Oriented assembly of invisible probes: towards single mRNA imaging in living cells

Nanostructure impact on electrocatalysis in gold nanodimers via electrochemiluminescence microscopy

This study explores the mechanism of enhanced electrochemiluminescence (ECL) due to the coupling effect in gold nanodimers (Au NDs) with precisely controlled interparticle distances via electrochemiluminescence microscopy (ECLM). Our research revealed that the enhancement in ECL was predominantly attributed to increased charge density and elevated electric fields resulting from overlapping electrochemical double layers. These findings offer new insights into the fundamental processes that govern nanostructure-mediated electrocatalysis, opening up exciting possibilities for future applications.

Medical and molecular biophysical techniques as substantial tools in the era of mRNA-based vaccine technology

The COVID-19 pandemic prompted the advancement of vaccine technology using mRNA delivery into the host cells. Consequently, mRNA-based vaccines have emerged as a practical approach against SARS-CoV-2 owing to their inherent properties, such as cost-effectiveness, rapid manufacturing, and preservation. These features are vital, especially in resource-constrained regions. Nevertheless, the design of mRNA-based vaccines is intricately intertwined with the refinement of biophysical technologies, thereby establishing their high potential. The preparation of mRNA-based vaccines involves a sequence of phases combining medical and molecular biophysical technologies. Furthermore, their efficiency depends on the capability to optimize their positive attributes, thus paving the way for their subsequent preclinical and clinical evaluations. Using biophysical techniques, the characterization of nucleic acids extends from their initial formulation to their cellular internalization abilities and encapsulation in biomolecule complexes, such as lipid nanoparticles (LNPs), for designing mRNA-based LNPs. Furthermore, nanoparticles are subjected to a series of careful screening steps to assess their physical and chemical characteristics before achieving an optimum formulation suitable for preclinical and clinical studies. This review provides a comprehensive understanding of the fundamental role of biophysical techniques in the complex development of mRNA-based vaccines and their role in the recent success during the COVID-19 pandemic.

Dark-field imaging and fluorescence dual-mode detection of microRNA-21 in living cells by core-satellite plasmonic nanoprobes

The in situ precise quantification and simultaneous imaging of low abundance microRNAs (miRNAs) within living cells is critical for cancer diagnosis, yet it remains a significant challenge. Leveraging the excellent sensitivity and spatiotemporal resolution of dark-field microscopy (DFM) and fluorescence imaging, we have successfully devised a novel detection approach using dual-signal reporter probes (DSRPs). These probes allow for highly sensitive detection of miRNA-21 in living cells via toehold-mediated strand displacement cascades. The DSRPs were constructed by Au nanoparticles and Ag nanoclusters core-satellite nanostructures. After the recognition of miRNA-21, the strand displacement cascades were triggered, inducing the disassembly of the Au/Ag core-satellite nanostructure with apparent scattering intensity decrease and peak wavelength shifts. Additionally, the fluorescence of Ag clusters could be recovered and further enhanced when in close proximity to specific guanine-rich strands. The dual-signal response capability enables the accurate detection of miRNA-21 from 1 fM to 1 nM, with a limit of detection reached 0.75 fM. DFM and fluorescent imaging of living cells efficiently confirms the applicable detection of miRNA-21 in complex detection media. The biosensor based on DSRPs represents a promising nanoplatform for visual monitoring and imaging of biomolecules in living cells, even at the single particle level.

CRISPR/Cas12a-Powered EC/FL Dual-Mode Controlled-Release Homogeneous Biosensor for Ultrasensitive and Cross-Validated Detection of Messenger Ribonucleic Acid

Accurate detection of cancer-associated mRNAs is beneficial to early diagnosis and potential treatment of cancer. Herein, for the first time, we developed a novel CRISPR/Cas12a-powered electrochemical/fluorescent (EC/FL) dual-mode controlled-release homogeneous biosensor for mRNA detection. A functionalized ssDNA P2-capped Fe3O4-NH2 loaded with methylene blue (P2@MB-Fe3O4-NH2) was synthesized as the signal probe, while survivin mRNA was chosen as the target RNA. In the presence of the target mRNA, the nicking endonuclease-mediated rolling circle amplification (NEM-RCA) was triggered to produce significant amounts of ssDNA, activating the collateral activity of Cas12a toward the surrounding single-stranded DNA. Thus, the ssDNA P1 completely complementary to ssDNA P2 was cleaved, resulting in that the ssDNA P2 bio-gate on Fe3O4-NH2 could not be opened due to electrostatic interactions. As a result, there was no or only a little MB in the supernatant after magnetic separation, and the measured EC/FL signal was exceedingly weak. On the contrary, the ssDNA P2 bio-gate was opened, enabling MB to be released into the supernatant, and generating an obvious EC/FL signal. Benefiting from the accuracy of EC/FL dual-mode cross-verification, high amplification efficiency, high specificity of NEM-RCA and CRISPR/Cas12a, and high loading of mesoporous Fe3O4-NH2 on signal molecules, the strategy shows aM-level sensitivity and single-base mismatch specificity. More importantly, the practical applicability of this dual-mode strategy was confirmed by mRNA quantification in complex serum environments and tumor cell lysates, providing a new way for developing a powerful disease diagnosis tool.

