Nanoreactors based on DNAzyme-functionalized magnetic nanoparticles activated by magnetic field

Systematic mapping of DNAzymes research from 1995 to 2019

DNAzymes (catalytic DNA) have gained significant diagnostic and therapeutic applications with increasing research output over the years. Functional oligonucleotides are used as molecular recognition elements within biosensors for detection of analytes and viral infections such as SARS-CoV-2. DNAzymes are also applied for silencing and regulating cancer specific genes. However, there has not been any report on systematic analysis to track research status, reveal hotspots, and map knowledge in this field. Therefore, in the present study, research articles on DNAzymes from 1995 to 2019 were extracted from Web of Science (SCI-Expanded) after which, 1037 articles were imported into Rstudio (version 3.6.2) and analysed accordingly. The highest number of articles was published in 2019 (n = 138), while the least was in 1995 (n = 1). The articles were published across 216 journals by 2344 authors with 2337 multi-author and 7 single authors. The most prolific authors were Li Y (n = 47), Liu J (n = 46), Wang L (n = 33), Willner I (n = 33) and Zhang L (n = 33). The top three most productive countries were China (n = 2018), USA (n = 447) and Canada (n = 251). The most productive institutions were Hunan University, China (n = 141), University of Illinois, USA (n = 139) and Fuzhou University, China (n = 101). Despite the increasing interest in this field, international collaborations between institutions were very low which requires immediate attention to mitigate challenges such as limited funding, access to facilities, and existing knowledge gap.

Inorganic nanoparticles coupled to nucleic acid enzymes as analytical signal amplification tools

Nucleic acid enzymes (NAzymes) are a class of nucleic acid molecules with catalytic activity, which can be modulated by the presence of different species such as metal ions, genetic biomarkers, small molecules or proteins, among others. NAzymes offer several important advantages for development of novel bioanalytical strategies, resulting from their functionality as specific recognition elements and as amplified analytical signal generators, making them ideal candidates for developing highly specific bioanalytical strategies for the detection of a wide variety of targets. When coupled with the exceptional features of inorganic nanoparticles (NPs), the sensitivity of the assays can be significantly improved, allowing the detection of targets using many different detection techniques including visual readout, spectrophotometry, fluorimetry, electrochemiluminescence, voltammetry, and single-particle inductively coupled plasma-mass spectrometry. Here we provide an overview of the fundamentals of novel strategies developed to achieve analytical signal amplification based on the use of NAzymes coupled with inorganic NPs. Some representative examples of such strategies for the highly sensitive detection of different targets will be presented, including metal ions, proteins, DNA- or RNA-based biomarkers, and small molecules or microorganisms. Furthermore, future prospective challenges will be discussed.

Recent progress in magnetic applications for micro- and nanorobots

In recent years, magnetic micro- and nanorobots have been developed and extensively used in many fields. Actuated by magnetic fields, micro- and nanorobots can achieve controllable motion, targeted transportation of cargo, and energy transmission. The proper use of magnetic fields is essential for the further research and development of micro- and nanorobotics. In this article, recent progress in magnetic applications in the field of micro- and nanorobots is reviewed. First, the achievements of manufacturing micro- and nanorobots by incorporating different magnetic nanoparticles, such as diamagnetic, paramagnetic, and ferromagnetic materials, are discussed in detail, highlighting the importance of a rational use of magnetic materials. Then the innovative breakthroughs of using different magnetoelectric devices and magnetic drive structures to improve the micro- and nanorobots are reviewed. Finally, based on the biofriendliness and the precise and stable performance of magnetic micro- and nanorobots in microbial environments, some future challenges are outlined, and the prospects of magnetic applications for micro- and nanorobots are presented.

Harnessing the physicochemical properties of DNA as a multifunctional biomaterial for biomedical and other applications

The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions of DNA. Here, the primary product of interest has been crosslinked, hydrated polymers, or hydrogels. State-of-the-art applications of macroscopic, DNA-based hydrogels in the fields of environment, electrochemistry, biologics delivery, and regenerative therapy have been extensively reviewed. Additionally, the review encompasses the status of DNA as a clinically and commercially viable material and provides insight into future possibilities.

Spatially Constrained DNA Nanomachines To Accelerate Kinetics in Response to External Input: Design and Bioanalysis

Cells take advantage of the spatial organization to accelerate the reaction kinetics of diverse components within a crowded intracellular environment. Inspired by this, we hereby designed a principle of spatial constraint to overcome limitations of response kinetics in DNAzyme-powered DNA nanomachines. First, we proposed the type-1 of spatially constrained DNA nanomachines (scDN-1) by co-localizing the aptamer probe and power unit (DNAzyme), allowing the DNA nanomachines to accomplish faster cyclic cleavage of DNAzyme as intramolecular reactions. To expand the scDN into the clinical practice, Type 2 spatially constrained DNA nanomachines (scDN-2) with constrained antibody probes were then constructed through Holliday junction assembly, which increased the effective local concentration to obtain the improved kinetics. With an accelerated response kinetics, this design principle allows DNA nanomachines to accomplish the response to tumor markers in real patients' samples within 30 min, significantly broadening the bioanalytical applications of DNA nanomachines to clinical practice.

