Quantification of mRNA in Single Cells Based on Dimerization-Induced Photoluminescence Nonblinking of Quantum Dots

Photoluminescence (PL) intermittency (or "blinking") is a unique characteristic of single quantum dot (QD) emission. Here, we report a novel single-molecule detection strategy for the intracellular mRNA of interest using the mRNA-induced nonblinking QD dimers as probes. The working principle of the method is that the DNA hybrid of the target DNA (or mRNA) with a biotin-modified ssDNA probe can induce two blinking streptavidin-modified QDs (SAV-QDs) conjugated. The formed QD dimer as a bright spot showed a nonblinking emission property, observed with total inner reflection fluorescence microscopy (TIRFM). In theory, one nonblinking spot indicated a target DNA (or mRNA). The experimental results from single-spot fluorescence trajectory analysis and single-particle brightness analysis based on TIRFM and fluorescence correlation spectroscopy (FCS) techniques verified this dimerization process of QDs or its induced nonblinking emission. Employing a target DNA with the same base sequences to Survivin mRNA as a model, the detection strategy was used to detect the target DNA concentration based on the linear relationship between the percentage of the nonblinking spots and the target DNA concentration. This single-molecule detection strategy was also successfully used for determining Survivin mRNA in a single HeLa cell. The method can simplify the hybridization steps, eliminate self-quenching and photobleaching of fluorophores, and reduce the influence of unspecific binding on the detection.

A novel binding-induced DNAzyme motor triggered by survivin mRNA

The accurate and sensitive detection of survivin mRNA is of great significance for cancer diagnosis and treatment. However, limited by the low-abundance mRNA in live cells, most strategies of survivin mRNA detection that were one-to-one signal-triggered model (one target triggered one signal) were inapplicable in practice. Here, we reported a binding-induced DNAzyme motor triggered by the survivin mRNA, which was a one-to-more signal-triggered model (one target triggered more signals), amplifying the detection signal and enhancing the sensitivity. The nanomotor is constructed by assembling several DNAzyme motor strands silenced by the blocker strands, and dozens of FAM-labeled substrate strands on a single gold nanoparticle (AuNP), forming three-dimensional DNA tracks. Through building the survivin mRNA bridge between the blocker and the DNAzyme motor strand, the binding-induced DNA nanomotor could be triggered by survivin mRNA. The operation of the DNAzyme motor was self-powered. And each walking step of the DNAzyme motor was fueled by DNAzyme-catalyzed substrate cleavage, along with the cleavage of the fluorescent molecule, resulting in autonomous and progressive walking along the AuNP-based tracks, and the fluorescence increase. The DNAzyme motor exhibited excellent sensitivity and remarkable specificity for survivin mRNA, providing the potential for cell image.

Upconversion Luminescence-Initiated and GSH-Responsive Self-Driven DNA Motor for Automatic Operation in Living Cells and In Vivo

In light of the worthy design flexibility and the good signal amplification capacity, the recently developed DNA motor (especially the DNA walker)-based fluorescent biosensors can offer an admirable choice for realizing bioimaging. However, this attractive biosensing strategy not only has the disadvantage of uncontrollable initiation but also usually demands the supplement of exogenous driving forces. To handle the above obstacles, some rewarding solutions are proposed here. First, on the surface of an 808 nm near-infrared light-excited low-heat upconversion nanoparticle, a special ultraviolet upconversion luminescence-initiated three-dimensional (3D) walking behavior is performed by embedding a photocleavage linker into the sensing elements, and such light-controlled target recognition can perfectly overcome the pre-triggering of the biosensor during the biological delivery to significantly boost the sensing precision. After that, a peculiar self-driven walking pattern is constructed by employing MnO₂ nanosheets as an additional nanovector to physically absorb the sensing frame, for which the reduction of the widespread glutathione in the biological medium can bring about sufficient self-supplied Mn²⁺ to guarantee the walking efficiency. By selecting an underlying next-generation broad-spectrum cancer biomarker (survivin messenger RNA) as the model target, we obtain that the newly formed autonomous 3D DNA motor shows a commendable sensitivity (where the limit of detection is down to 0.51 pM) and even an outstanding specificity for distinguishing single-base mismatching. Beyond this sound assay performance, our sensing approach is capable of working as a powerful imaging platform for accurately operating in various living specimens such as cells and bodies, showing a favorable diagnostic ability for cancer care.

