Smart Tumor Cell-Derived DNA Nano-Tree Assembly for On-Demand Macrophages Reprogramming

Without coordinated strategies to balance the population and activity of tumor cells and polarized macrophages, antitumor immunotherapy generally offers limited clinical benefits. Inspired by the "eat me" signal, a smart tumor cell-derived proximity anchored non-linear hybridization chain reaction (Panel-HCR) strategy is established for on-demand regulation of tumor-associated macrophages (TAMs). The Panel-HCR is composed of a recognition-then-assembly module and a release-then-regulation module. Upon recognizing tumor cells, a DNA nano-tree is assembled on the tumor cell surface and byproduct strands loaded with CpG oligodeoxynucleotides (CpG-ODNs) are released depending on the tumor cell concentration. The on-demand release of CpG-ODNs can achieve efficient regulation of M2 TAMs into the M1 phenotype. Throughout the recognition-then-assembly process, tumor cell-targeted bioimaging is implemented in single cells, fixed tissues, and living mice. Afterward, the on-demand release of CpG-ODNs regulate the transformation of M2 TAMs into the M1 phenotype by stimulating toll-like receptor 9 to activate the NF-κB pathway and increasing inflammatory cytokines. This release-then-regulation process is verified to induce strong antitumor immune responses both in vitro and in vivo. Altogether, this proposed strategy holds tremendous promise for on-demand antitumor immunotherapy.

A Novel miRNA Detection Method Using Loop-Mediated Isothermal Amplification

A novel ligation-based loop-mediated isothermal amplification has been developed for miRNA detection. Two stem-loop structure DNA linker A/B probes which hybridized with miRNA were designed to establish a rapid and ultrasensitive miRNA-LAMP system for miRNA detection. Target miR-200a was used to template the ligation of Linker A/B probes with SplintR Ligase and used as a dumbbell-shaped amplicon. By adding BIP/FIP and Bst 2.0 DNA polymerase, the LAMP reaction was carried out, which brought greatly improved amplification efficiency. The double-stranded DNA fluorescent dye EvaGreen was added for the detection of amplification product to achieve the quantification of the target miRNA. This method can detect miRNA in a linear range of seven orders of magnitude, with a detection limit of 100 fM. Therefore, this ultrasensitive miRNA-LAMP assay provides a new path for the highly sensitive quantitative analysis of miRNA, thereby bringing convenience to clinical diagnosis and prognostic research.

Attomolar analyte sensing techniques (AttoSens): a review on a decade of progress on chemical and biosensing nanoplatforms

Detecting the ultra-low abundance of analytes in real-life samples, such as biological fluids, water, soil, and food, requires the design and development of high-performance biosensing modalities. The breakthrough efforts from the scientific community have led to the realization of sensing technologies that measure the analyte's ultra-trace level, with relevant sensitivity, selectivity, response time, and sampling efficiency, referred to as Attomolar Analyte Sensing Techniques (AttoSens) in this review. In an AttoSens platform, 1 aM detection corresponds to the quantification of 60 target analyte molecules in 100 μL of sample volume. Herein, we review the approaches listed for various sensor probe design, and their sensing strategies that paved the way for the detection of attomolar (aM: 10^-18 M) concentration of analytes. A summary of the technological advances made by the diverse AttoSens trends from the past decade is presented.

Ultrasensitive ratiometric electrochemiluminescence for detecting atxA mRNA using luminol-encapsulated liposome as effectively amplified signal labels

It is an advantageous way to quickly identify the toxicity of Bacillus anthracis (B. anthracis) by detecting the transcription product of the atxA gene. Herein, a novel ultrasensitive ratiometric electrochemiluminescence (ECL) biosensor with competitive mechanism and double amplified signal ways was proposed for detecting the atxA mRNA. The K2S2O8 was used as cathodic emitter and silver metal-organic gels (AgMOG) was used as ECL enhancer. The AgMOG could accelerate the electro-catalytic reduction of S2O82- to SO4˙-, which reacted with dissolved oxygen, resulting in strong cathodic ECL. Meanwhile, luminol was encapsulated in liposome as anodic amplified signal labels and the luminol anion radical also reacted with dissolved oxygen to create the anodic ECL emission. We immobilized luminol-encapsulated liposomes on the surface of AgMOG through the hybridization of DNA and mRNA. This would provide a competitive mechanism involving dissolved oxygen between K2S2O8 and luminol. Benefiting from the competitive mechanism and amplified signal ways, this ratiometric biosensor achieved a wide linear relationship range from 10 to 300 fM with a low limit of detection (8.13 fM). Considering the accessible operation, favorable performance, and high universality of this strategy, this work may be used to analyze other mRNAs of bacteria.