Magnetic Nanoparticles for Nanomedicine

The field of nanomedicine has recently emerged as a product of the expansion of a range of nanotechnologies into biomedical science, pharmacology and clinical practice. Due to the unique properties of nanoparticles and the related nanostructures, their applications to medical diagnostics, imaging, controlled drug and gene delivery, monitoring of therapeutic outcomes, and aiding in medical interventions, provide a new perspective for challenging problems in such demanding issues as those involved in the treatment of cancer or debilitating neurological diseases. In this review, we evaluate the role and contributions that the applications of magnetic nanoparticles (MNPs) have made to various aspects of nanomedicine, including the newest magnetic particle imaging (MPI) technology allowing for outstanding spatial and temporal resolution that enables targeted contrast enhancement and real-time assistance during medical interventions. We also evaluate the applications of MNPs to the development of targeted drug delivery systems with magnetic field guidance/focusing and controlled drug release that mitigate chemotherapeutic drugs’ side effects and damage to healthy cells. These systems enable tackling of multiple drug resistance which develops in cancer cells during chemotherapeutic treatment. Furthermore, the progress in development of ROS- and heat-generating magnetic nanocarriers and magneto-mechanical cancer cell destruction, induced by an external magnetic field, is also discussed. The crucial roles of MNPs in the development of biosensors and microfluidic paper array devices (µPADs) for the detection of cancer biomarkers and circulating tumor cells (CTCs) are also assessed. Future challenges concerning the role and contributions of MNPs to the progress in nanomedicine have been outlined.

Photocaged FRET nanoflares for intracellular microRNA imaging

Herein, we developed photocaged FRET nanoflares for spatiotemporal microRNA imaging in living cells. In other words, the probes will not work until they are exposed to UV light.

RNA imaging by chemical probes

Sequence-specific detection of intracellular RNA is one of the most important approaches to understand life phenomena. However, it is difficult to detect RNA in living cells because of its variety and scarcity. In the last three decades, several chemical probes have been developed for RNA detection in living cells. These probes are composed of DNA or artificial nucleic acid and hybridize with the target RNA in a sequence-specific manner. This hybridization triggers a change of fluorescence or a chemical reaction. In this review, we classify the probes according to the associated fluorogenic mechanism, that is, interaction between fluorophore and quencher, environmental change of fluorophore, and template reaction with/without ligation. In addition, we introduce examples of RNA imaging in living cells.

Towards Nanomaterials for Cancer Theranostics: A System of DNA-Modified Magnetic Nanoparticles for Detection and Suppression of RNA Marker in Cancer Cells

Theranostics of cancer using smart biocompatible materials can enable early cancer diagnostics and treatment. Here, we report on a DNA-nanoparticle functional material, which can simultaneously report the presence of an mRNA cancer biomarker and trigger its degradation in cultured cells. The nanodevice consists of two species of magnetic beads, each of which is conjugated with different components of a multicomponent deoxyribozyme (DZ) sensor. The system is activated only under two conditions: (i) in the presence of a specific target mRNA and (ii) when a magnetic field is applied. We demonstrate that delivery of such a system is markedly enhanced by the application of a magnetic field. The system not only fluorescently detects target mRNA in cultured MCF-7 cancer cells, but also induces its downregulation. Thus, the two-component magnetic nanoparticle system has characteristics of a material that can be used for cancer theranostics.

Molecular Engineering of Functional Nucleic Acid Nanomaterials toward In Vivo Applications

Recent advances in nanotechnology and engineering have generated many nanomaterials with unique physical and chemical properties. Over the past decade, numerous nanomaterials are introduced into many research areas, such as sensors for environmental monitoring, food safety, point-of-care diagnostics, and as transducers for solar energy transfer. Meanwhile, functional nucleic acids (FNAs), including nucleic acid enzymes, aptamers, and aptazymes, have attracted major attention from the biomedical community due to their unique target recognition and catalytic properties. Benefiting from the recent progress of molecular engineering strategies, the physicochemical properties of nanomaterials are endowed by the target recognition and catalytic activity of FNAs in the presence of a target analyte, resulting in numerous smart nanoprobes for diverse applications including intracellular imaging, drug delivery, in vivo imaging, and tumor therapy. This progress report focuses on the recent advances in designing and engineering FNA-based nanomaterials, highlighting the functional outcomes toward in vivo applications. The challenges and opportunities for the future translation of FNA-based nanomaterials into clinical applications are also discussed.

