Fluorescent-Raman Binary Star Ratio Probe for MicroRNA Detection and Imaging in Living Cells

Tailoring strategies of SERS tags-based sensors for cellular molecules detection and imaging

As an emerging nanoprobe, surface enhanced Raman scattering (SERS) tags hold significant promise in sensing and bioimaging applications due to their attractive merits of anti-photobleaching ability, high sensitivity and specificity, multiplex, and low background capabilities. Recently, several reviews have proposed the application of SERS tags in different fields, however, the specific sensing strategies of SERS tags-based sensors for cellular molecules have not yet been systematically summarized. To provide beneficial and comprehensive insights into the advanced SERS tags technique at the cellular level, this review systematically elaborated on the latest advances in SERS tags-based sensors for cellular molecules detection and imaging. The general SERS tags-based sensing strategies for biomolecules and ions were first introduced according to molecular classes. Then, aiming at such molecules located in the extracellular, cellular membrane and intracellular regions, the tailored strategies by designing and manipulating SERS tags were summarized and explored through several key examples. Finally, the challenges and perspectives of developing high performance of advanced SERS tags were briefly discussed to provide effective guidance for further development and extended applications.

Face-to-face Assembly Strategy of Au Nanocubes: Induced Generation of Broad Hotspot Regions for SERS-Fluorescence Dual-Signal Detection of Intracellular miRNAs

While designing anisotropic noble metal nanoparticles (NPs) can enhance the signal intensity of Raman dyes, more sensitive surface-enhanced Raman scattering (SERS) probes can be designed by oriented self-assembly of noble metal nanomaterials into dimers or higher-order nanoclusters. In this study, we engineered a self-assembly strategy in living cells for real-time fluorescence and SERS dual-channel detection of intracellular microRNAs (miRNAs), using Mg2+-dependent 8-17E DNAzyme sequences as the driving motors, gold nanocubes (AuNCs) as the driver components, and three-branched double-stranded DNA as the linking tool. The assembly selects adenine in DNA as a reporter molecule, simplifying the labeling process of Raman reporter molecules and reducing the synthesis process. In addition, adenine is stably distributed between the faces of AuNCs and the wide hotspot region gives good reproducibility of the adenine SERS signal. In this strategy, the SERS channel was consistently stable and more sensitive compared to the fluorescence channel. Among them, the detection limit of the SERS channel was 2.1 pM and the coefficient of variation was 1.26% in the in vitro liquid phase and 1.49% in MCF-7 cells. The strategy successfully achieved accurate tracking and quantification of miRNA-21 in cancer cells, showing good reproducibility in complex samples as well as cells. The reported strategy provides ideas for exploring intracellular specific triggering of nanoparticles for precise control of self-assembly.

SERS-based methods for the detection of genomic biomarkers of cancer

Genomic biomarkers of cancer are based on changes in nucleic acids, which include abnormal expression levels of some miRNAs, point mutations in DNA sequences, and altered levels of DNA methylation. The presence of tumor-related nucleic acids in body fluids (blood, saliva, or urine) makes it possible to achieve a non-invasive early-stage cancer diagnosis. Currently existing techniques for the discovery of nucleic acids require complex, time-consuming, costly assays and have limited multiplexing abilities. Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopy technique that is able to provide molecular specificity combined with trace sensitivity. SERS has gained research attention as a tool for the detection of nucleic acids because of its promising potential: label-free SERS can decrease the complexity of assays currently used with fluorescence-based detection due to the absence of the label, while labeled SERS may outperform the gold standard in terms of the multiplexing ability. The first papers about SERS-based methods for the measurement of genomic biomarkers were written in 2008, and since then, more than 150 papers have been published. The aim of this paper is to review and evaluate the proposed SERS-based methods in terms of their level of development and their potential for liquid biopsy application, as well as to contribute to their further evolution by attracting research attention to the field. This goal will be reached by grouping, on the basis of their experimental protocol, all the published manuscripts on the topic and evaluating each group in terms of its limit of detection and applicability to real body fluids. Thus, the methods are classified according to their working principles into five main groups, including capture-based, displacement-based, sandwich-based, enzyme-assisted, and specialized protocols.

