Functional Imaging with Nucleic-Acid-Based Sensors: Technology, Application and Future Healthcare Prospects

An Emission-Based Probe for the Detection and Quantification of DNA and RNA

Sequence-independent detection of low concentrations of nucleic acids is important for applications in forensics and diagnostics. An emission-based probe for detecting and quantifying DNA and RNA utilizing a water-soluble dicationic tetraphenylethene (TPE) derivativewas developed. The recognition is based on the electrostatic and other non-covalent interactions between the phosphate backbone of nucleic acids and the cationic probe, which cause the restriction of rotation of the aryl units of the probe, ensuing in the enhancement of the fluorescence signal. The binding was validated by different spectroscopic techniques and also by electrophoretic mobility shift assay. The probable mode of binding with the nucleic acids was studied by blind-docking studies that correlated well with the experimental results.

Generation of DNAzyme in Bacterial Cells by a Bacterial Retron System

DNAzymes are catalytically active single-stranded DNAs in which DNAzyme 10-23 (Dz 10-23) consists of a catalytic core and a substrate-binding arm that reduces gene expression through sequence-specific mRNA cleavage. However, the in vivo application of Dz 10-23 depends on exogenous delivery, which leads to its inability to be synthesized and stabilized in vivo, thus limiting its application. As a unique reverse transcription system, the bacterial retron system can synthesize single-stranded DNA in vivo using ncRNA msr/msd as a template. The objective of this work is to reduce target gene expression using Dz 10-23 generated in vivo by the retron system. In this regard, we successfully generated Dz 10-23 by cloning the Dz 10-23 coding sequence into the retron msd gene and tested its ability to reduce specific gene expression by examining the mRNA levels of cfp encoding cyan fluorescence protein and other functional genes such as mreB and ftsZ. We found that Dz had different repressive effects when targeting different mRNA regions, and in general, the repressive effect was stronger when targeting downstream of mRNAs. Our results also suggested that the reduction effect was due to cleavage of the substrate mRNA by Dz 10-23 rather than the antisense effect of the substrate-binding arm. Therefore, this study not only provided a retron-based method for the intracellular generation of Dz 10-23 but also demonstrated that Dz 10-23 could reduce gene expression by cleaving target mRNAs in cells. We believe that this new strategy would have great potential in the regulation of gene expression.

Advances in the use of nanomaterials for nucleic acid detection in point-of-care testing devices: A review

The outbreak of the coronavirus (COVID-19) has heightened awareness of the importance of quick and easy testing. The convenience, speed, and timely results from point-of-care testing (POCT) in all vitro diagnostic devices has drawn the strong interest of researchers. However, there are still many challenges in the development of POCT devices, such as the pretreatment of samples, detection sensitivity, specificity, and so on. It is anticipated that the unique properties of nanomaterials, e.g., their magnetic, optical, thermal, and electrically conductive features, will address the deficiencies that currently exist in POCT devices. In this review, we mainly analyze the work processes of POCT devices, especially in nucleic acid detection, and summarize how novel nanomaterials used in various aspects of POCT products can improve performance, with the ultimate aims of offering new ideas for the application of nanomaterials and the overall development of POCT devices.

Coupled Multiphysics Modelling of Sensors for Chemical, Biomedical, and Environmental Applications with Focus on Smart Materials and Low-Dimensional Nanostructures

Low-dimensional nanostructures have many advantages when used in sensors compared to the traditional bulk materials, in particular in their sensitivity and specificity. In such nanostructures, the motion of carriers can be confined from one, two, or all three spatial dimensions, leading to their unique properties. New advancements in nanosensors, based on low-dimensional nanostructures, permit their functioning at scales comparable with biological processes and natural systems, allowing their efficient functionalization with chemical and biological molecules. In this article, we provide details of such sensors, focusing on their several important classes, as well as the issues of their designs based on mathematical and computational models covering a range of scales. Such multiscale models require state-of-the-art techniques for their solutions, and we provide an overview of the associated numerical methodologies and approaches in this context. We emphasize the importance of accounting for coupling between different physical fields such as thermal, electromechanical, and magnetic, as well as of additional nonlinear and nonlocal effects which can be salient features of new applications and sensor designs. Our special attention is given to nanowires and nanotubes which are well suited for nanosensor designs and applications, being able to carry a double functionality, as transducers and the media to transmit the signal. One of the key properties of these nanostructures is an enhancement in sensitivity resulting from their high surface-to-volume ratio, which leads to their geometry-dependant properties. This dependency requires careful consideration at the modelling stage, and we provide further details on this issue. Another important class of sensors analyzed here is pertinent to sensor and actuator technologies based on smart materials. The modelling of such materials in their dynamics-enabled applications represents a significant challenge as we have to deal with strongly nonlinear coupled problems, accounting for dynamic interactions between different physical fields and microstructure evolution. Among other classes, important in novel sensor applications, we have given our special attention to heterostructures and nucleic acid based nanostructures. In terms of the application areas, we have focused on chemical and biomedical fields, as well as on green energy and environmentally-friendly technologies where the efficient designs and opportune deployments of sensors are both urgent and compelling.

DNA nanomachine for visual detection of structured RNA and double stranded DNA

Visual detection of ssRNA and dsDNA amplicons was achieved at room temperature without the need for a probe-analyte annealing stage. This approach uses a DNA nanostructure equipped with two analyte-binding arms. Highly selective binding of the third arm leads to the formation of a G-quadruplex structure capable of changing the solution color.

