Immobilization of Oligonucleotides on Metal-Dielectric Nanostructures for miRNA Detection

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.

Role of probe design and bioassay configuration in surface enhanced Raman scattering based biosensors for miRNA detection

The accurate design of labelled oligo probes for the detection of miRNA biomarkers by Surface Enhanced Raman Scattering (SERS) may improve the exploitation of the plasmonic enhancement. This work, thus, critically investigates the role of probe labelling configuration on the performance of SERS-based bioassays for miRNA quantitation. To this aim, highly efficient SERS substrates based on Ag-decorated porous silicon/PDMS membranes are functionalized according to bioassays relying on a one-step or two-step hybridization of the target miRNA with DNA probes. Then, the detection configuration is varied to evaluate the impact of different Raman reporters and their labelling position along the oligo sequence on bioassay sensitivity. At high miRNA concentration (100-10 nM), a significantly increased SERS intensity is detected when the reporters are located closer to the plasmonic surface compared to farther probe labelling positions. Counterintuitively, a levelling-off of the SERS intensity from the different configurations is recorded at low miRNA concentration. Such effect is attributed to the increased relative contribution of Raman hot-spots to the whole SERS signal, in line with the electric near field distribution simulated for a simplified model of the Ag nanostructures. However, the beneficial effect of reducing the reporter-to-surface distance is partially retained for a two-step hybridization assay thanks to the less sterically hindered environment in which the second hybridization occurs. The study thus demonstrates an improvement of the detection limit of the two-step assay by tuning the probe labelling position, but sheds at the same time light on the multiple factors affecting the sensitivity of SERS-based bioassays.

A Y-shape-structured electrochemiluminescence biosensor based on carbon quantum dots and locked nucleic acid probe for microRNA determination with single-base resolution

Since microRNAs (miRNAs) are predictors of tumorigenesis, accurate identification and quantification of miRNAs with highly similar sequences are expected to reflect tumor diagnosis and treatment. In this study, a highly selective and sensitive electrochemiluminescence (ECL) biosensor was constructed for miRNAs determination based on Y-shaped junction structure equipped with locked nucleic acids (LNA), graphene oxide-based nanocomposite to enrich luminophores, and conductive matrix. Specifically, two LNA-modified probes were designed for specific miRNA recognition, that is, a dual-amine functionalized hairpin capture probe and a signal probe. A Y-shaped DNA junction structure was generated on the electrode surface upon miRNA hybridizing across the two branches, so as to enhance the selectivity. Carbon quantum dots-polyethylene imine-graphene oxide (CQDs-PEI-GO) nanocomposites were developed to enrich luminophores CQDs, and thus enhancing the ECL intensity. For indirect signal amplification, an electrochemically activated poly(2-aminoterephthalic acid) (ATA) film decorated with gold nanoparticles was prepared on electrode as an effective matrix to accelerate the electron transfer. The fabricated ECL biosensor achieved sensitive determination of miRNA-222 with a limit-of-detection (LOD) as low as 1.95 fM (S/N = 3). Notably, Y-shaped junction structures equipped with LNA probes endowed ECL biosensor with salient single-base discrimination ability and anti-interference capacity. Overall, the proposed Y-shaped ECL biosensor has considerable promise for clinical biomarker determination.

Entropy-driven DNA circuit with two-stage strand displacement for elegant and robust detection of miRNA let-7a

MicroRNAs (miRNAs) research in cancer diagnosis is expanding, on account of miRNAs were demonstrated to be key indicator of gene expression and hopeful candidates for biomarkers. In this study, a stable miRNA-let-7a fluorescent biosensor was successfully designed based on an exonuclease Ⅲ-assisted two-stage strand displacement reaction (SDR). First, an entropy-driven SDR containing a three-chain structure of the substrate is used in our designed biosensor, leading to reduce the reversibility of the target recycling process in each step. The target acts on the first stage to start the entropy-driven SDR, which generates the trigger used to stimulate the exonuclease Ⅲ-assisted SDR in the second stage. At the same time, we design a SDR one-step amplification strategy as a comparison. Expectly, this developed two-stage strand displacement system has a low detection limit of 25.0 pM as well as a broad detection range of 4 orders of magnitude, making it more sensitive than the SDR one-step sensor, whose detection limit is 0.8 nM. In addition, this sensor has high specificity across members of the miRNA family. Therefore, we can take advantage of this biosensor to promote miRNA research in cancer diagnosis sensing systems.

