DNA nanolantern-based split aptamer probes for in situ ATP imaging in living cells and lighting up mitochondria

A dual-switch electrochemical aptasensor for label-free detection of thrombin and ATP based on split aptamers

BACKGROUND

Aptamers, consisting of specialized single-stranded nucleic acids, are engineered through the SELEX technique to recognize specific targets with strong affinity. Aptamers are exceptionally useful in various sensor technologies, such as fluorescence-based sensors, electrochemical sensors, and colorimetric detection systems. Due to its high sensitivity, specificity and fast response, electrochemical aptasensor shows great application prospects in analytical detection, food safety, and environmental monitoring. However, one aptasensor can usually detect only one type of target, limiting its universality in practical applications.

RESULTS

Here, we constructed a dual-switch and label-free electrochemical aptasensor based on split aptamer and nuclease. The feasibility, specificity, and sensitivity of the aptasensor were investigated by using thrombin and adenosine triphosphate (ATP) as targets. Split aptamer can not only capture target specifically but also form a stable sandwich structure with the target. In the presence of thrombin, it triggered a hydrolysis reaction of exonuclease I, leading to a decrease in the impedance signal. Differently, the presence of ATP could form a sandwich structure with split aptamers, leading to an increase in output signals. The aptasensor achieved sensitive and specific detection of thrombin and ATP, with low detection limits of 0.76 pM and 0.27 pM, respectively.

SIGNIFICANCE AND NOVELTY

The aptasensor realized the detection of two targets without replacing any reagents or equipment, which greatly saved time and cost. Furthermore, electrochemical impedance spectroscopy (EIS) uses impedance as an output signal, showing great application prospects in electrochemical aptasensors as label-free and simple methods. Because of its simplicity, label-free, and sensitivity in complex samples, the split aptamer-assisted aptasensor provides new ideas and methods in early diagnosis of diseases.

Functionalizing tetrahedral framework nucleic acids-based nanostructures for tumor in situ imaging and treatment

Timely in situ imaging and effective treatment are efficient strategies in improving the therapeutic effect and survival rate of tumor patients. In recent years, there has been rapid progress in the development of DNA nanomaterials for tumor in situ imaging and treatment, due to their unsurpassed structural stability, excellent material editability, excellent biocompatibility and individual endocytic pathway. Tetrahedral framework nucleic acids (tFNAs), are a typical example of DNA nanostructures demonstrating superior stability, biocompatibility, cell-entry performance, and flexible drug-loading ability. tFNAs have been shown to be effective in achieving timely tumor in situ imaging and precise treatment. Therefore, the progress in the fabrication, characterization, modification and cellular internalization pathway of tFNAs-based functional systems and their potential in tumor in situ imaging and treatment applications were systematically reviewed in this article. In addition, challenges and future prospects of tFNAs in tumor in situ imaging and treatment as well as potential clinical applications were discussed.

Accelerated diagnosis: a crosslinking catalytic hairpin assembly system for rapid and sensitive SARS-CoV-2 RNA detection

The COVID-19 pandemic has underscored the urgent need for rapid and reliable strategies for early detection of SARS-CoV-2. In this study, we propose a DNA nanosphere-based crosslinking catalytic hairpin assembly (CCHA) system for the rapid and sensitive SARS-CoV-2 RNA detection. The CCHA system employs two DNA nanospheres functionalized with catalytic hairpin assembly (CHA) hairpins. The presence of target SARS-CoV-2 RNA initiated the crosslinking of DNA nanospheres via CHA process, leading to the amplification of fluorescence signals. As a result, the speed of SARS-CoV-2 diagnosis was enhanced by significantly increasing the local concentration of the reagents in a crosslinked DNA product, leading to a detection limit of 363 fM within 5 min. The robustness of this system has been validated in complex environments, such as fetal bovine serum and saliva. Hence, the proposed CCHA system offers an efficient and simple approach for rapid detection of SARS-CoV-2 RNA, holding substantial promise for enhancing COVID-19 diagnosis.