Electrochemical Biosensors for Detection of MicroRNA as a Cancer Biomarker: Pros and Cons

Cancer is the second most fatal disease in the world and an early diagnosis is important for a successful treatment. Thus, it is necessary to develop fast, sensitive, simple, and inexpensive analytical tools for cancer biomarker detection. MicroRNA (miRNA) is an RNA cancer biomarker where the expression level in body fluid is strongly correlated to cancer. Various biosensors involving the detection of miRNA for cancer diagnosis were developed. The present review offers a comprehensive overview of the recent developments in electrochemical biosensor for miRNA cancer marker detection from 2015 to 2020. The review focuses on the approaches to direct miRNA detection based on the electrochemical signal. It includes a RedOx-labeled probe with different designs, RedOx DNA-intercalating agents, various kinds of RedOx catalysts used to produce a signal response, and finally a free RedOx indicator. Furthermore, the advantages and drawbacks of these approaches are highlighted.

DNA Walking and Rolling Nanomachine for Electrochemical Detection of miRNA

miRNAs, a class of endogenous noncoding RNAs, are involved in many crucial biological processes, which have emerged as a new set of biomarkers for disease theranostics. Exploring efficient signal amplification strategy is highly desired to pursue a highly sensitive miRNA biosensing platform. DNA nanotechnology shows great promise in the fabrication of amplified miRNA biosensors. In this work, a novel DNA walking and rolling nanomachine is developed for highly sensitive and selective detection of miRNA. Particularly, this approach programs two forms of dynamic DNA nanomachines powered by corresponding enzymes, which are well integrated. It is able to achieve a limit of detection as low as 39 × 10^-18 m, along with excellent anti-interfering performance and clinical applications. In addition, by designing pH-controlled detachable intermolecular DNA triplex, the main sensing elements can be conveniently reset, which fulfills the requirements of point-of-care profiling of miRNA. The high consistency between the proposed approach and quantitative real-time polymerase chain reaction validates the robustness and reliability. Therefore, it is anticipated that the DNA walking and rolling nanomachine has attractive application prospects in miRNA assay for biological researches and clinical diagnosis.

Target-triggered configuration change of DNA tetrahedron for SERS assay of microRNA 122

A surface-enhanced Raman scattering (SERS) method is proposed for the assay of microRNA 122 based on configuration change of DNA tetrahedron. Firstly, a DNA tetrahedron was self-assembled with one vertex labeled with toluidine blue (TB). Then, it was immobilized on the porous Ni/SiO₂@PEI@Au as a SERS platform, which was characterized by scanning electron microscopy (SEM) and X-ray diffraction (XRD). At this time, the DNA tetrahedron was contracted; so, the TB is close to AuNPs and the Raman signal is high. When target microRNA 122 existed, with the nicking enzyme amplification strategy, a great deal of DNA signal chains (S5) was obtained, which can extend the contracted DNA tetrahedron and change it into a three-dimensional DNA tetrahedron. In this case, the TB was far from AuNPs, resulting in a lower Raman signal. Due to the configuration change of DNA tetrahedron, the Raman signal at 1624 cm^-1 (with the excitation wavelength of 633 nm) has a linear relationship with the logarithm concentration of microRNA 122. This SERS assay has high sensitivity for microRNA 122 with a determination range from 0.01 aM to 10 fM and a detection limit of 0.009 aM. The recoveries from spiked samples were in the range 95 to 109%. This SERS strategy is designed based on the target-triggered configuration change of DNA tetrahedron, which can give new insight for DNA structures in bioanalysis. Graphical abstract A sensitive surface-enhanced Raman scattering (SERS) biosensor was developed to detect microRNA 122 using the configuration change of DNA tetrahedron to indirectly control the position of TB and hot spot.

