FRET Nanoflares for Intracellular mRNA Detection: Avoiding False Positive Signals and Minimizing Effects of System Fluctuations

Environmentally responsive plasmonic nanoassemblies for biosensing

Assemblies of plasmonic nanoparticles enable new modalities for biosensing.

Fluorescence and photoacoustic dual-mode imaging of tumor-related mRNA with a covalent linkage-based DNA nanoprobe

A fluorescence and photoacoustic dual-mode DNA nanoprobe based on covalent linkage was developed for detecting tumor-associated mRNA.

Polydopamine-assisted versatile modification of a nucleic acid probe for intracellular microRNA imaging and enhanced photothermal therapy

MicroRNAs play an important role in various biological processes, and their aberrant expression is closely associated with various human diseases, especially cancer. Real-time monitoring of microRNAs in living cells may help us to understand their role in cellular processes, which can further provide a basis for diagnosis and treatment. In this study, polydopamine was used to assist the versatile modification of a nucleic acid probe for intracellular microRNA imaging and enhanced photothermal therapy. Polydopamine can be covalently linked with a thiol-terminated nucleic acid probe through the Michael addition reaction under slightly alkaline conditions. This modification is mild and can be performed directly in an aqueous solution, which can better resist hydrolysis than the traditional modification processes, resulting in a nanoprobe with better stability and higher loading of nucleic acids. This prepared nanoprobe can easily enter cells without transfection agents and then realize the imaging of intracellular miRNA through fluorescence restoration. Moreover, the coating of PDA can enhance the photothermal conversion efficiency of the nanoprobe, making it suitable for photothermal therapy of cancer. It is expected that the PDA-based versatile modification can help to construct a promising platform for tumor imaging and treatment.

Polydopamine can assist the versatile modification of a nucleic acid probe for intracellular miRNA responsed fluorescence imaging and enhanced photothermal therapy.

Energy transfer-based biodetection using optical nanomaterials

This review focuses on recent progress in the development of FRET probes and the applications of FRET-based sensing systems.

Recent progress in live cell mRNA/microRNA imaging probes based on smart and versatile nanomaterials

We summarize the recent progress in live cell mRNA/miRNA imaging probes based on various versatile nanomaterials, describing their structures and their working principles of bio-imaging applications.

In Situ Spatial Complementation of Aptamer-Mediated Recognition Enables Live-Cell Imaging of Native RNA Transcripts in Real Time

Direct cellular imaging of the localization and dynamics of biomolecules helps to understand their function and reveals novel mechanisms at the single-cell resolution. In contrast to routine fluorescent-protein-based protein imaging, technology for RNA imaging remains less well explored because of the lack of enabling technology. Herein, we report the development of an aptamer-initiated fluorescence complementation (AiFC) method for RNA imaging by engineering a green fluorescence protein (GFP)-mimicking turn-on RNA aptamer, Broccoli, into two split fragments that could tandemly bind to target mRNA. When genetically encoded in cells, endogenous mRNA molecules recruited Split-Broccoli and brought the two fragments into spatial proximity, which formed a fluorophore-binding site in situ and turned on fluorescence. Significantly, we demonstrated the use of AiFC for high-contrast and real-time imaging of endogenous RNA molecules in living mammalian cells. We envision wide application and practical utility of this enabling technology to in vivo single-cell visualization and mechanistic analysis of macromolecular interactions.

Near-infrared triggered strand displacement amplification for MicroRNA quantitative detection in single living cells

Two hairpin functionalized AuNRs were designed for NIR-laser triggered strand displacement amplification for microRNA quantitative analysis in single living cells.

As an important modulator of gene expression, microRNA (miRNA) has been described as a promising biomarker for the early diagnosis of cancers. A non-invasive method for real-time sensitive imaging and monitoring of miRNA in living cells is in urgent demand. Although some amplified methods have been developed, few can be programmed to assemble single intelligent nanostructures to realize sensitive intracellular miRNA detection without extra addition of an enzyme or catalytic fuel. Herein, two programmable oligonucleotide hairpin probe functionalized gold nanorods (THP-AuNRs) were designed to develop a near-infrared (NIR) laser triggered target strand displacement amplification (SDA) approach for sensitive miRNA imaging quantitative analysis in single living cells and multicellular tumor spheroids (MCTSs). Such a NIR-triggered SDA strategy achieves facile and sensitive monitoring of a model oncogenic miRNA-373 in various cancer lines and MCTS simulated tumor tissue. Notably, using a linear regression equation derived from miRNA mimics, a quantitative method of miRNA in single living cells was realized due to the high sensitivity. This provides a new way for sensitive real-time monitoring of intracellular miRNA, and may be promising for miRNA-based biomedical applications.