Synthesis of rare-earth metal-organic frameworks to construct high-resolution sensing array for multiplex anions detection, cell imaging and blood phosphorus monitoring

Accurate detection and differentiation of multiple anions is still a difficult problem due to their wide variety, structural similarity, and mutual interference. Hence, four rare-earth metal-organic frameworks (RE-MOFs) including Dy-MOFs, Er-MOFs, Tb-MOFs and Y-MOFs are successfully prepared by using TCPP as the ligand and rare-earth ions as the metal center via coordination chelation. It is found that 7 anions can light up their fluorescence. Thus, a high-resolution sensing array based on RE-MOFs nanoprobes is employed to differentiate these anions from intricate analytes in real-time scenarios. The distinctive host-guest response promotes the RE-MOFs nanoprobes to selectively extract the target anions from the complex samples. By taking advantage of the cross-response between RE-MOFs nanoprobes and anions, it allows to create an array for detecting target analytes using pattern recognition. Additionally, RE-MOFs nanoprobes also facilitate the quantitative analysis of these anions (PO43-, H2PO4-, HPO42-, F-, S2-, CO32- and C2O42-). More importantly, the exceptional effectiveness of this method has been demonstrated through various successful applications, including quality monitoring of 8 toothpaste brands, intracellular phosphate imaging, and blood phosphorus detection in mice with vascular calcification. These findings provide robust evidence for the efficacy and reliability of the RE-MOFs nanoprobes array for anion recognition.

Dynamic DNA Nanostructures for Cell Manipulation

Dynamic DNA nanostructures are DNA nanostructures with reconfigurable elements that can undergo structural transformations in response to specific stimuli. Thus, anchoring dynamic DNA nanostructures on cell membranes is an attractive and promising strategy for well-controlled cell manipulation. Here, we review the latest progress in dynamic DNA nanostructures for cell manipulation. Commonly used mechanisms for dynamic DNA nanostructures are first introduced. Subsequently, we summarize the anchoring strategies for dynamic DNA nanostructures on cell membranes and list possible applications (including programming cell membrane receptors, controlling ligand activity and drug delivery, capturing and releasing cells, and assembling cells into clusters). Finally, insights into the remaining challenges are presented.

Self-assembly of DNA nanospheres with controllable size and self-degradable property for enhanced antitumor chemotherapy

Controllable size, self-degradability and targeting property are important for a precise improvement of anticancer effects and reduction of side effects of drug vehicles. Here, a series of DNA nanospheres with controllable size and self-degradation ability were constructed through the hybridization of two i-motif strands and two linker strands for targeted cancer therapy. DNA nanospheres with different sizes were fabricated by regulating the linker sequence, and their pH-responsive self-degradation property was realized by the introduction of the i-motif strand. Moreover, the ZY11 aptamer was introduced to endow the DNA nanospheres with targeting property toward SMMC-7721 cancer cells. The results revealed that the appropriate size of DNA nanospheres (80 nm) highly promoted the internalization by mammalian cells. The results of DLS, AFM and CD spectra showed that the DNA nanospheres were stable in a physiological environment but they self-degraded in a slightly acidic environment due to the existence of the i-motif strand. Moreover, the fluorescence of DOX@AP-NSs2 was triple at pH = 5.0 than at pH = 7.4, which further confirmed the pH-responsive drug release performance. The above results proved that the use of DOX@AP-NSs2 is a promising approach to accelerate the rapid release of drugs into the tumors and avoid drug leakage into the normal tissue. The results at a cellular level and in vivo confirmed the pH-responsive targeted antitumor effect. Hence, the novel DNA nanospheres with controllable size and self-degradable property represent a potential tool for targeted drug delivery and cancer therapy.