Recent Advances in the DNA-Mediated Multi-Mode Analytical Methods for Biological Samples

DNA-mediated nanotechnology has become a research hot spot in recent decades and is widely used in the field of biosensing analysis due to its distinctive properties of precise programmability, easy synthesis and high stability. Multi-mode analytical methods can provide sensitive, accurate and complementary analytical information by merging two or more detection techniques with higher analytical throughput and efficiency. Currently, the development of DNA-mediated multi-mode analytical methods by integrating DNA-mediated nanotechnology with multi-mode analytical methods has been proved to be an effective assay for greatly enhancing the selectivity, sensitivity and accuracy, as well as detection throughput, for complex biological analysis. In this paper, the recent progress in the preparation of typical DNA-mediated multi-mode probes is reviewed from the aspect of deoxyribozyme, aptamer, templated-DNA and G-quadruplex-mediated strategies. Then, the advances in DNA-mediated multi-mode analytical methods for biological samples are summarized in detail. Moreover, the corresponding current applications for biomarker analysis, bioimaging analysis and biological monitoring are introduced. Finally, a proper summary is given and future prospective trends are discussed, hopefully providing useful information to the readers in this research field.

Nucleic Acid Probes in Bio-Imaging and Diagnostics: Recent Advances in ODN-Based Fluorescent and Surface-Enhanced Raman Scattering Nanoparticle and Nanostructured Systems

Raman nanoparticle probes are a potent class of optical labels for the interrogation of pathological and physiological processes in cells, bioassays, and tissues. Herein, we review the recent advancements in fluorescent and Raman imaging using oligodeoxyribonucleotide (ODN)-based nanoparticles and nanostructures, which show promise as effective tools for live-cell analysis. These nanodevices can be used to investigate a vast number of biological processes occurring at various levels, starting from those involving organelles, cells, tissues, and whole living organisms. ODN-based fluorescent and Raman probes have contributed to the achievement of significant advancements in the comprehension of the role played by specific analytes in pathological processes and have inaugurated new possibilities for diagnosing health conditions. The technological implications that have emerged from the studies herein described could open new avenues for innovative diagnostics aimed at identifying socially relevant diseases like cancer through the utilization of intracellular markers and/or guide surgical procedures based on fluorescent or Raman imaging. Particularly complex probe structures have been developed within the past five years, creating a versatile toolbox for live-cell analysis, with each tool possessing its own strengths and limitations for specific studies. Analyzing the literature reports in the field, we predict that the development of ODN-based fluorescent and Raman probes will continue in the near future, disclosing novel ideas on their application in therapeutic and diagnostic strategies.

Trimer structures formed by target-triggered AuNPs self-assembly inducing electromagnetic hot spots for SERS-fluorescence dual-signal detection of intracellular miRNAs

Accurate quantitative, in situ and temporal tracking imaging of tumor-associated miRNAs in living cells could provide a basis for cancer diagnosis and prognosis. In this strategy, a surface-enhanced Raman scattering (SERS)-fluorescence (FL) dual-spectral sensor (DSS) was constructed based on the nanoscale photophysical properties of AuNPs, mediated by functionalized DNA, to achieve rapid imaging of FL and accurate SERS quantification of intracellular miRNAs. The dual-spectrum sensor in the strategy is highly sensitive, specific and reproducibly stable. The LOD values of the dual spectra were 3.58 pM (SERS) as well as 11.8 pM (FL) with RSD values less than 2.69%. The bispectral sensor self-assembled into a trimer by the lapidation of Y-type DNA under the excitation of the target, generating a stable enhanced electric field coupling; and selected adenine located in the enhanced electric field as the reporter molecule, simplifying the labeling process and variables of the Raman reporter molecule, distinguishing it from other traditional methods. This strategy successfully achieved accurate tracking and quantification of miR-21 in cancer cells and showed good stability in the cells. The reported probes are potential tools for reliable monitoring of biomolecular dynamics in living cells.