Real-Time Monitoring of the In Situ Microfluidic Synthesis of Ag Nanoparticles on Solid Substrate for Reliable SERS Detection

A sharpened control over the parameters affecting the synthesis of plasmonic nanostructures is often crucial for their application in biosensing, which, if based on surface-enhanced Raman spectroscopy (SERS), requires well-defined optical properties of the substrate. In this work, a method for the microfluidic synthesis of Ag nanoparticles (NPs) on porous silicon (pSi) was developed, focusing on achieving a fine control over the morphological characteristics and spatial distribution of the produced nanostructures to be used as SERS substrates. To this end, a pSi membrane was integrated in a microfluidic chamber in which the silver precursor solution was injected, allowing for the real-time monitoring of the reaction by UV-Vis spectroscopy. The synthesis parameters, such as the concentration of the silver precursor, the temperature, and the flow rate, were varied in order to study their effects on the final silver NPs' morphology. Variations in the flow rate affected the size distribution of the NPs, whereas both the temperature and the concentration of the silver precursor strongly influenced the rate of the reaction and the particle size. Consistently with the described trends, SERS tests using 4-MBA as a probe showed how the flow rate variation affected the SERS enhancement uniformity, and how the production of larger NPs, as a result of an increase in temperature or of the concentration of the Ag precursor, led to an increased SERS efficiency.

A fluorescence nanoprobe for detecting the effect of different oxygen and nutrient conditions on breast cancer cells' migration and invasion

Cancer cell migration and invasion are initial steps for tumor metastasis, which increases patient mortality. The tumor microenvironment is characterized as being hypoxic and nutrient deficient. Previous studies have suggested that hypoxia induces tumor metastasis, while the low nutrient content is not beneficial for tumor metastasis. Thus, it is necessary to develop a simple probe to study the changes in cancer migration and invasion. Herein, we designed a nanoprobe based on gold nanoparticles (Au NPs) to monitor the effect of different oxygen and nutrient conditions on the migration and invasion of breast cancer cells through detecting the changes in levels of RAB-22a and MMP-2 mRNA in living cells. After incubating MCF-7 and MDA-MB-231 cells with different concentrations of oxygen and nutrients, fluorescence imaging assays were used to evaluate migration and invasion. This work provides a new insight in the effect of different tumor microenvironments on cell migration and invasion.

A 3D hydrogel based on chitosan and carbon dots for sensitive fluorescence detection of microRNA-21 in breast cancer cells

Hydrogels are 3D polymeric networks with great swelling capability in water and appropriate chemical, mechanical and biological features which make it feasible to maintain bioactive substances. Herein, we fabricated carbon dots-chitosan nanocomposite hydrogels via reacting carbon dots synthesized from various aldehyde precursors with chitosan after that functionalized with ssDNA probe for detection of microRNA-21 in MCF-7 cancer cells. More importantly, three fluorescent hydrogels were produced using schiff base reaction (forming imine bonds) among the amine in chitosan and aldehyde groups on the CDs surface. Furthermore, the hydrogel films, CDs and CDs-chitosan nanocomposite hydrogels were characterized by UV-vis absorption and fluorescence spectra, FT-IR, scanning electron microscope (SEM) and transmission electron microscopy (TEM). The DNA hydrogel bioassay strategy revealed a great stability and a superb sensitivity for microRNA-21, with a suitable linear range (0.1-125 fM) and a detection limit (0.03 fM). For sample analysis, the biosensors exhibited good linearity with MCF-7 cancer cell concentrations from 1000 to 25000, 1000-25000 and 1000-6000 cells mL^-1 and detection limit of 310, 364 and 552 cells mL^-1, for glutaraldehyde, nitrobezaldehyde and benzaldehyde based nanocomposite hydrogels, respectively. In addition, cell viability consequences demonstrated low probe cytotoxicity, so nanocomposite hydrogels was utilized to multicolor imaging of MCF-7 cancer cells.