DNA-Programed Plasmon Rulers Decrypt Single-Receptor Dimerization on Cell Membrane

Decrypting the dynamics of receptor dimerization on cell membranes bears great importance in identifying the mechanisms regulating diverse cellular activities. In this regard, long-term monitoring of single-molecule behavior during receptor dimerization allows deepening insight into the dimerization process and tracking of the behavior of individual receptors, yet this remains to be realized. Herein, real-time observation of the receptor tyrosine kinases family (RTKs) at single-molecule level based on plasmon rulers was achieved for the first time, which enabled precise regulation and dynamic monitoring of the dimerization process by DNA programming with excellent photostability. Additionally, those nanoprobes demonstrated substantial application in the regulation of RTKs protein dimerization/phosphorylation and activation of downstream signaling pathways. The proposed nanoprobes hold considerable potential for elucidating the molecular mechanisms of single-receptor dimerization as well as the conformational transitions upon dimerization, providing a new paradigm for the precise manipulation and monitoring of specific single-receptor crosslink events in biological systems.

A Reversible Plasmonic Nanoprobe for Dynamic Imaging of Intracellular pH during Endocytosis

Understanding the pH evolution during endocytosis is essential for our comprehension of the fundamental processes of biology as well as effective nanotherapeutic design. Herein, we constructed a plasmonic Au@PANI core-shell...

Dual Imaging of Poly(ADP-ribose) Polymerase-1 and Endogenous H2O2 for the Diagnosis of Cancer Cells Using Silver-Coated Gold Nanorods

The imaging of tumor-related multitarget molecules is of great significance to raise the diagnostic accuracy for malignant tumors. Poly(ADP-ribose) polymerase-1 (PARP-1) has emerged as a potential clinical biomarker for tumor diagnosis due to its specific overexpression in cancer cells. High levels of H₂O₂ in the tumor microenvironment play vital roles in driving cancer progression. Inspired by these achievements, we employed a silver-coated gold nanorod (Au@Ag NR) as a plasmonic probe for dual imaging of intracellular PARP-1 and H₂O₂ under a dark-field microscope (DFM). Au@Ag NR was used not only to distinguish tumor cells from normal cells but also to induce the apoptosis of cancer cells owing to the etching of Ag shell by H₂O₂, accompanied by the color change from green to orange. On the other hand, Au@Ag NRs modified with active double-stranded DNA (dsDNA) could be utilized to image PARP-1 in cancer cells and quantitatively detect PARP-1 in vitro by naked eyes or DFM. The reason is that PARP-1 polymerized nicotinamideadenine dinucleotide (NAD⁺) into large and hyperbranched poly(ADP-ribose) polymer (PAR) on the surface of Au@Ag NRs, preventing the Ag shell from being etched by H₂O₂. As the PARP-1 activity increased, a blue-shift of the adsorption peak occurred along with a color change from pale pink to green, which could be recognized by naked eyes. Under DFM, its scattering light varied obviously from red to green. The proposed dual-imaging strategy holds good prospects in cancer diagnosis.

Individual Plasmonic Nanoprobes for Biosensing and Bioimaging: Recent Advances and Perspectives

With the advent of nanofabrication techniques, plasmonic nanoparticles (PNPs) have been widely applied in various research fields ranging from photocatalysis to chemical and bio-sensing. PNPs efficiently convert chemical or physical stimuli in their local environment into optical signals. PNPs also have excellent properties, including good biocompatibility, large surfaces for the attachment of biomolecules, tunable optical properties, strong and stable scattering light, and good conductivity. Thus, single optical biosensors with plasmonic properties enable a broad range of uses of optical imaging techniques in biological sensing and imaging with high spatial and temporal resolution. This work provides a comprehensive overview on the optical properties of single PNPs, the description of five types of commonly used optical imaging techniques, including surface plasmon resonance (SPR) microscopy, surface-enhanced Raman scattering (SERS) technique, differential interference contrast (DIC) microscopy, total internal reflection scattering (TIRS) microscopy, and dark-field microscopy (DFM) technique, with an emphasis on their single plasmonic nanoprobes and mechanisms for applications in biological imaging and sensing, as well as the challenges and future trends of these fields.