Functionalized photosensitive metal-organic framework as a theranostic nanoplatform for turn-on detection of MicroRNA and photodynamic therapy

Developing a theranostic platform integrating precise diagnostic and efficient treatment is significant but challenging. Here, we reported a new theranostic platform - hairpin probe - photosensitizing MOFs (HPMOF) composed of photosensitizing MOFs (PMOFs) and hairpin probes labeled with fluorophore and quencher, in which PMOF played the role of photosensitizer and nanocarrier of the hairpin probe. The HPMOF was covered with a layer of ZIF-8 to achieve the dual-layered nanotheranostics (HPMOF@ZIF-8). The HPMOF@ZIF-8 achieved high DNA loading capacity and intracellular delivery for tumor-related miRNA imaging. Moreover, HPMOF@ZIF-8 could generate reactive oxygen species with high efficiency, which induced cell apoptosis, leading to efficient photodynamic therapy. Due to the different expression of miRNA between normal cells and cancer cells, the HPMOF@ZIF-8 could recognize cancer cells through imaging of miRNA, leading to more accurate treatment of cancer, providing a promising theranostic nanoplatform.

Three-Dimensional Surface-Enhanced Raman Scattering Platform with Hotspots Built by a Nano-mower for Rapid Detection of MRSA

Methicillin-resistant Staphylococcus aureus (MRSA) has become one of the greatest threats to human health due to its strong drug resistance, wide distribution range, and high infection rate. Rapid identification of MRSA strains is very important for accurate diagnosis and early treatment of MRSA infections. Here, we introduced an Exo III-assisted nanomotor mower to build 3D hotspots for rapid detection of MRSA by surface-enhanced Raman scattering (SERS). As the bacteria bound to the aptamer, two trigger chains were released from the double-stranded structure, and the nano-mowers were activated by opening a hairpin probe on gold nanoparticles (AuNPs). With the continued cleavage of Exo III and cyclic release of the trigger chain, multiple hairpin DNAs on the AuNPs were cleaved to increase the motor power. The resulting nano-mower continued slicing protective DNA from larger AuNPs, exposing the AuNPs. Without the protection of DNA, Mg²⁺ in the buffer induced spontaneous aggregation of the AuNPs, and a large number of hotspots were formed for SERS measurements. Under optimal conditions, MRSA can be detected within 40 min, and the concentration of MRSA showed a good linear relationship with the SERS intensity at 1342 cm^-1, with a limit of detection as low as 1 CFU/mL and a wide linear range (10⁰ to 10⁷ CFU/mL). This strategy creates a rapid bacterial detection method that performs well on actual samples utilizing portable Raman spectroscopy instruments, with potential applications in food detection, water detection, clinical treatment, and diagnosis.

Fluorescence-Raman dual-mode quantitative detection and imaging of small-molecule thiols in cell apoptosis with DNA-modified gold nanoflowers

The monitoring of small-molecule thiols (especially glutathione) has attracted widespread attention due to their involvement in numerous physiological processes in living organisms and cells. In this work, a dual-mode nanosensor was designed to detect small-molecule thiols, which is based on the "on-off" switch of fluorescence resonance energy transfer (FRET) and surface-enhanced Raman scattering (SERS). Briefly, DNA was modified by Cy5 (signal probe) and disulfide bonds (recognition element). Gold nanoflowers (AuNFs) were used as the fluorescence-quenching and SERS-enhancing substrate. However, small-molecule thiols can cleave disulfide bonds and release short Cy5-labeled chains, causing the recovery of the fluorescence signal and a decrease of the SERS signal. The nanosensor showed a sensitive response to small-molecule thiols represented by GSH, with a linear range of 0.01-3 mM and a detection limit of 913 nM. In addition, it competed with other related biological interferences and presented good stability and better selectivity towards small-molecule thiols. Most importantly, the developed nanosensor had been successfully applied to in situ imaging and quantitative monitoring of the concentration of small-molecule thiols which changed during T-2 toxin-induced apoptosis in HeLa cells. Meanwhile, nanosensors are also versatile with their potential applications and can be easily extended to the detection and imaging of other human cell lines. The proposed method combines the dual advantages of fluorescence and SERS, which has broad prospects for in situ studies of physiological processes involving small-molecule thiols in biological systems.