Nanocarriers with multi-locked DNA valves targeting intracellular tumor-related mRNAs for controlled drug release

The fabrication of well-behaved drug delivery systems that can transport drugs to specifically treat cancer cells rather than normal cells is still a tremendous challenge. A novel drug delivery system with two types of tumor-related mRNAs as "keys" to open the multiple valves of the nanocarrier to control drug release was developed. Hollow mesoporous silica nanoparticles were employed as the nanocarrier and dual DNAs targeting two intracellular mRNAs were employed as "multi-locks" to lock up the nanocarrier. When the nanocarrier enters the cancer cells, the overexpressed endogenous mRNA keys hybridize with the DNA multi-locks to open the valves and release the drug. Each single mRNA could not trigger the opening of the locks to release the cargo. Therefore, the nanocarrier can be applied for specific chemotherapy against cancer cells with minor side effects to normal cells. The current strategy could provide an important avenue towards advancing the practical applications of drug delivery systems used for cancer therapy.

A fluorescent turn on nanoprobe for simultaneous visualization of dual-targets involved in cell apoptosis and drug screening in living cells

Herein, a novel dual-responsive two-color fluorescent nanoprobe has been designed for the fluorescence activation imaging of cell apoptosis in living cells. The nanoprobe consists of a gold nanoparticle core functionalized with a dense layer of DNA aptamers and peptides, which shows high affinity and specific response to cytochrome c (Cyt c) and caspase-3, respectively. The formation of the aptamer-Cyt c complex and the cleavage of the specific peptide by caspase-3 can liberate the dye labelled aptamers and peptides from the surface of gold nanoparticles, and then recover their fluorescence. The turn-on and specific recognition properties of our nanoprobe allow for the sensitive and selective detection of Cyt c concentration and caspase-3 activity both in solutions and in living cells. The here proposed nanoprobe with the abilities of real-time monitoring the cell apoptosis and evaluating the apoptosis-related drug efficacy might serve as a potential interesting tool for studying the molecular mechanisms of apoptosis regulation or screening the apoptosis-based drugs.

Developing a Fluorescent Toolbox To Shed Light on the Mysteries of RNA

Technologies that detect and image RNA have illuminated the complex roles played by RNA, redefining the traditional and superficial role first outlined by the central dogma of biology. Because there is such a wide diversity of RNA structure arising from an assortment of functions within biology, a toolbox of approaches have emerged for investigation of this important class of biomolecules. These methods are necessary to detect and elucidate the localization and dynamics of specific RNAs and in doing so unlock our understanding of how RNA dysregulation leads to disease. Current methods for detecting and imaging RNA include in situ hybridization techniques, fluorescent aptamers, RNA binding proteins fused to fluorescent reporters, and covalent labeling strategies. Because of the inherent diversity of these methods, each approach comes with a set of strengths and limitations that leave room for future improvement. This perspective seeks to highlight the most recent advances and remaining challenges for the wide-ranging toolbox of technologies that illuminate RNA's contribution to cellular complexity.

Dual-channel sensing strategy based on gold nanoparticles cooperating with carbon dots and hairpin structure for assaying RNA and DNA

By employing the attractive performance of fluorescent carbon dots and the assistant of hairpin structure, an innovative dual-channel biosensor on the basis of gold nanoparticles (AuNPs) for detecting multiple nucleotide sequences has been successfully proposed. In brief, the fluorescence of carbon dots (CDs) was quenched in the absence of the targets, and the hairpin structure was hybridized with the AuNPs-DNA and resulted in recovering the fluorescence. Instead, the presence of breast cancer (BRCA1) RNA/DNA could specifically bind with its contrary sequence to release the CDs from AuNPs, hence leading to the fluorescence recovery as a positive signal. Again, the hairpin structure can be released in the presence of thymidine kinase (TK1) RNA/DNA, thus induced a fluorescence quenching accordingly. Subsequently, the prepared sensing model was applied to detect BRCA1 RNA/DNA respectively accompanied with a linear range of 4-120nM as well as a detection limit of 1.5nM and 2.1nM, and 10-120nM as well as a detection limit of 3.6nM and 4.5nM for TK1 RNA/DNA respectively. More importantly, this sensing model could assay any possible gene sequence or aptamer-substrate complexes by appropriately programming.