Aggregation-Induced Synergism by Hydrophobic-Driven Self-Assembly of Amphiphilic Oligonucleotides

The evident contradiction between high local-concentration-based substrate reactivity and free-diffusion-based high reaction efficiency remains one of the important challenges in chemistry. Herein, we propose an efficient aggregation-induced synergism through the hydrophobic-driven self-assembly of amphiphilic oligonucleotides to generate high local concentration whereas retaining high reaction efficiency through hydrophobic-based aggregation, which is important for constructing efficient DNA nanomachines for ultrasensitive applications. MicroRNA-155, used as a model, triggered strand displacement amplification of the DNA monomers on the periphery of the 3D DNA nanomachine and generated an amplified fluorescent response for its sensitive assay. The local concentration of substrates was increased by a factor of at least 9.0×10⁵ through hydrophobic-interaction-based self-assembly in comparison with the traditional homogeneous reaction system, achieving high local-concentration-based reactivity and free-diffusion-based enhanced reaction efficiency. As expected, the aggregation-induced synergism by hydrophobic-driven self-assembly of amphiphilic oligonucleotides created excellent properties to generate a 3D DNA nanomachine with potential as an assay for microRNA-155 in cells. Most importantly, this approach can be easily expanded for the bioassay of various biomarkers, such as nucleotides, proteins, and cells, offering a new avenue for simple and efficient applications in bioanalysis and clinical diagnosis.

A Lamping U-Shaped Fiber Biosensor Detector for MicroRNA

This study presents a U-shaped optical fiber developed for a facile application of microRNA detection. It is fabricated by the lamping process and packaged in a quartz tube to eliminate human negligence. In addition, silanization and electrostatic self-assembly are employed to bind gold nanoparticles and miRNA-133a probe onto the silicon dioxide of the fiber surface. For Mahlavu of hepatocellular carcinoma (HCC), detection is determined by the wavelength shift and transmission loss of a U-shaped optical fiber biosensor. The spectral sensitivity of wavelength and their coefficient of determination are found at −218.319 nm/ ng/mL and 0.839, respectively. Concurrently, the sensitivity of transmission loss and their coefficient of determination are found at 162.394 dB/ ng/mL and 0.984, respectively. A method for estimating the limit of detection of Mahlavu is at 0.0133 ng/mL. The results show that the proposed U-shaped biosensor is highly specific to miRNA-133a and possesses good sensitivity to variations in specimen concentration. As such, it could be of substantial value in microRNA detection.

Label-free and enzyme-free detection of microRNA based on a hybridization chain reaction with hemin/G-quadruplex enzymatic catalysis-induced MoS2 quantum dots via the inner filter effect

A new simple, sensitive and specific strategy for microRNA analysis has been described based on a hybridization chain reaction with hemin/G-quadruplex enzymatic catalysis-induced MoS2 quantum dots via the inner filter effect. The target microRNA triggers the hybridization chain reaction between two DNA probes to generate long dsDNA with many hemin/G-quadruplex DNAzymes in the presence of hemin. With the assistance of H2O2, the produced hemin/G-quadruplex DNAzyme could oxidize o-phenylenediamine (OPD) to 2,3-diaminophenazine (DAP) directly, resulting in the fluorescence quenching of MoS2 quantum dots via the inner filter effect. As an example, the fluorescence response of MoS2 quantum dots is linearly related with the logarithm of the microRNA let-7a concentration with a detection limit of 42 fM. The proposed label-free assay has promising potential to be applied in practical diagnosis.

Photofabrication of polymeric biomicrofluidics: New insights into material selection

We propose a versatile method to evaluate the suitability of polymers for the fabrication of microfluidic devices for biomedical applications, based on the concept that the selection and the design of convenient materials should involve different properties depending on the final microfluidic application. Here polymerase chain reaction (PCR) is selected as biological model and target microfluidic reaction. A class of photocured siloxanes is introduced as device building polymers and copolymerization is adopted as strategy to finely tune and optimize the final material properties. All-polymeric flexible devices are easily fabricated exploiting the rapidity of the photopolymerization reaction: they resist to thermal cycles without leakage or de-bonding (i.e., without separation of different chip parts made of the same material bonded together), show very limited water swelling and permeability, are bioinert and prevent the inhibition of the biochemical reaction. PCR is thus successfully conducted in the photocured microfluidic devices made with a specifically designed siloxane copolymer.

Advanced methods for microRNA biosensing: a problem-solving perspective

MicroRNAs (miRNAs) present several features that make them more difficult to analyze than DNA and RNA. For this reason, efforts have been made in recent years to develop innovative platforms for the efficient detection of microRNAs. The aim of this review is to provide an overview of the sensing strategies able to deal with drawbacks and pitfalls related to microRNA detection. With a critical perspective of the field, we identify the main challenges to be overcome in microRNA sensing, and describe the areas where several innovative approaches are likely to come for managing those issues that put limits on improvement to the performances of the current methods. Then, in the following sections, we critically discuss the contribution of the most promising approaches based on the peculiar properties of nanomaterials or nanostructures and other hybrid strategies which are envisaged to support the adoption of these new methods useful for the detection of miRNA as biomarkers of practical clinical utility. Graphical abstract ᅟ.