Algorithm-Assisted Detection and Imaging of microRNAs in Living Cancer Cells via the Disassembly of Plasmonic Core-Satellite Probes Coupled with Strand Displacement Amplification

Acute detection and high-resolution imaging of microRNAs (miRNAs) in living cancer cells have attracted great attention in clinical diagnosis and therapy. However, current methods suffer from low detection sensitivity or heavy dependence on expensive and sophisticated spectrometers. Herein, a novel algorithm-assisted system of detecting and imaging miRNAs in living cancer cells was developed via the disassembly of plasmonic core-satellite probes coupled with strand displacement amplification (SDA). The target miRNAs in the system could trigger the disassembly of plasmonic core-satellite probes, leading to the color change in the scattering light of the probes, which could be captured by dark-field microscopy (DFM). The concentration of the target miRNAs was obtained by analyzing the dark-field image based on the proposed algorithm with a detection limit of 2 pM for miRNA-21. Thus, the performance in terms of simplicity and sensitivity of the system compared with one of the conventional spectrophotometers was well presented, which could inspire more clinical applications of inexpensive, intelligent, and rapid screening of cancer cells. The application software based on the proposed algorithm running on the Android platform was also developed, demonstrating the potential of remote diagnosis.

A DNA-functionalized biomass nanoprobe for the targeted photodynamic therapy of tumor and ratiometric fluorescence imaging-based visual cancer cell identification/antitumor drug screening

Survivin is widely expressed in tumor tissue, in which the in situ ratiometric fluorescence imaging of intracellular survivin mRNA can provide accurate information for the diagnosis and treatment of cancers, as well as the screening of antitumor drugs. However, the development of a nanoprobe that can be used simultaneously in the diagnosis and treatment of tumors and the screening of antitumor drugs remains a challenge. In an effort to address these requirements, a multifunctional biomass nanoprobe was developed for the photodynamic therapy (PDT) of tumors as well as cancer cell identification and antitumor drug screening based on the ratiometric fluorescence imaging of intracellular survivin mRNA. This nanoprobe was assembled from near-infrared (NIR) biomass quantum dots (BQDs), single-stranded DNA and NIR dye (dylight680) labeled single-stranded DNA. The BQDs contain a large number of chlorophyll molecules, meaning that they can produce a large amount of singlet oxygen under NIR light irradiation, thus realizing the PDT of a tumor. However, the specific binding of the nanoprobe to intracellular survivin mRNA causes the release of dylight680 and reduces the fluorescence resonance energy transfer (FRET) efficiency between the BQDs and dylight680 in the probe, thereby achieving the ratiometric fluorescence imaging of survivin mRNA. Therefore, the prepared nanoprobe can not only be used in the diagnosis of cancers, but also in the targeted PDT of tumors.

In vivo mRNA imaging based on tripartite DNA probe mediated catalyzed hairpin assembly

Herein, we develop a novel tripartite DNA probe to transport phosphorothioated substrate hairpins and an aptamer for the intramolecular CHA circuit, which achieves detection of a low amount of specific mRNA in living cells and mice. Our study provides an improved strategy to promote in vivo fluorescence imaging applications in early-stage clinical diagnosis.

Metallic Nanoparticle-Based Optical Cell Chip for Nondestructive Monitoring of Intra/Extracellular Signals

The biosensing platform is noteworthy for high sensitivity and precise detection of target analytes, which are related to the status of cells or specific diseases. The modification of the transducers with metallic nanoparticles (MNPs) has attracted attention owing to excellent features such as improved sensitivity and selectivity. Moreover, the incorporation of MNPs into biosensing systems may increase the speed and the capability of the biosensors. In this review, we introduce the current progress of the developed cell-based biosensors, cell chip, based on the unique physiochemical features of MNPs. Mainly, we focus on optical intra/extracellular biosensing methods, including fluorescence, localized surface plasmon resonance (LSPR), and surface-enhanced Raman spectroscopy (SERS) based on the coupling of MNPs. We believe that the topics discussed here are useful and able to provide a guideline in the development of new MNP-based cell chip platforms for pharmaceutical applications such as drug screening and toxicological tests in the near future.

Advances in DNA/RNA detection using nanotechnology

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.