Simultaneous Imaging of Endogenous Survivin mRNA and On-Demand Drug Release in Live Cells by Using a Mesoporous Silica Nanoquencher

The design of multifunctional drug delivery systems capable of simultaneous target detection, imaging, and therapeutics in live mammalian cells is critical for biomedical research. In this study, by using mesoporous silica nanoparticles (MSNs) chemically modified with a small-molecule dark quencher, followed by sequential drug encapsulation, MSN capping with a dye-labeled antisense oligonucleotide, and bioorthogonal surface modification with cell-penetrating poly(disulfide)s, the authors have successfully developed the first mesoporous silica nanoquencher (qMSN), characterized by high drug-loading and endocytosis-independent cell uptake, which is able to quantitatively image endogenous survivin mRNA and release the loaded drug in a manner that depends on the survivin expression level in tumor cells. The authors further show that this novel drug delivery system may be used to minimize potential cytotoxicity encountered by many existing small-molecule drugs in cancer therapy.

Rational Engineering of a Dynamic, Entropy-Driven DNA Nanomachine for Intracellular MicroRNA Imaging

We rationally engineered an elegant entropy-driven DNA nanomachine with three-dimensional track and applied it for intracellular miRNAs imaging. The proposed nanomachine is activated by target miRNA binding to drive a walking leg tethered to gold nanoparticle with a high density of DNA substrates. The autonomous and progressive walk on the DNA track via the entropy-driven catalytic reaction of intramolecular toehold-mediated strand migration leads to continuous disassembly of DNA substrates, accompanied by the recovery of fluorescence signal due to the specific release of a dye-labeled substrate from DNA track. Our nanomachine outperforms the conventional intermolecular reaction-based gold nanoparticle design in the context of an improved sensitivity and kinetics, attributed to the enhanced local effective concentrations of working DNA components from the proximity-induced intramolecular reaction. Moreover, the nanomachine was applied for miRNA imaging inside living cells.

A label-free visual platform for self-correcting logic gate construction and sensitive biosensing based on enzyme-mimetic coordination polymer nanoparticles

In molecular logic gates, the occurrence of erroneous procedures is a frequently encountered and critical problem in data transmission, and thus it is highly desirable to develop novel logic systems with self-correction abilities. Herein, based on the horseradish peroxidase (HRP)-like activity of the novel metal coordination polymer nanoparticles formed between Cu²⁺ and guanosine monophosphate (GMP), denoted as Cu-GMP CPNs, a label-free visual platform was constructed and successfully utilized for both self-correcting logic gate construction and sensitive biosensing. The HRP-mimicking ability of Cu-GMP CPNs was verified and utilized for the sensitive detection of both H₂O₂ and glucose. More importantly, a set of logic gates (AND, OR, NOR, INHIBIT, and XNOR) were fabricated, in which two intermediate outputs, i.e., color change and precipitate formation, were combined in an "AND" mode to produce the final output, and thus the as-proposed logic system exhibited the self-correction ability to automatically correct the erroneous intermediate outputs induced by interfering substances such as HRP. Moreover, in addition to the unique feature of self-correction, the as-proposed logic system also exhibited the advantages of simple operation, rapid response and easy detection of the visual outputs by the naked eye, thus expanding its practical applications to a variety of fields. Therefore, the label-free visual platform we have proposed here offers a promising strategy for logic gate fabrication and may pave the way for the development of novel molecular computing with self-correction abilities.

Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes

RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.

Fluorescence Resonance Energy Transfer-Based DNA Tetrahedron Nanotweezer for Highly Reliable Detection of Tumor-Related mRNA in Living Cells

Accurate detection and imaging of tumor-related mRNA in living cells hold great promise for early cancer detection. However, currently, most probes designed to image intracellular mRNA confront intrinsic interferences arising from complex biological matrices and resulting in inevitable false-positive signals. To circumvent this problem, an intracellular DNA nanoprobe, termed DNA tetrahedron nanotweezer (DTNT), was developed to reliably image tumor-related mRNA in living cells based on the FRET (fluorescence resonance energy transfer) "off" to "on" signal readout mode. DTNT was self-assembled from four single-stranded DNAs. In the absence of target mRNA, the respectively labeled donor and acceptor fluorophores are separated, thus inducing low FRET efficiency. However, in the presence of target mRNA, DTNT alters its structure from the open to closed state, thus bringing the dual fluorophores into close proximity for high FRET efficiency. The DTNT exhibited high cellular permeability, fast response and excellent biocompatibility. Moreover, intracellular imaging experiments showed that DTNT could effectively distinguish cancer cells from normal cells and, moreover, distinguish among changes of mRNA expression levels in living cells. The DTNT nanoprobe also exhibits minimal effect of probe concentration, distribution and laser power as other ratiometric probe. More importantly, as a result of the FRET "off" to "on" signal readout mode, the DTNT nanoprobe almost entirely avoids false-positive signals due to intrinsic interferences, such as nuclease digestion, protein binding and thermodynamic fluctuations in complex biological matrices. This design blueprint can be applied to the development of powerful DNA nanomachines for biomedical research and clinical early diagnosis.

