DNAzyme-functionalized gold nanoparticles for biosensing

Advances and Trends in miRNA Analysis Using DNAzyme-Based Biosensors

miRNAs are endogenous small, non-coding RNA molecules that function in post-transcriptional regulation of gene expression. Because miRNA plays a pivotal role in maintaining the intracellular environment, and abnormal expression has been found in many cancer diseases, detection of miRNA as a biomarker is important for early diagnosis of disease and study of miRNA function. However, because miRNA is present in extremely low concentrations in cells and many types of miRNAs with similar sequences are mixed, traditional gene detection methods are not suitable for miRNA detection. Therefore, in order to overcome this limitation, a signal amplification process is essential for high sensitivity. In particular, enzyme-free signal amplification systems such as DNAzyme systems have been developed for miRNA analysis with high specificity. DNAzymes have the advantage of being more stable in the physiological environment than enzymes, easy to chemically synthesize, and biocompatible. In this review, we summarize and introduce the methods using DNAzyme-based biosensors, especially with regard to various signal amplification methods for high sensitivity and strategies for improving detection specificity. We also discuss the current challenges and trends of these DNAzyme-based biosensors.

Integrating high-performing electrochemical transducers in lateral flow assay

Lateral flow assays (LFAs) are the best-performing and best-known point-of-care tests worldwide. Over the last decade, they have experienced an increasing interest by researchers towards improving their analytical performance while maintaining their robust assay platform. Commercially, visual and optical detection strategies dominate, but it is especially the research on integrating electrochemical (EC) approaches that may have a chance to significantly improve an LFA's performance that is needed in order to detect analytes reliably at lower concentrations than currently possible. In fact, EC-LFAs offer advantages in terms of quantitative determination, low-cost, high sensitivity, and even simple, label-free strategies. Here, the various configurations of EC-LFAs published are summarized and critically evaluated. In short, most of them rely on applying conventional transducers, e.g., screen-printed electrode, to ensure reliability of the assay, and additional advances are afforded by the beneficial features of nanomaterials. It is predicted that these will be further implemented in EC-LFAs as high-performance transducers. Considering the low cost of point-of-care devices, it becomes even more important to also identify strategies that efficiently integrate nanomaterials into EC-LFAs in a high-throughput manner while maintaining their favorable analytical performance. Graphical abstract.

Integrating high-performing electrochemical transducers in lateral flow assay

Lateral flow assays (LFAs) are the best-performing and best-known point-of-care tests worldwide. Over the last decade, they have experienced an increasing interest by researchers towards improving their analytical performance while maintaining their robust assay platform. Commercially, visual and optical detection strategies dominate, but it is especially the research on integrating electrochemical (EC) approaches that may have a chance to significantly improve an LFA’s performance that is needed in order to detect analytes reliably at lower concentrations than currently possible. In fact, EC-LFAs offer advantages in terms of quantitative determination, low-cost, high sensitivity, and even simple, label-free strategies. Here, the various configurations of EC-LFAs published are summarized and critically evaluated. In short, most of them rely on applying conventional transducers, e.g., screen-printed electrode, to ensure reliability of the assay, and additional advances are afforded by the beneficial features of nanomaterials. It is predicted that these will be further implemented in EC-LFAs as high-performance transducers. Considering the low cost of point-of-care devices, it becomes even more important to also identify strategies that efficiently integrate nanomaterials into EC-LFAs in a high-throughput manner while maintaining their favorable analytical performance.

Attaching DNA to Gold Nanoparticles With a Protein Corona

DNA-functionalized gold nanoparticles (AuNPs) have been widely used in directed assembly of materials, biosensors, and drug delivery. This conjugate may encounter proteins in these applications and proteins may affect not only DNA adsorption but also the function of the attached DNA. Bovine serum albumin (BSA) with many cysteine residues can strongly adsorb on AuNPs and this conjugate showed high colloidal stability against salt, acid and base. Similar protection effects were also observed with a few other common proteins including catalase, hemoglobin, glucose oxidase, and horseradish peroxidase. DNA oligonucleotides without a thiol label can hardly displace adsorbed BSA, and BSA cannot displace pre-adsorbed DNA either, indicating a strongly kinetically controlled system. Thiolated DNA can be attached at a low density on the AuNPs with a BSA corona. The BSA corona did not facilitate the hybridization of the conjugated DNA, while a smaller peptide, glutathione allowed faster hybridization. Overall, proteins increase the colloidal stability of AuNPs, and they do not perturb the gold-thiol bond in the DNA conjugate, although a large protein corona may inhibit the hybridization function of DNA.