"Loading-type" Plasmonic Nanoparticles for Detection of Peroxynitrite in Living Cells

To date, plasmon resonance energy transfer (PRET)-based analytical approaches still inevitably suffer from limitations, such as lack of appropriate acceptor-donor pairs and the extra requirements of active groups of acceptors, which place great obstacles in extending the application of such methods, especially in the area of living cell studies. Herein, we design and fabricate a kind of "loading-type" plasmonic nanomaterials constituting gold nanoparticles as donors of PRET coated with mesoporous silicon, in which organic small molecules (CHCN) as acceptors of PRET were loaded (Au@MSN-CHCN). This "loading-type" strategy could conveniently integrate acceptor-donor pairs into one nanoparticle, so as to achieve the goal of sensitive detection of biomolecules in a complex physiological microenvironment. Based on the change of PRET efficiency of Au@MSN-CHCN induced by the specific reaction between CHCN and peroxynitrite (ONOO^-), ONOO^-, which plays an irreplaceable role in a series of physiological and pathological processes, is sensitively and selectively detected. Furthermore, in situ imaging of exogenous and endogenous ONOO^- in living cells was achieved even at a single nanoparticle level. This work provides a general approach to construct PRET probes for visualizing various biomolecules in living cells.

Activatable CRISPR Transcriptional Circuits Generate Functional RNA for mRNA Sensing and Silencing

CRISPR-dCas9 systems that are precisely activated by cell-specific information facilitate the development of smart sensors or therapeutic strategies. We report the development of an activatable dCas9 transcriptional circuit that enables sensing and silencing of mRNA in living cells using hybridization-mediated structure switching for gRNA activation. The gRNA is designed with the spacer sequence blocked by a hairpin structure, and mRNA hybridization induces gRNA structure switching and activates the transcription of reporter RNA. An mRNA sensor developed using a light-up RNA reporter shows high sensitivity and fast-response imaging of survivin mRNA in cells under drug treatments and different cell lines. Furthermore, a feedback circuit is engineered by incorporating a small hairpin RNA in the reporter RNA, demonstrating a smart strategy for dynamic sensing and silencing of survivin with induced tumor cell apoptosis. This circuit illustrates a broadly applicable platform for the development of cell-specific sensing and therapeutic strategies.

Single-Particle Assay of Poly(ADP-ribose) Polymerase-1 Activity with Dark-Field Optical Microscopy

Poly(ADP-ribose) polymerase-1 (PARP-1), over expression in vast majority of cancer cells, is a potential biomarker for clinical diagnosis. However, very limited detection methods have been developed so far, especially for in situ intracellular imaging. Here, we developed a spectral-resolved single-particle detection method for detection of PARP-1 in vitro and in situ intracellular imaging with dark-field microscopy (DFM). A gold nanoparticle (50 nm) modified with active DNA duplex (Au₅₀-dsDNA) was used as a scattering probe. Under the function of active dsDNA, PARP-1 catalyzed to synthesize the hyperbranched poly (ADP-ribose) polymer (PAR) by using nicotinamideadenine dinucleotide as substrates, forming Au₅₀-dsDNA@PAR. Then, negatively charged PAR adsorbed positively charged AuNPs (8 nm) to form Au₅₀-dsDNA@PAR@Au₈. As a result, a notable red shift occurred in localized surface plasmon resonance scattering spectra of Au₅₀, accompanying with obvious color change. Thus, PARP-1 has been detected with a linear range from 0.2 to 10 mU based on the scattering spectra change. The detection limit was 2 orders of magnitude lower than previously reported methods. Probes showed distinct different colors in cancer cells and normal cells, realizing in situ imaging of intracellular PARP-1 at a single-particle level. Compared with previously reported fluorescence imaging methods, the proposed strategy avoided sophisticated label procedures, which has great potential to be used for clinical diagnosis and PARP-1 inhibitor research.