In Situ Monitoring of Intracellular ATP Variation Based on a Thermoregulated Polymer Nanocomposite

It is necessary to develop reliable chemiluminescence strategies for determination of intracellular adenosine triphosphate (ATP), which is vital in life science and clinical diagnosis. However, the current chemiluminescence methods based on firefly luciferase suffered from low delivery efficiency, unsatisfied targeting performance, and autohydrolysis in living biosystem. To circumvent these drawbacks, a thermoresponsive polymer nanocomposite modified with firefly luciferase and ATP aptamer (PFLNC@aptamer) was fabricated, which targeted ATP and determined the intracellular ATP levels via measuring the chemiluminescence signals at different temperatures. The PFLNC@aptamer exhibited capability for the enzymolysis efficiency regulation, increased 21.0% with temperature change from 37.0 to 25.0 °C. The ATP detection limit was 3.3 nM with a linear relationship from 10.0 nM to 0.1 mM. Moreover, the thermoresponsive nanocomposite could also effectively avoid the interference during delivering firefly luciferase into the living cells and effectively discriminate ATP via the immobilized ATP aptamer, which further confirmed its reliability for practical applications. It paves a specific avenue for effective intracellular ATP monitoring in fundamental and applied research.

Development of the DNA-based biosensors for high performance in detection of molecular biomarkers: More rapid, sensitive, and universal

The molecular biomarkers are molecules that are closely related to specific physiological states. Numerous molecular biomarkers have been identified as targets for disease diagnosis and biological research. To date, developing highly efficient probes for the precise detection of biomarkers has become an attractive research field which is very important for biological and biochemical studies. During the past decades, not only the small chemical probe molecules but also the biomacromolecules such as enzymes, antibodies, and nucleic acids have been introduced to construct of biosensor platform to achieve the detection of biomarkers in a highly specific and highly efficient way. Nevertheless, improving the performance of the biosensors, especially in clinical applications, is still in urgent demand in this field. A noteworthy example is the Corona Virus Disease 2019 (COVID-19) that breaks out globally in a short time in 2020. The COVID-19 was caused by the virus called SARS-CoV-2. Early diagnosis is very important to block the infection of the virus. Therefore, during these months scientists have developed dozens of methods to achieve rapid and sensitive detection of the virus. Nowadays some of these new methods have been applied for producing the commercial detection kit and help people against the disease worldwide. DNA-based biosensors are useful tools that have been widely applied in the detection of molecular biomarkers. The good stability, high specificity, and excellent biocompatibility make the DNA-based biosensors versatile in application both in vitro and in vivo. In this paper, we will review the major methods that emerged in recent years on the design of DNA-based biosensors and their applications. Moreover, we will also briefly discuss the possible future direction of DNA-based biosensors design. We believe this is helpful for people interested in not only the biosensor field but also in the field of analytical chemistry, DNA nanotechnology, biology, and disease diagnosis.

DNA nanolantern-mediated catalytic hairpin assembly nanoamplifiers for simultaneous detection of multiple microRNAs

Simultaneous detection of multiple microRNAs (miRNAs) with high sensitivity can give accurate and reliable information for clinical applications. By uniformly anchoring hairpin probes on the surface of DNA nanolantern, a three-dimensional DNA nanostructure contains abundant and adjustable modification sites, highly integrated DNA nanoprobes were designed and developed as catalytic hairpin assembly (CHA)-based signal amplifiers for enzyme-free signal amplification detection of target miRNAs. The nanolantern-based CHA (NLC) amplifiers, which were facilely prepared via a simple "one-pot" annealing method, showed enhanced biostability, improved cell internalization efficiency, accelerated CHA reaction kinetics, and increased signal amplification capability compared to the single-stranded DNA hairpin probes used in traditional CHA reaction. By co-assembling multiple hairpin probes on a DNA nanolantern surface, as-prepared NLC amplifiers were demonstrated to work well for highly sensitive and specific imaging, expression level fluctuation analysis of two miRNAs in living cells, and miRNAs-guided tumor imaging in living mice. The proposed DNA nanolantern-based nanoamplifier strategy might provide a feasible way to promote the cellular and in vivo applications of nucleic acid probes.