Fluorescence and SERS Imaging for the Simultaneous Absolute Quantification of Multiple miRNAs in Living Cells

The simultaneous imaging and quantification of multiple intracellular microRNAs (miRNAs) are particularly desirable for the early diagnosis of cancers. However, simultaneous direct imaging with absolute quantification of multiple intracellular RNAs remains a great challenge, particularly for miRNAs, which have significantly different expression levels in living cells. We designed dual-signal switchable (DSS) nanoprobes using the fluorescence-Raman signal switch. The intracellular uptake and dynamic behaviors of the probe are monitored by its fluorescence signal. Meanwhile, real-time quantitative detection of multiple miRNAs is made possible by measurements of the surface-enhanced Raman spectroscopy (SERS) ratios. Moreover, the signal 1:n ratio amplification mode only responds to low-abundance miRNA (asymmetric signal amplification mode) for simultaneous visualization and quantitative detection of significantly different levels of miRNAs in living cells. miR-21 and miR-203 were successfully detected in living MCF-7 cells, in agreement with in vitro results from the same batch of cell lysates. The reported dual-spectrum imaging method promises to offer a new strategy for the intracellular imaging and detection of various types of biomolecules.

Microfluidic chip based micro RNA detection through the combination of fluorescence and surface enhanced Raman scattering techniques

We present a novel microfluidic chip based method for the detection of micro RNA (miRNA) via the combination of fluorescence and surface enhanced Raman scattering (SERS) spectroscopies. First, silver nanoparticles (Ag NPs) are immobilized onto a glass slide, forming a SERS enhancing substrate. Then a specificially designed molecular beacon (MB) is attached to the SERS substrate. The 3' end of the MB is decorated with a thiol group to facilitate the attachment of the MB, while the 5' end of the MB is labeled with an organic dye 6-FAM, which is used both as the fluorophore and SERS reporter. In the absence of target miRNA, the MB will form a hairpin structure, making 6-FAM close to the Ag NPs. Hence, the fluorescence of 6-FAM will be quenched and the Raman signal of 6-FAM will be enhanced. On the contrary, with target miRNA present, hybridization between the miRNA and MB will unfold the MB and increase the distance between 6-FAM and the Ag NPs. Thus the fluorescence of 6-FAM will recover and the SERS signal of 6-FAM will decrease. So the target miRNA will simultaneously introduce opposite changing trends in the intensities of the fluorescence and SERS signals. By combining the opposite changes in the two optical spectra, an improved sensitivity and linearity toward the target miRNA is achieved as compared with using solely fluorescence or SERS. Moreover, introducing the microfluidic chip can reduce the reaction time, reagent dosage and complexity of detection. With the improved sensitivity and simplicity, we anticipate that the presented method can have great potential in the investigation of miRNA related diseases.

Rapid and sensitive detection of microRNA via the capture of fluorescent dyes-loaded albumin nanoparticles around functionalized magnetic beads

MicroRNAs (miRNAs) play important roles in gene regulation and cancer development. Nowadays, it is still a challenge to detect low-abundance miRNAs. Here, we present a magnetic fluorescent miRNA sensing system for the rapid and sensitive detection of miRNAs from cell lysates and serum samples. In this system, albumin nanoparticles (Alb NPs) were prepared from inherent biocompatible bovine serum albumin (BSA). A large number of fluorescent dyes were loaded into Alb NPs to make Alb NPs serve as signal molecular nanocarriers for signal amplification. Benefited from the reactive functional groups-carboxyl groups of Alb NPs, p19 protein, a viral protein that can bind and sequester short RNA duplex effectively and selectively, was modified successfully to the surface of the fluorescent dyes-loaded Alb NPs, thus enabling the probe:target miRNA duplex recognition and binding. Followed by the introduction of gold nanoparticles coated magnetic microbeads (Au NPs-MBs), which were prepared through a novel and simple method, the system combined the merits of the rapid and efficient collection given by MBs with the good affinities to attach probe molecules endowed by the coated gold layer. A broad linear detection range of 10fM-10nM and a low detection limit of 9fM were obtained within 100min by detecting a model target miRNA-21. The feasibility of this method for rapid and sensitive quantification might advance the use of miRNAs as biomarkers in clinical praxis significantly.