RNA-Cleaving DNAzymes: Old Catalysts with New Tricks for Intracellular and In Vivo Applications

DNAzymes are catalytically active DNA molecules that are normally isolated through in vitro selection methods, among which RNA-cleaving DNAzymes that catalyze the cleavage of a single RNA linkage embedded within a DNA strand are the most studied group of this DNA enzyme family. Recent advances in DNA nanotechnology and engineering have generated many RNA-cleaving DNAzymes with unique recognition and catalytic properties. Over the past decade, numerous RNA-cleaving, DNAzymes-based functional probes have been introduced into many research areas, such as in vitro diagnostics, intracellular imaging, and in vivo therapeutics. This review focus on the fundamental insight into RNA-Cleaving DNAzymes and technical tricks for their intracellular and in vivo applications, highlighting the recent progress in the clinical trial of RNA-Cleaving DNAzymes with selected examples. The challenges and opportunities for the future translation of RNA-cleaving DNAzymes for biomedicine are also discussed.

Enzymatic Nanocomposites with Radio Frequency Field-Modulated Activity

The control over enzymatic activity by physical stimuli is of interest to many applications in medicine, biotechnology, synthetic biology, and nanobionics. Although the main focus has been on optically responsive systems, alternative strategies to modulate the enzymatic activity of hybrid systems are needed. Here we describe a radiofrequency (RF) field controlled catalytic activity of an enzymatic sol-gel composite. Specifically, the activity of bovine carbonic anhydrase entrapped in sol-gel-derived magnetite (enzyme@ferria) composite was accelerated by a factor of 460% compared to its initial value, by applying the RF field of 937 A/m, with fast response time. This acceleration is reversible and its magnitude controllable. An acceleration mechanism, based on RF-induced heating of the magnetite by the Néel relaxation effect, is proposed and proven. The entrapment within a sol-gel matrix solves the problem of enhancing activity by heating without denaturing the enzyme. RF-controlled enzymatic composites can be potentially applied as biological RF sensors or to control biochemical reactions within living organisms.

MicroRNA Detection through DNAzyme-Mediated Disintegration of Magnetic Nanoparticle Assemblies

DNA-assembled nanoparticle superstructures offer numerous bioresponsive properties that can be utilized for point-of-care diagnostics. Functional DNA sequences such as deoxyribozymes (DNAzymes) provide novel bioresponsive strategies and further extend the application of DNA-assembled nanoparticle superstructures. In this work, we describe a microRNA detection biosensor that combines magnetic nanoparticle (MNP) assemblies with DNAzyme-assisted target recycling. The DNA scaffolds of the MNP assemblies contain substrate sequences for DNAzyme and can form cleavage catalytic structures in the presence of target DNA or RNA sequences, leading to rupture of the scaffolds and disintegration of the MNP assemblies. The target sequences are preserved during the cleavage reaction and release into the suspension to trigger the digestion of multiple DNA scaffolds. The high local concentration of substrate sequences in the MNP assemblies reduces the diffusion time for target recycling. The concentration of released MNPs, which is proportional to the concentration of the target, can be quantified by a 405 nm laser-based optomagnetic sensor. For the detection of let-7b in 10% serum, after 1 h of isothermal reaction at 50 °C, we found a linear detection range between 10 pM and 100 nM with a limit of detection of 6 pM. For the quantification of DNA target in buffer solution, a limit of detection of 1.5 pM was achieved. Compared to protein enzyme-based microRNA detection methods, the proposed DNAzyme-based biosensor has an increased stability, a reduced cost and a possibility to be used in living cells, all of which are valuable features for biosensing applications.

Composition-Tunable Hollow Au/Ag SERS Nanoprobes Coupled with Target-Catalyzed Hairpin Assembly for Triple-Amplification Detection of miRNA

Detecting disease-related biomarkers is of great significance for disease diagnosis and therapy. In this work, we develop an ultrasensitive surface-enhanced Raman scattering (SERS) biosensor for the detection of an acute myocardial infarction-related miRNA (miR-133a) using composition-adjustable hollow Ag/Au nanosphere-based SERS probes coupled with the target-catalyzed hairpin assembly (CHA) strategy. Bimetallic probes displaying high stability and a strong surface plasmon resonance effect were synthesized with a controllable ratio of silver and gold by a galvanic replacement method and then captured by a duplex linker produced in the CHA process to accomplish signal amplification. In this way, the target miR-133a can be detected in a wide linear range with a detection limit of 0.306 fM and high selectivity over other miRNAs expressed in human hearts. Practical applications in human blood samples reveal the strong anti-interference ability and ideal sensitivity of our developed sensing platform in physiological environments, benefiting its potential biomedical applications.

FaptaSyme: A Strategy for Converting a Monomer/Oligomer-Nonselective Aptameric Sensor into an Oligomer-Selective One

Aptameric sensors can bind molecular targets and produce output signals, a phenomenon that is used in bioassays. In some cases, it is important to distinguish between monomeric and oligomeric forms of a target. Here, we propose a strategy to convert a monomer/oligomer-nonselective sensor into an oligomer-selective sensor. We designed an aptazyme that produced a high fluorescent output in the presence of oligomeric α-synuclein (a molecular marker of Parkinson's disease) but not its monomeric form. The strategy is potentially useful in the design of point-of-care tests for the diagnosis of neurodegenerative diseases.