Label-Free SERS Discrimination and In Situ Analysis of Life Cycle in Escherichia coli and Staphylococcus epidermidis

Surface enhanced Raman spectroscopy (SERS) has been proven suitable for identifying and characterizing different bacterial species, and to fully understand the chemically driven metabolic variations that occur during their evolution. In this study, SERS was exploited to identify the cellular composition of Gram-positive and Gram-negative bacteria by using mesoporous silicon-based substrates decorated with silver nanoparticles. The main differences between the investigated bacterial strains reside in the structure of the cell walls and plasmatic membranes, as well as their biofilm matrix, as clearly noticed in the corresponding SERS spectrum. A complete characterization of the spectra was provided in order to understand the contribution of each vibrational signal collected from the bacterial culture at different times, allowing the analysis of the bacterial populations after 12, 24, and 48 h. The results show clear features in terms of vibrational bands in line with the bacterial growth curve, including an increasing intensity of the signals during the first 24 h and their subsequent decrease in the late stationary phase after 48 h of culture. The evolution of the bacterial culture was also confirmed by fluorescence microscope images.

Quantification of MicroRNAs by Coupling Cyclic Enzymatic Amplification with Microfluidic Voltage-Assisted Liquid Desorption Electrospray Ionization Mass Spectrometry

Quantitative assay of microRNAs (miRNAs) with mass spectrometric detection currently suffers from two major disadvantages, i.e., being insufficient in sensitivity and requiring an extraction or chromatographic separation prior to MS detection. In this work, we developed a facile and sensitive assay of targeted miRNAs based on the combination of cyclic enzymatic amplification (CEA) with microfluidic voltage-assisted liquid desorption electrospray ionization tandem mass spectrometry (VAL-DESI-MS/MS). The single-stranded DNA (ssDNA) probe was designed to have a sequence complementary to the miRNA target with an extension of a two-base nucleotide fragment (i.e., CpC) at the 3'-position as MS signal reporter, thus being easy to prepare and high in stability. In the proposed CEA-VAL-DESI-MS/MS assay, an ssDNA probe was added to a sample solution, forming a DNA-miRNA hybrid. Duplex-specific nuclease (DSN) was then added to cleave specifically the DNA probe in the heteroduplex strands. As the hybridization-cleavage cycle repeated itself for many rounds, a large quantity of CpC molecules was produced that was quantified by VAL-DESI-MS/MS with accuracy and specificity. miRNA-21 was tested as the model target. The assay had a linear calibration equation in the range from 2.5 pM to 1.0 nM with a limit of detection of 0.25 pM. Determination of miRNA-21 in cellular samples was demonstrated. miRNA-21 was found to be 95.3 ± 13.95 amol ( n = 3) in 100 mouse peritoneal macrophages with a recovery of 94.2 ± 2.6% ( n = 3). Interestingly, analysis of exosomes secreted from these cells revealed that exposure of the cells to chemical stimuli caused a 3-fold increase in exosomal level of miRNA-21. The results suggest that the proposed assay may provide an accurate and cost-effective means for quantification of targeted miRNAs in biomedical samples.

Progress in the Development of SERS-Active Substrates Based on Metal-Coated Porous Silicon

The present work gives an overview of the developments in surface-enhanced Raman scattering (SERS) with metal-coated porous silicon used as an active substrate. We focused this review on the research referenced to SERS-active materials based on porous silicon, beginning from the patent application in 2002 and enclosing the studies of this year. Porous silicon and metal deposition technologies are discussed. Since the earliest studies, a number of fundamentally different plasmonic nanostructures including metallic dendrites, quasi-ordered arrays of metallic nanoparticles (NPs), and metallic nanovoids have been grown on porous silicon, defined by the morphology of this host material. SERS-active substrates based on porous silicon have been found to combine a high and well-reproducible signal level, storage stability, cost-effective technology and handy use. They make it possible to identify and study many compounds including biomolecules with a detection limit varying from milli- to femtomolar concentrations. The progress reviewed here demonstrates the great prospects for the extensive use of the metal-coated porous silicon for bioanalysis by SERS-spectroscopy.