Highly Selective and Sensitive microRNA-210 Assay Based on Dual-Signaling Electrochemical and Photocurrent-Polarity-Switching Strategies

Highly sensitive and selective microRNA (miRNA) assay is of great significance for disease diagnosis and therapy. Herein, a magnetic-assisted electrochemistry (EC)-photoelectrochemistry (PEC) dual-mode biosensing platform was developed for miRNA-210 detection based on dual-signaling EC and photocurrent-polarity-switching PEC strategies. Porous magnetic Fe₃O₄ octahedra with a large surface area were synthesized by calcining Fe-based metal-organic frameworks. Subsequently, the magnetic photoelectric materials (Fe₃O₄@CdS) were developed by the successive ionic layer adsorption and reaction method in Cd²⁺ and S^2- solutions. Then, the self-assembled DNA nanoprisms contained three thiols/hanging arms that could capture miRNA-210 efficiently and were anchored to the Fe₃O₄@CdS octahedra via the Cd-S bond. When miRNA-210 was present, the double-stranded DNA concatemers [the self-assembled duplex helixes based on a pair of methylene blue (MB)-labeled single-stranded DNAs (AP1 and AP2) through the hybridization chain reaction and then intercalated with adriamycin (Dox) into their grooves] were connected with the Fe₃O₄@CdS-DNA nanoprisms. MB and Dox not only acted as the electrochemical probes but also synergistically switched the photocurrent polarity of the Fe₃O₄@CdS octahedra. Thus, miRNA-210 was assayed sensitively and selectively via the proposed EC-PEC dual-mode biosensing platform. Additionally, the abovementioned recognition steps occurred in a homogeneous system, and the effects of the impurities and interferences on the miRNA-210 assay could be easily avoided by magnetic separation due to the good magnetic properties of Fe₃O₄ octahedra. The proposed EC-PEC dual-mode biosensing platform showed a wide range of potential applications in bioanalysis and early diagnosis of disease.

Duplex-Specific Nuclease-Triggered Fluorescence Immunoassay Based on Dual-Functionalized AuNP for Acetochlor, Metolachlor, and Propisochlor

Given the great harm of pesticide residues to the environment and public health, exploring ultrasensitive and low-cost methods for their quantitative analysis becomes intensely necessary. Herein, we proposed a double-functionalized gold nanoparticle (AuNP) probe as a signal amplification immunoassay for the detection of acetochlor (ATC), metolachlor, and propisochlor. The AuNP was modified with IgG and fluorophore-labeled duplex DNA by a polyadenine-based freezing method. The quenched fluorescence can be effectively recovered via duplex-specific nuclease (DSN) with excellent cleaving activity. This approach provided limits of detection (LODs) down to 0.03 ng/mL for ATC, 0.10 ng/mL for metolachlor, 0.14 ng/mL for propisochlor, and 0.08 ng/mL for their mixture. The average recoveries of ATC, metolachlor, and propisochlor were 93.0-106.6% from a corn sample, which are in good agreement with the commercial kit (R² = 0.9995). This "turn-off" fluorescence immunoassay presents considerable potential in the analysis of chloroacetamide herbicide due to its simple process of probe preparing and ultrahigh sensitivity.

Target-Triggered Nanomaterial Self-Assembly Induced Electromagnetic Hot-Spot Generation for SERS-Fluorescence Dual-Mode In Situ Monitoring MiRNA-Guided Phototherapy

A multifunctional theranostic nanosystem that integrates dynamic monitoring and therapeutic functions is necessary for precision tumor medicine. Herein, an entropy-driven self-assembly nanomachine is developed that overcomes the mechanism differences of different diagnostic modes and is applied to miRNA surface-enhanced Raman scattering (SERS)-fluorescence dual-mode dynamic monitoring and synergy phototherapy. It is worth noting that the activated dual-mode theranostic nanosystem (DTN) is capable of tumor in situ fluorescence imaging and SERS absolute quantification of the target. After being internalized into tumor cells, the DTN nanosystem is activated by the DNA cascade chain displacement of the target miR-21, resulting in the secondary release of fluorophores and the assembly of core-satellite structures (CS structures). The coupling of localized surface plasmon resonances (LSPRs) in the CS structure results in the formation of numerous enhanced electric fields (hot spot) in the nanogap of the CS structure. Then the DTN nanosystem greatly improves the sensitivity and repeatability of Raman detection by converting trace targets into numerous adenines residing in the electromagnetic hot spot of the CS structure. Meanwhile, the CS structure and the loaded photosensitizer are used for synergy phototherapy under the guidance of fluorescence imaging. This proposed strategy is confirmed by in vivo and in vitro results, and it provides new ideas for tumor SERS-fluorescence dual-mode diagnosis and effective tumor therapy.