Integration of a peptide–DNA conjugate with multiple cyclic signal amplification for the ultrasensitive detection of cathepsin B activity

We integrate a peptide–DNA conjugate with multiple cyclic signal amplification for the sensitive detection of cathepsin B activity.

Gold Nanoparticles-Based Multipedal DNA Walker for Ratiometric Detection of Circulating Tumor Cell

Sensitive and accurate quantification of circulating tumor cell (CTC) can provide new insights for early diagnosis and prognosis of cancers. Herein, we have developed a multipedal DNA walker for ultrasensitive detection of CTC for the first time. Generally, a number of walker strands are simply modified on gold nanoparticle (AuNPs). The integrated aptamer sequence can specially interact with the transmembrane receptor protein of CTC and facilitate the enrichment of AuNPs on the surface of cells. After a low speed centrifugation, the complex of CTC and AuNPs could be precipitated and the supernate represents decreased UV-vis absorbance response of AuNPs. On the other hand, since multiple walker strands are modified on a single AuNP, hybridization with several tracks on the electrode occurs simultaneously for the following nicking endonuclease-catalyzed cleaving. Experimental results verify that the rate of multipedal walking is much faster. In addition, TCEP-mediated electrochemical amplification is employed to further enhance the electrochemical signal. By comparing the variations of electrochemical and UV-vis absorbance responses, ultrahigh sensitivity for CTC assay is achieved. The limit of detection is down to 1 cell/mL. The results of selectivity confirmation and blood sample test are also satisfactory. This AuNPs-based multipedal DNA walker offers a speedy analysis of CTC and shows great potential use for early clinical diagnosis and treatment of cancers.

Functional chimera aptamer and molecular beacon based fluorescent detection of Staphylococcus aureus with strand displacement-target recycling amplification

A fluorescent detection of Staphylococcus aureus (S. aureus) is established based on a finely designed functional chimera sequence, a molecular beacon (MB), and strand displacement target recycling. The chimera sequence, which consists of the aptamer sequence of S. aureus and the complementary sequence of MB, can form a hairpin structure due to the existence of intramolecular complementary regions. When S. aureus is present, it binds to the aptamer region of the chimera, opens the hairpin and unlocks the complementary sequence of MB. Subsequently, the MB is opened and intensive fluorescence signal is restored. To increase the sensitivity of the detection, signal amplification is achieved through strand displacement-based target recycling. With the catalysis of Nb. Bpu10I nicking endonuclease and Bsm DNA polymerase, the MB sequence can be cleaved and then elongated to form a complete duplex with the chimera, during which S. aureus is displaced from the chimera and proceeded to the next round of the reaction. This assay displays a linear correlation between the fluorescence intensity and the logarithm of the concentration of S. aureus within a broad concentration range from 80 CFU/mL to 8 × 10⁶ CFU/mL. The detection limit of 39 CFU/mL can be derived. The assay was applied to detect S. aureus in different water samples, and satisfactory recovery and repeatability were achieved. Hence the designed chimera sequence and established assay have potential application in environmental pollution monitoring.

Bipedal DNA Walker Based Electrochemical Genosensing Strategy

DNAs are one of the most fundamental molecules for life. Quantification of specific sequences is of great importance for biological research and clinical diagnosis. In order to determine extremely low abundant DNAs, we herein develop a novel electrochemical genosensor taking advantage of a smart bipedal DNA walking machine. Magnetic nanomaterials are first employed to enrich target DNA. Strand displacement amplification initiated by target DNA is then designed on the surface of the nanomaterials, the products of which can be used to trigger bipedal DNA walking on the surface of an electrode. Benefiting from triple amplification, ultrahigh sensitivity is achieved for electrochemical analysis of DNA. More importantly, the proposed strategy opens a new avenue for employing the bipedal DNA walker for sensitive detection of various biomolecules with signal amplification.