Activated Plasmonic Nanoaggregates for Dark-Field in Situ Imaging for HER2 Protein Imaging on Cell Surfaces

Dark-field microscopy (DFM) based on localized surface plasmon resonance (LSPR) was used for observation of experimental phenomena, which is a hopeful nondamaging and non-photobleaching biological imaging technique. In this strategy, plasma nanoaggregates with stronger scattering efficiency were formed in the presence of the target, causing a "turn-on" phenomenon, when asymmetry modified AuNPs were introduced as probes with zero LSPR background. First, Au₁-N₃ probe and Au₂-C≡C probe were designed for the cycloaddition between azide and alkyne to form AuNP dimers under catalytic action by Cu⁺, which was obtained from the reduction of Cu²⁺ by sodium ascorbate. The two kinds of probes were successfully used for the detection of Cu²⁺ in rat serum. Then, to apply this concept to protein on cells, DNA and antibody were modified on the probes. DNA1/Au₁-N₃ probe and anti-HER2/Au₂-C≡C probe were proposed for HER2 protein DFM on cells. By designing an aptamer sequence in primer, the rolling circle amplification (RCA) was introduced in HER2 DFM on cells, and the image signal was much brighter than that from no-RCA. The unique design made it easier to discriminate the target signal from background noise in cell DFM. This method might be used in the fields of molecular diagnostics and cell imaging.

A single promoter system co-expressing RNA sensor with fluorescent proteins for quantitative mRNA imaging in living tumor cells

Genetically encoded light-up RNA aptamers afford a valuable platform for developing RNA sensors toward live cell imaging. However, quantitative imaging of intracellular RNAs remains a grand challenge. Here we reported a novel genetically encoded RNA sensor strategy using a plasmid that expresses a splittable fusion of the RNA sensor and the GFP mRNA in an individual transcript using a single promoter system. This splittable fusion design enables synchronous co-expression of the RNA sensor with GFP mRNA while alleviates the interference with correct folding of RNA aptamers due to intramolecular hybridization. This single-promoter system is applied to ratiometric imaging of survivin mRNA in tumor cells. The results reveal that the ratiometric images dynamically correlated with survivin mRNA concentrations and allow quantitative imaging of survivin mRNA in different tumor cells. The RNA sensor strategy may provide a new paradigm for developing a robust imaging platform for quantitative mRNA studies in living cells.

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.

Dynamic Single Molecular Rulers: Toward Quantitative Detection of MicroRNA-21 in Living Cells

Innovative techniques to measure microRNA (miRNA) in vivo could greatly improve the fundamental understanding of complex cellular processes. Herein, we report a novel method for real-time, quantitative miRNA detection inside living cells based on core-satellite plasmon rulers (PRs). This approach allows for the statistical analysis of single hybridization event caused by target miRNA. We investigated hundreds of satellite leaving events and found that the distribution of the time range for one strand displacement event is miRNA concentration-dependent, which obeyed Poisson statistics. Probing several such PRs under dark-field microscopy would provide precise determination of miRNA in vitro and in living cells, without photobleaching or blinking of the fluorophores. We believe the simple and practical approach on the basis of dynamic PRs with single-molecule sensitivity combined with statistical analysis hold promising potential to visualize native nucleic acids with short sequence and low-abundance.

Exploration of the Kinetics of Toehold-Mediated Strand Displacement via Plasmon Rulers

DNA/RNA strand displacement is one of the most fundamental reactions in DNA and RNA circuits and nanomachines. In this work, we reported an exploration of the dynamic process of the toehold-mediated strand displacement via core-satellite plasmon rulers at the single-molecule level. Applying plasmon rulers with unlimited lifetime, single-strand displacement triggered by the invader that resulted in stepwise leaving of satellite from the core was continuously monitored by changes of scattering signal for hours. The kinetics of strand displacement in vitro with three different toehold lengths have been investigated. Also, the study revealed the difference in the kinetics of strand displacement between DNA/RNA and DNA/DNA duplexes. For the kinetics study in vivo, influence from the surrounding medium has been evaluated using both phosphate buffer and cell lysate. Applying core-satellite plasmon rulers with high signal/noise ratio, kinetics study in living cells proceeded for the first time, which was not possible by conventional methods with a fluorescent reporter. The plasmon rulers, which are flexible, easily constructed, and robust, have proven to be effective tools in exploring the dynamical behaviors of biochemical reactions in vivo.

A low cost mobile phone dark-field microscope for nanoparticle-based quantitative studies

Dark-field microscope (DFM) analysis of nanoparticle binding signal is highly useful for a variety of research and biomedical applications, but current applications for nanoparticle quantification rely on expensive DFM systems. The cost, size, limited robustness of these DFMs limits their utility for non-laboratory settings. Most nanoparticle analyses use high-magnification DFM images, which are labor intensive to acquire and subject to operator bias. Low-magnification DFM image capture is faster, but is subject to background from surface artifacts and debris, although image processing can partially compensate for background signal. We thus mated an LED light source, a dark-field condenser and a 20× objective lens with a mobile phone camera to create an inexpensive, portable and robust DFM system suitable for use in non-laboratory conditions. This proof-of-concept mobile DFM device weighs less than 400g and costs less than $2000, but analysis of images captured with this device reveal similar nanoparticle quantitation results to those acquired with a much larger and more expensive desktop DFMM system. Our results suggest that similar devices may be useful for quantification of stable, nanoparticle-based activity and quantitation assays in resource-limited areas where conventional assay approaches are not practical.