A two-photon fluorescence silica nanoparticle-based FRET nanoprobe platform for effective ratiometric bioimaging of intracellular endogenous adenosine triphosphate

Two-photon fluorescence imaging is one of the most attractive imaging techniques for monitoring important biomolecules in the biomedical field due to its advantages of low light scattering, high penetration depth, and suppressed photodamage/phototoxicity under near-infrared excitation. However, in actual biological imaging, organic two-photon fluorescent dyes have disadvantages such as high biological toxicity and their fluorescence efficiency is easily affected by the complex environment in organisms. In this study, a novel nanoprobe platform with two-photon dye-doped silica nanoparticles was developed for FRET-based ratiometric biosensing and bioimaging, with endogenous ATP chosen as the target for detection. The nanoprobe has three components: (1) a two-photon dye-doped silica nanoparticle core, which serves as an energy donor for FRET; (2) amino-modified hairpin primers with carboxy fluorescein as an energy acceptor for FRET; (3) an aptamer acting as a recognition unit to realize the probing function. The nanoprobe showed ratiometric fluorescence responses for ATP detection with high sensitivity and high selectivity in vivo. Moreover, the nanoprobe showed satisfactory ratiometric two-photon fluorescence imaging of endogenous ATP in living cells and tissues (penetration depth of 190 nm). These results indicated that novel two-photon silica nanoparticles can be constructed by doping a two-photon fluorescent dye into silica nanoparticles, and they can effectively solve the disadvantages of two-photon fluorescent dyes. These excellent performances indicate that this novel nanoprobe platform will become a very valuable molecular imaging tool, which can be widely used in the biomedical field for drug screening and disease diagnosis and other related research.

Dual-Mode SERS and Electrochemical Detection of miRNA Based on Popcorn-like Gold Nanofilms and Toehold-Mediated Strand Displacement Amplification Reaction

MicroRNA (miRNA) has emerged as one of the ideal target biomarker analytes for cancer detection because its abnormal expression is closely related to the occurrence of many cancers. In this work, we combined three-dimensional (3D) popcorn-like gold nanofilms as novel surface-enhanced Raman scattering (SERS)-electrochemistry active substrates with toehold-mediated strand displacement reactions (TSDRs) to construct a DNA molecular machine for SERS-electrochemistry dual-mode detection of miRNA. 3D popcorn-like spatial structures generated more active "hot spots" and thus enhanced the sensitivity of SERS and electrochemical signals. Besides, the TSDRs showed high sequence-dependence and high specificity. The addition of target miRNA will trigger the molecular machine to perform two TSDRs in the presence of signal DNA strands modified by R6G (R6G-DNA), thus achieving an enzyme-free amplification detection of miRNA with a low limit of detection of 0.12 fM (for the SERS method) and 2.2 fM (for the electrochemical method). This biosensor can also serve as a universally amplified and sensitive detection platform for monitoring different biomarkers, such as cancer-related DNA, messenger RNA, or miRNA molecules, with high selectivity by changing the corresponding probe sequence.

Detection of cell-surface sialic acids and photodynamic eradication of cancer cells using dye-modified polydopamine-coated gold nanobipyramids

A nanoprobe based on polydopamine-coated gold nanobipyramids surface modified with molecules of a phenylboronic acid-substituted distyryl boron dipyrromethene has been fabricated and characterised using various physical and spectroscopic methods. It serves as an ultrasensitive sensor for sialic acids on the surface of cancer cells based on its dual surface-enhanced Raman scattering and fluorescence response. This biomarker can also trigger the photodynamic activity of these nanobipyramids, effectively eradicating the cancer cells mainly through apoptosis as shown by various bioassays.