomimetic systems.

In-Situ Encapsulation of Protein into Nanoscale Hydrogen-Bonded Organic Frameworks for Intracellular Biocatalysis

Hydrogen-bonded organic frameworks (HOFs) are porous materials with great potential for biological applications. The self-assembly of HOFs and biomacromolecules, however, is challenging. We report herein the self-assembly of nanoscale HOFs (nHOFs) to encapsulate protein for intracellular biocatalysis. The self-assembly of tetrakis(4-amidiniumphenyl)methane and azobenzenedicarboxylate can encapsulate protein in situ to form protein@nHOFs under mild conditions. This strategy is applicable to proteins with different surface charge and molecular weight, showing a high protein encapsulation efficiency and minimal effect on protein activity. A cellular delivery study shows that the protein@TA-HOFs can efficiently enter cells and retain enzyme activity for biochemical catalysis in living cells for neuroprotection. Our strategy paves new avenues for interfacing nHOFs with biological settings and sheds light on expanding nHOFs as a platform for biomacromolecule delivery and disease treatment.

Glycoengineering artificial receptors for microglia to phagocytose Aβ aggregates

Oligomeric and fibrillar amyloid-β (Aβ) are principally internalized via receptor-mediated endocytosis (RME) by microglia, the main scavenger of Aβ in the brain. Nevertheless, the inflammatory cascade will be evoked after vast Aβ aggregate binding to pattern recognition receptors on the cell membrane, which then significantly decreases the expression of these receptors and further deteriorate Aβ deposition. This vicious circle will weaken the ability of microglia for Aβ elimination. Herein, a combination of metabolic glycoengineering and self-triggered click chemistry is utilized to engineer microglial membranes with ThS as artificial Aβ receptors to promote microglia to phagocytose Aβ aggregates. Additionally, to circumvent the undesirable immune response during the process of the bioorthogonal chemistry reaction and Aβ-microglial interaction, Mn-porphyrin metal-organic frameworks (Mn-MOFs) with superoxide dismutase (SOD) and catalase (CAT) mimic activity are employed to carry N-azidoacetylmannosamine (AcManNAz) and eradicate over-expressed reactive oxygen species (ROSs). The artificial Aβ receptors independent of a signal pathway involved in immunomodulation as well as Mn-MOFs with antioxidant properties can synergistically promote the phagocytosis and clearance of Aβ with significantly enhanced activity and negligible adverse effects. The present study will not only provide valuable insight into the rational design of the microglial surface engineering strategy via bioorthogonal chemistry, but also hold great potential for other disease intervention associated with receptor starvation.

Artificial Cells Based on DNA Nanotechnology

Artificial cells have led to many potential applications in synthetic biology and served as useful platforms to study biological phenomena. With increasing development of DNA nanotechnology, DNA-based nanostructures with various morphologies have been constructed for protein mimicking. These biomimicking elements can be assembled on cell membrane involved in various cellular activities, as well as be constructed as signaling networks inside cells. DNA nanotechnology provides an efficient approach to accomplish multiple functions, including signal recognition, transduction, and output. Here, we review a myriad of predominant studies on the construction of artificial cells based on DNA nanotechnology, including the morphological and functional mimic of membrane proteins, biosensors for monitoring the cellular microenvironment, and construction of DNA-based signal feedback networks. We also provide a comprehensive insight into DNA-based artificial cells, on the basis of current challenges and scientific requirements, which will prompt their reasonable designs in the future.

Aptamer-Functionalized DNA Nanostructures for Biological Applications

DNA nanostructures hold great promise for various applications due to their remarkable properties, including programmable assembly, nanometric positional precision, and dynamic structural control. The past few decades have seen the development of various kinds of DNA nanostructures that can be employed as useful tools in fields such as chemistry, materials, biology, and medicine. Aptamers are short single-stranded nucleic acids that bind to specific targets with excellent selectivity and high affinity and play critical roles in molecular recognition. Recently, many attempts have been made to integrate aptamers with DNA nanostructures for a range of biological applications. This review starts with an introduction to the features of aptamer-functionalized DNA nanostructures. The discussion then focuses on recent progress (particularly during the last five years) in the applications of these nanostructures in areas such as biosensing, bioimaging, cancer therapy, and biophysics. Finally, challenges involved in the practical application of aptamer-functionalized DNA nanostructures are discussed, and perspectives on future directions for research into and applications of aptamer-functionalized DNA nanostructures are provided.

Dual-Signal Readout of DNA Methylation Status Based on the Assembly of a Supersandwich Electrochemical Biosensor without Enzymatic Reaction

A highly sensitive and selective biosensing system was designed to analyze DNA methylation using a dual-signal readout technique in combination with the signal amplification of supersandwich DNA structure. Through the ingenious design of target-triggered cascade of hybridization chain reaction, one target DNA could initiate the formation of supersandwich structure with multiple signal probes. As a result, one-to-multiple amplification effect was achieved, which conferred high sensitivity to target molecular recognition. Based on probe 1 labeled with ferrocene and probe 2 modified with methylene blue, the target DNA was clearly recognized by two electrochemical signals at independent potentials, which was helpful for the acquisition of more accurate detection results. Taking advantage of bisulfite conversion, the methylation status of cytosine (C) was changed to nucleic acid sequence status, which facilitated the hybridization-based detection without enzymatic reaction. Consequently, the methylated DNA was detected at the femtomolar level with satisfactory analytical parameters. The proposed system was effectively used to assess methylated DNA in human blood serum samples, illuminating the possibility of the sensing platform for applications in disease diagnosis and biochemistry research.