DNAzyme Based Nanomachine for in Situ Detection of MicroRNA in Living Cells

The capability of in situ detection of microRNA in living cells with signal amplification strategy is of fundamental importance, and it will open up a new opportunity in development of diagnosis and prognosis of many diseases. Herein we report a swing DNA nanomachine for intracellular microRNA detection. The surfaces of Au nanoparticles (NPs) are modified by two hairpin DNA. We observe that one DNA (MB2) will open its hairpin structure upon partial hybridization with target miR-21 after entering into cells, and the other part of its hairpin structure could further react with the other hairpin DNA (MB1) to form a Zn²⁺-specific DNAzyme. This results in the disruption of MB1 through shearing action and the release of fluorescein Cy5. To provide an intelligent DNA nanomachine, MB2 is available again with the shearing action to bind with MB1, which provides effective signal amplification. This target-responsive, DNA nanomachine-based method showed a detection limit of 0.1 nM in vitro, and this approach could be an important step toward intracellular amplified detection and imaging of various analytes in living cells.

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.

Analytical methods based on the light-scattering of plasmonic nanoparticles at the single particle level with dark-field microscopy imaging

This minireview summarizes analytical methods based on the light-scattering of gold nanoparticles with the dark-field microscopy imaging technique at the single particle level.

Noise Reduction Method for Quantifying Nanoparticle Light Scattering in Low Magnification Dark-Field Microscope Far-Field Images

Nanoparticles have become a powerful tool for cell imaging and biomolecule, cell and protein interaction studies, but are difficult to rapidly and accurately measure in most assays. Dark-field microscope (DFM) image analysis approaches used to quantify nanoparticles require high-magnification near-field (HN) images that are labor intensive due to a requirement for manual image selection and focal adjustments needed when identifying and capturing new regions of interest. Low-magnification far-field (LF) DFM imagery is technically simpler to perform but cannot be used as an alternate to HN-DFM quantification, since it is highly sensitive to surface artifacts and debris that can easily mask nanoparticle signal. We now describe a new noise reduction approach that markedly reduces LF-DFM image artifacts to allow sensitive and accurate nanoparticle signal quantification from LF-DFM images. We have used this approach to develop a "Dark Scatter Master" (DSM) algorithm for the popular NIH image analysis program ImageJ, which can be readily adapted for use with automated high-throughput assay analyses. This method demonstrated robust performance quantifying nanoparticles in different assay formats, including a novel method that quantified extracellular vesicles in patient blood sample to detect pancreatic cancer cases. Based on these results, we believe our LF-DFM quantification method can markedly decrease the analysis time of most nanoparticle-based assays to impact both basic research and clinical analyses.

Plasmon-induced light concentration enhanced imaging visibility as observed by a composite-field microscopy imaging system

The plasmon-induced light concentration (PILC) effect, which has been supposed to be responsible for lots of linear and nonlinear enhanced optical signals such as Raman and high-harmonic generation, is hard to directly observe. Herein, we developed a scattered light based composite-field microscopy imaging (iCFM) system by coupling the oblique and vertical illumination modes, which were adopted in dark- and bright-field microscopy imaging systems, respectively, and through which iCFM system monochromatic background (MCB) images are available, to directly observe the PILC effect in far-field scattering microscopy imaging. Owing to the PILC effect, the scattering signal gain of plasmonic nanoparticles was found to be larger than that of the background, and the imaging visibility of plasmonic nanoparticles was improved by 2.4-fold for silver nanoparticles (AgNPs) and 1.6-fold for gold nanorods (AuNRs). Successful observation of the PILC effect visually together with application in enhanced visibility in cancer cell imaging by this composite illumination system might open an exciting prospect of light scattering microscopy imaging techniques with largely increased visibility.

Plasmonic nanohalo optical probes for highly sensitive imaging of survivin mRNA in living cells

A novel strategy for sensitive detection of survivin mRNA based on Rayleigh light scattering spectroscopy of AuNP nanohalo probes.

Distance mediated electrochemiluminescence enhancement of CdS thin films induced by the plasmon coupling of gold nanoparticle dimers

Theoretical and experimental studies of plasmon enhanced electrochemiluminescence of CdS QDs by gold nanoparticle monomers and dimers.