Selective, pH-Dependent Colorimetric and Fluorimetric Detection of Quadruplex DNA with 4-Dimethylamino(phenyl)-Substituted Berberine Derivatives

The 9- and 12-dimethylaminophenyl-substituted berberine derivatives 3 a and 3 b were readily synthesized by Suzuki-Miyaura reactions and shown to be useful fluorescent probes for the optical detection of quadruplex DNA (G4-DNA). Their association with the nucleic acids was investigated by spectrometric titrations, CD and LD spectroscopy, and with DNA-melting analysis. Both ligands bind to duplex DNA by intercalation and to G4-DNA by terminal π stacking. At neutral conditions, they bind with higher affinity (Kb =105 -106  M-1 ) to representative quadruplex forming oligonucleotides 22AG, c-myc, c-kit, and a2, than to duplex calf thymus (ct) DNA (Kb =5-7×104  M-1 ). At pH 5, however, the affinity of 3 a towards G4-DNA 22AG is higher (Kb =1.2×106  M-1 ), whereas the binding constant towards ct DNA is lower (Kb =3.9×103  M-1 ) than under neutral conditions. Notably, the association of the ligand with DNA results in characteristic changes of the absorption and emission properties under specific conditions, which may be used for optical DNA detection. Other than the parent berberine, the ligands do not show a noticeable increase of their very low intrinsic emission intensity upon association with DNA at neutral conditions. In contrast, a fluorescence light-up effect was observed upon association to duplex (Φfl =0.01) and quadruplex DNA (Φfl =0.04) at pH 5. This fluorimetric response to G4-DNA association in combination with the distinct, red-shifted absorption under these conditions provides a simple and conclusive optical detection of G4-DNA at lower pH.

Berberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA

A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms (Kb = 2-7 × 105 M-1) and induces a slight stabilization of G4-DNA toward thermally induced unfolding, mostly pronounced for the telomeric quadruplex 22AG. The ligand likely binds by aggregation and intercalation with ct DNA and by terminal stacking with G4-DNA. Thus, this compound represents one of the rare examples of phosphate-substituted DNA binders. In an aqueous solution, the title compound has a very weak fluorescence intensity (Φfl < 0.01) that increases significantly upon binding to G4-DNA (Φfl = 0.01). In contrast, the association with duplex DNA was not accompanied by such a strong fluorescence light-up effect (Φfl < 0.01). These different fluorimetric responses upon binding to particular DNA forms are proposed to be caused by the different binding modes and may be used for the selective fluorimetric detection of G4-DNA.

Hydrogel-Based Technologies for the Diagnosis of Skin Pathology

Hydrogels, swellable hydrophilic polymer networks fabricated through chemical cross-linking or physical entanglement are increasingly utilized in various biomedical applications over the past few decades. Hydrogel-based microparticles, dressings and microneedle patches have been explored to achieve safe, sustained and on-demand therapeutic purposes toward numerous skin pathologies, through incorporation of stimuli-responsive moieties and therapeutic agents. More recently, these platforms are expanded to fulfill the diagnostic and monitoring role. Herein, the development of hydrogel technology to achieve diagnosis and monitoring of pathological skin conditions are highlighted, with proteins, nucleic acids, metabolites, and reactive species employed as target biomarkers, among others. The scope of this review includes the characteristics of hydrogel materials, its fabrication procedures, examples of diagnostic studies, as well as discussion pertaining clinical translation of hydrogel systems.

Hydrophobic Interaction: A Promising Driving Force for the Biomedical Applications of Nucleic Acids

The comprehensive understanding and proper use of supramolecular interactions have become critical for the development of functional materials, and so is the biomedical application of nucleic acids (NAs). Relatively rare attention has been paid to hydrophobic interaction compared with hydrogen bonding and electrostatic interaction of NAs. However, hydrophobic interaction shows some unique properties, such as high tunability for application interest, minimal effect on NA functionality, and sensitivity to external stimuli. Therefore, the widespread use of hydrophobic interaction has promoted the evolution of NA-based biomaterials in higher-order self-assembly, drug/gene-delivery systems, and stimuli-responsive systems. Herein, the recent progress of NA-based biomaterials whose fabrications or properties are highly determined by hydrophobic interactions is summarized. 1) The hydrophobic interaction of NA itself comes from the accumulation of base-stacking forces, by which the NAs with certain base compositions and chain lengths show properties similar to thermal-responsive polymers. 2) In conjugation with hydrophobic molecules, NA amphiphiles show interesting self-assembly structures with unique properties in many new biosensing and therapeutic strategies. 3) The working-mechanisms of some NA-based complex materials are also dependent on hydrophobic interactions. Moreover, in recent attempts, NA amphiphiles have been applied in organizing macroscopic self-assembly of DNA origami and controlling the cell-cell interactions.

Nanodelivery Systems for Topical Management of Skin Disorders

Topical drug delivery has inherent advantages over other administration routes. However, the existence of stratum corneum limits the diffusion to small and lipophilic drugs. Fortunately, the advancement of nanotechnology brings along opportunities to address this challenge. Taking the unique features in size and surface chemistry, nanocarriers such as liposomes, polymeric nanoparticles, gold nanoparticles, and framework nucleic acids have been used to bring drugs across the skin barrier to epidermis and dermis layers. This article reviews the development of these formulations and focuses on their applications in the treatment of skin disorders such as acne, skin inflammation, skin infection, and wound healing. Existing hurdles and further developments are also discussed.

Colorimetric and Fluorimetric DNA Detection with a Hydroxystyryl-Quinolizinium Photoacid and Its Application for Cell Imaging

The combination of styryl dye properties with the acidity and strong photoacidity of the 2,2'-[(1''-hydroxy-4''-methyl-(E)-2'',6''-phenylene)]-bisquinolizinium enables the detection of DNA by distinct absorption and emission color changes and the fluorimetric detection of DNA in cells with epifluorescence and confocal fluorescence microscopy.

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.