Silver nanoparticle@DNA tetrahedron-based colorimetric detection of HIV-related DNA with cascade strand displacement amplification

DNA tetrahedron-modified silver nanoparticles (AgNPs) were achieved via amino-silver chemistry for the first time and were applied as a colorimetric biosensor for detecting HIV-related DNA. Target DNA initiated strand displacement polymerization and nicking endonuclease-aided cycles were involved to link DNA tetrahedron-modified AgNPs, reporting colorimetric responses. This developed method showed excellent specificity and sensitivity. A wide linear range from 1 to 15 000 nM was achieved with a limit of detection of 0.84 nM. Moreover, it was successfully applied to determine DNA in blood serum samples.

A high-energy-state biomimetic enzyme of oxygen-deficient MnTiO3 nanodiscs for sensitive electrochemical sensing of the superoxide anion

A high-energy-state biomimetic enzyme for the superoxide anion is presented by inducing surface oxygen defects in MnTiO₃ nanodiscs.

DNA-Functionalized Porous Fe3O4 Nanoparticles for the Construction of Self-Powered miRNA Biosensor with Target Recycling Amplification

Herein, we have developed an ultrasensitive self-powered biosensor for miRNA assay based on biofuel cells. The system is composed of indium tin oxide cathode and graphene oxide/gold nanoparticle/glucose oxidase anode. Redox probe of [Fe(CN)₆]^3- is entrapped inside porous Fe₃O₄ nanoparticles by DNA. However, in the presence of target miRNA, hybridization reaction occurs between miRNA and DNA, which initiates the release of [Fe(CN)₆]^3-. Moreover, duplex specific nuclease is further employed to trigger target recycling amplification. As a result, much more redox probes are released and the open circuit voltage is significantly increased. A "signal-on" self-powered biosensor for miRNA quantification is thus developed. The detection range is from 10 aM to 10 fM; meanwhile, the limit of detection is as low as 1.4 aM, which is superior to that in most reported methods. Therefore, the proposed biosensor is expected to be a powerful point-of-care tool for miRNA diagnostics, which may have wide applications in the future.

An aptamer biosensor for leukemia marker mRNA detection based on polymerase-assisted signal amplification and aggregation of illuminator

A novel electrochemical luminescence (ECL) aptamer biosensor via polymerase amplification is constructed for label-free detection of leukemia marker mRNA (miR-16). In order to achieve the ultrasensitive detection of the target mRNA, the cyclic target chain displacement polymerization of leukemia marker mRNA assisted with Klenow fragment of DNA polymerase is employed. The determination is carried out by recording the ECL emission of pyridine ruthenium (Ru(bpy)₃²⁺) complexes embedded into the assistance DNA (ADNA) loaded on the nanogold surface, after the hybridization reaction between the probe DNA (PDNA) and the remaining sequence of the CP's stem part, and the formation of a core-shell sun-like structure. The mercapto-modified capture DNA (CP) is immobilized on the surface of a magneto-controlled glassy carbon electrode by Au-S bond. The CP is opened and hybridized with the target mRNA to form double-stranded DNA. In the presence of polymerase, primer DNA, and bases (dNTPs), the primer chain gets access to its complementary sequence of the stem part and then triggers a polymerization of the DNA strand, leading to the release of mRNA and starting the next polymerization cycle. Finally, the composite of PDNA-covered and ADNA-covered (embedded with Ru(bpy)₃²⁺) gold nanoparticles (hereafter called AuNPs@(PDNA+ADNA-Ru(bpy)₃²⁺) is added, and the ECL intensity is recorded. Because of the polymerization cycle and the aggregation of the illuminator of Ru(bpy)₃²⁺, the detected signal is amplified significantly. The results showed that the corresponding ECL signal has a good linear relationship with a logarithm of target mRNA concentration in the range of 1 × 10^-16 to 1 × 10^-7 mol/L, with a detection limit of 4.3 × 10^-17 mol/L. The mRNA spiked in the human serum sample is determined, and the recoveries are from 97.2 to 102.0%. This sensor demonstrates good selectivity, stability, and reproducibility. Graphical abstract ᅟ.

Ultrasensitive electrochemical detection of miRNA based on DNA strand displacement polymerization and Ca2+-dependent DNAzyme cleavage

An ultrasensitive electrochemical sensing strategy for the detection of miRNA is developed combining strand displacement polymerization and a DNAzyme-catalyzed cleavage reaction.