Crosslinking catalytic hairpin assembly for high-contrast imaging of multiple mRNAs in living cells

A novel DNA nanotetrad mediated crosslinking catalytic hairpin assembly has been developed for high-contrast imaging of multiple mRNAs in living cells.

Plasmon Coupling Effect-Enhanced Imaging of Metal Ions in Living Cells Using DNAzyme Assembled Core-Satellite Structures

We demonstrate a core-satellite plasmonic nanoprobe assembled via metal-ion-dependent DNA-cleaving DNAzyme linker for imaging intercellular metal ion based on plasmon coupling effect at a single-particle level. As metal ions are present in the system, the DNAzyme linker will be cleaved, and thus, disassembly of the core-satellite nanoprobes occurs, which results in distinct blue shift of the scattering spectra of Au core-satellite probes and naked color change of the scattering light. This change in scattering spectra has been supported by theoretical simulations. As a proof of concept, sensitive detection of Cu²⁺ with a limit of detection down to 67.2 pM has been demonstrated. The nanoprobes have been further utilized for intracellular Cu²⁺ imaging in living cells. The results demonstrate that the present strategy provides a promising platform for detection and imaging of metal ions in living cells and could be potentially applied to imaging other interesting target molecules simply by substituting the oligonucleotide sequence.

Ultrasensitive MicroRNA Assay via Surface Plasmon Resonance Responses of Au@Ag Nanorods Etching

Quantification of trace serum circulate microRNAs is extremely important in clinical diagnosis but remains a great challenge. Herein we developed an ultrasensitive platform for microRNA 141 (miR-141) detection based on a silver coated gold nanorods (Au@Ag NRs) etching process accompanied by surface plasmon resonance (SPR) shift. Both SPR absorption and scattering responses were monitored. Combined amplification cascades of catalyzed hairpin assembly (CHA) and hybridization chain reaction (HCR) with the sensitive SPR responses of plasmonic Au@Ag NRs, the proposed bioassay exhibited ultrahigh sensitivity toward miRNA-141 with dynamic range from 5.0 × 10^-17 M to 1.0 × 10^-11 M. With target concentration higher than 1.0 × 10^-13 M, the color of the solution changed obviously that could be observed with naked eyes. Under dark-field microscopy observation of individual particle, a limit of detection down to 50 aM could be achieved. Owing to the superior sensitivity and selectivity, the proposed method was applied to detecting trace microRNA in serum. Similar SPR assays could be developed simply by redesigning the switching aptamer for the detections of other microRNAs or targets such as small molecule, DNA, or protein. Considering the convenient operation, good performance and simple observation modes of this method, it may have great potential in trace bioanalysis for clinical applications.

In Situ Detection and Imaging of Telomerase Activity in Cancer Cell Lines via Disassembly of Plasmonic Core-Satellites Nanostructured Probe

The label-free localized surface plasmon resonance (LSPR) detection technique has been identified as a powerful means for in situ investigation of biological processes and localized chemical reactions at single particle level with high spatial and temporal resolution. Herein, a core-satellites assembled nanostructure of Au₅₀@Au₁₃ was designed for in situ detection and intracellular imaging of telomerase activity by combining plasmonic resonance Rayleigh scattering spectroscopy with dark-field microscope (DFM). The Au₅₀@Au₁₃ was fabricated by using 50 nm gold nanoparticles (Au₅₀) as core and 13 nm gold nanoparticles (Au₁₃) as satellites, both of them were functionalized with single chain DNA and gathered proximity through the highly specific DNA hybridization with a nicked hairpin DNA (O1) containing a telomerase substrate (TS) primer as linker. In the presence of telomerase, the telomeric repeated sequence of (TTAGGG)_n extended at the 3'-end of O1 would hybridized with its complementary sequences at 5'-ends. This led the telomerase extension product of O1 be folded to form a rigid hairpin structure. As a result, the Au₅₀@Au₁₃ was disassembled with the releasing of O1 and Au₁₃-S from Au₅₀-L, which dramatically decreased the plasmon coupling effect. The remarkable LSPR spectral shift was observed accompanied by a detectable color change from orange to green with the increase of telomerase activity at single particle level with a detection limit of 1.3 × 10^-13 IU. The ability of Au₅₀@Au₁₃ for in situ imaging intracellular telomerase activity, distinguishing cancer cells from normal cells, in situ monitoring the variation of cellular telomerase activity after treated with drugs were also demonstrated.