Toward Universal SERS Detection of Disease Signaling Bioanalytes Using 3D Self-Assembled Nonplasmonic near-Quantum-Scale Silicon Probe

Currently, the quantum-scale surface-enhanced Raman scattering (SERS) properties of Si materials have yet to be discovered for universal biosensing applications. In this study, a potential universal biosensing probe is generated by activating the SERS functionality of Si nanostructures through near quantum-scale (nQS) engineering. We introduce herein 3D nonplasmonic Si nanomesh structure with nQS defects for SERS biosensing applications. Through ionization of a single-crystal defect-free Si wafer, highly defect-rich Si subnano-orbs (sNOs) are fabricated and self-assemble as connective 3D Si nanomesh structures with enhanced SERS biosensing activity. By amending the laser ionization and ion-ion interactions, we observe the controlled synthesis of engineered nQS defects in the form of nQS-grain boundary disorder or surface nQS voids within the interconnected Si sNOs. To our knowledge, it is shown here for the first time that defect-rich Si nanomesh structures exhibit enhanced Raman activity, with the nQS morphological and crystallographic defects acting as the prime SERS contributors without a plasmonic contribution. The SERS biosensing sensitivity with the synthesized defect-rich Si nanomesh structures without an additional plasmonic material was evaluated using of a tripeptide biomarker l-glutathione (GSH); we observe an enhancement factor value of ∼10² for the GSH biomolecules with 10^-9 M sensitivity, a phenomena to our knowledge that has yet to be reported. Additionally, the SERS detection of multiple disease-signaling biomolecules (cysteine, tryptophan, and methionine) is achieved at very low analyte concentration (10^-9 M). These results indicate a potential new dimension to universal SERS biosensing applications with these unique nonplasmonic defect-rich 3D nQS-Si nanostructures.

Ratiometric electrochemical assay for sensitive detecting microRNA based on dual-amplification mechanism of duplex-specific nuclease and hybridization chain reaction

We propose a ratiometric electrochemical assay for detecting microRNA (miRNA) on the basis of dual-amplification mechanism by using distinguishable electrochemical signals from thionine (Thi) and ferrocene (Fc). The thiol-modified and ferrocene-labeled hairpin capture probes (CP) are first immobilized on an Au electrode via Au-S reaction. The target miRNA hybridizes with CP and unfolding the hairpin structure of CP to form miRNA-DNA duplexes. Then, kamchatka crab duplex specific nuclease (DSN) specifically cleaves the DNA in miRNA-DNA duplexes, leading to the release of miRNA and another cleaves cycle, meanwhile, numerous Fc leaves away from the electrode surface and leads to the signal-off of Fc. The residual fragment on electrode surface acts as a HCR primer to form dsDNA polymers through in situ HCR with the presence of the primer and two probes (HDNA and HDNA'), resulting in the capture of numerous DNA/Au NPs/Thi and the signal-on of Thi. The dual-amplification mechanism significantly amplifies the decrease of Fc signal and the increase of Thi signal for ratiometric readout (I_Thi/I_Fc), thus providing a sensitive method for the selective detection of miR-141 with a detection limit down to 11aM. The dual-signal ratiometric outputs have an intrinsic self-calibration to the effects from system, which is promising to be applied in biosensing and clinical diagnosis.

SERS-active metal-dielectric nanostructures integrated in microfluidic devices for label-free quantitative detection of miRNA

In this work, SERS-based microfluidic PDMS chips integrating silver-coated porous silicon membranes were used for the detection and quantitation of microRNAs (miRNAs), which consist of short regulatory non-coding RNA sequences typically over- or under-expressed in connection with several diseases such as oncogenesis. In detail, metal–dielectric nanostructures which provide noticeable Raman enhancements were functionalized according to a biological protocol, adapted and optimized from an enzyme-linked immunosorbent assay (ELISA), for the detection of miR-222. Two sets of experiments based on different approaches were designed and performed, yielding a critical comparison. In the first one, the labelled target miRNA is revealed through hybridization to a complementary thiolated DNA probe, immobilized on the silver nanoparticles. In the second one, the probe is halved into shorter strands (half1 and half2) that interact with the complementary miRNA in two steps of hybridization. Such an approach, taking advantage of the Raman labelling of half2, provides a label-free analysis of the target. After suitable optimisation of the procedures, two calibration curves allowing quantitative measurements were obtained and compared on the basis of the SERS maps acquired on the samples loaded with several miRNA concentrations. The selectivity of the two-step assay was confirmed by the detection of target miR-222 mixed with different synthetic oligos, simulating the hybridization interference coming from similar sequences in real biological samples. Finally, that protocol was applied to the analysis of miR-222 in cellular extracts using an optofluidic multichamber biosensor, confirming the potentialities of SERS-based microfluidics for early-cancer diagnosis.