Divide and Control: Comparison of Split and Switch Hybridization Sensors

Hybridization probes have been intensively used for nucleic acid analysis in medicine, forensics and fundamental research. Instantaneous hybridization probes (IHPs) enable signalling immediately after binding to a targeted DNA or RNA sequences without the need to isolate the probe-target complex (e. g. by gel electrophoresis). The two most common strategies for IHP design are conformational switches and split approach. A conformational switch changes its conformation and produces signal upon hybridization to a target. Split approach uses two (or more) strands that independently or semi independently bind the target and produce an output signal only if all components associate. Here, we compared the performance of split vs switch designs for deoxyribozyme (Dz) hybridization probes under optimal conditions for each of them. The split design was represented by binary Dz (BiDz) probes; while catalytic molecular beacon (CMB) probes represented the switch design. It was found that BiDz were significantly more selective than CMBs in recognition of single base substitution. CMBs produced high background signal when operated at 55°C. An important advantage of BiDz over CMB is more straightforward design and simplicity of assay optimization.

Integrating Deoxyribozymes into Colorimetric Sensing Platforms

Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection. By using various signal transduction mechanisms, DNAzymes can be engineered into fluorescent, colorimetric, electrochemical and chemiluminescent biosensors. Among them, colorimetric sensors represent an attractive option as the signal can be easily detected by the naked eye. This reduces reliance on complex and expensive equipment. In this review, we will discuss the recent progress in the development of colorimetric biosensors that make use of DNAzymes and the prospect of employing these sensors in a range of chemical and biological applications.

A one-step colorimetric acid-base titration sensor using a complementary color changing coordination system

We report the development of a colorimetric sensor that allows for the quantitative measurement of the acid content via acid-base titration in a single-step. In order to create the sensor, we used a cobalt coordination system (Co-complex sensor) that changes from greenish blue colored Co(H2O)4(OH)2 to pink colored Co(H2O)6(2+) after neutralization. Greenish blue and pink are two complementary colors with a strong contrast. As a certain amount of acid is introduced to the Co-complex sensor, a portion of greenish blue colored Co(H2O)4(OH)2 changes to pink colored Co(H2O)6(2+), producing a different color. As the ratio of greenish blue and pink in the Co-complex sensor is determined by the amount of neutralization reaction occurring between Co(H2O)4(OH)2 and an acid, the sensor produced a spectrum of green, yellow green, brown, orange, and pink colors depending on the acid content. In contrast, the color change appeared only beyond the end point for normal acid-base titration. When we mixed this Co-complex sensor with different concentrations of citric acid, tartaric acid, and malic acid, three representative organic acids in fruits, we observed distinct color changes for each sample. This color change could also be observed in real fruit juice. When we treated the Co-complex sensor with real tangerine juice, it generated diverse colors depending on the concentration of citric acid in each sample. These results provide a new angle on simple but quantitative measurements of analytes for on-site usage in various applications, such as in food, farms, and the drug industry.

Postsynthetic Modification of DNA Phosphodiester Backbone for Photocaged DNAzyme

Photocaged (photoactivatable) biomolecules are powerful tools for noninvasive control of biochemical activities by light irradiation. DNAzymes (deoxyribozymes) are single-stranded oligonucleotides with a broad range of enzymatic activities. In this work, to construct photocaged DNAzymes, we developed a facile and mild postsynthetic method to incorporate an interesting photolabile modification (thioether-enol phosphate, phenol substituted, TEEP-OH) into readily available phosphorothioate DNA. Upon light irradiation, TEEP-OH transformed into a native DNA phosphodiester, and accordingly the DNAzymes with RNA-cleaving activities were turned "on" from its inactive and caged form. Activation of the TEEP-OH-caged DNAzyme by light was also successful inside live cells.

Poly-adenine-based programmable engineering of gold nanoparticles for highly regulated spherical DNAzymes

Enzyme complexes are assembled at the two-dimensional lipid membrane or prearranged on three-dimensional scaffolding proteins to regulate their catalytic activity in cells. Inspired by nature, we have developed gold nanoparticle-based spherical DNAzymes (SNAzymes) with programmably engineered activities by exploiting poly-adenine (polyA)-Au interactions. In a SNAzyme, AuNPs serve as the metal core, which is decorated with a functional shell of DNAzymes. Conventional thiolated DNAzyme-based assembly leads to disordered structures with suppressed activity. In contrast, by using an anchoring block of polyA tails, we find that the activity of SNAzymes can be programmably regulated. By using a polyA30 tail, SNAzymes demonstrated remarkably enhanced binding affinity compared to the thiolated DNAzyme-based assembly (∼75-fold) or individual DNAzymes in the solution phase (∼10-fold). More significantly, this increased affinity is directly translated to the sensitivity improvement in the SNAzyme-based lead sensor. Hence, this design of SNAzymes may provide new opportunities for developing biosensors and bioimaging probes for theranostic applications.