A cancer cell specific targeting nanocomplex for combination of mRNA-responsive photodynamic and chemo-therapy

Herein, a cancer cell specific targeting nanocomplex which combines photodynamic therapy with chemotherapy through precisely responding to the intracellular tumor-related mRNA is presented.

Stable, polyvalent aptamer-conjugated near-infrared fluorescent nanocomposite for high-performance cancer cell-targeted imaging and therapy

A novel nanocomposite with improved biostability has been designed and used for cancer cell-specific imaging and targeted therapy.

Uracil removal-inhibited ligase reaction in combination with catalytic hairpin assembly for the sensitive and specific detection of uracil-DNA glycosylase activity

Uracil removal-inhibited ligase reaction in combination with a catalytic hairpin assembly sensing strategy is demonstrated for UDG activity detection.

Plasmon Resonance Energy Transfer: Coupling between Chromophore Molecules and Metallic Nanoparticles

Plasmon resonance energy transfer (PRET) from a single metallic nanoparticle to the molecules adsorbed on its surface has attracted more and more attentions in recent years. Here, a molecular beacon (MB)-regulated PRET coupling system composed of gold nanoparticles (GNPs) and chromophore molecules has been designed to study the influence of PRET effect on the scattering spectra of GNPs. In this system, the chromophore molecules are tagged to the 5'-end of MB, which can form a hairpin structure and modified on the surface of GNPs by its thiol-labeled 3'-end. Therefore, the distance between GNPs and chromophore molecules can be adjusted through the open and close of the MB loop. From the peak shift, the PRET interactions of different GNPs-chromophore molecules coupling pairs have been calculated by discrete dipole approximation and the fitting results match well with the experimental data. Therefore, the proposed system has been successfully applied for the analysis of PRET situation between various metallic nanoparticles and chromophore molecules, and provides a useful tool for the potential application in screening the PRET-based nanoplasmonic sensors.

Dual-channel signals for intracellular mRNA detection via a PRET nanosensor

An intracellular nanosensor was designed and developed to accurately sense mRNA in living cells without false positive results.

A dual-colored ratiometric-fluorescent oligonucleotide probe for the detection of human telomerase RNA in cell extracts

A dual-colored ratiometric-fluorescent oligonucleotide probe is designed for the detection of human telomerase RNA (hTR) in cell extracts.

MnO2 nanosheet mediated "DD-A" FRET binary probes for sensitive detection of intracellular mRNA

The donor donor-acceptor (DD-A) FRET model has proven to have a higher FRET efficiency than donor-acceptor acceptor (D-AA), donor-acceptor (D-A), and donor donor-acceptor acceptor (DD-AA) FRET models. The in-tube and in-cell experiments clearly demonstrate that the "DD-A" FRET binary probes can indeed increase the FRET efficiency and provide higher imaging contrast, which is about one order of magnitude higher than the ordinary "D-A" model. Furthermore, MnO2 nanosheets were employed to deliver these probes into living cells for intracellular TK1 mRNA detection because they can adsorb ssDNA probes, penetrate across the cell membrane and be reduced to Mn2+ ions by intracellular GSH. The results indicated that the MnO2 nanosheet mediated "DD-A" FRET binary probes are capable of sensitive and selective sensing gene expression and chemical-stimuli changes in gene expression levels in cancer cells. We believe that the MnO2 nanosheet mediated "DD-A" FRET binary probes have the potential as a simple but powerful tool for basic research and clinical diagnosis.

FRET-based nanoprobes for simultaneous monitoring of multiple mRNAs in living cells using single wavelength excitation

We demonstrate a novel strategy using FRET-based nanoprobes for the simultaneous detection of multiple mRNAs with single wavelength excitation in living cells.

Gold-Quantum Dot Core-Satellite Assemblies for Lighting Up MicroRNA In Vitro and In Vivo

A high yield DNA-driven gold-quantum dot core-satellite is developed for miRNA detection in vitro and vivo. In the presence of the target miRNA, the DNA hairpin between core and satellite is ruined, resulting in the recovery of fluorescence. The limit of detection for miRNA-21 detection in living cells reaches 296 copies per cell.

Water-Soluble Nonconjugated Polymer Nanoparticles with Strong Fluorescence Emission for Selective and Sensitive Detection of Nitro-Explosive Picric Acid in Aqueous Medium

Water-soluble nonconjugated polymer nanoparticles (PNPs) with strong fluorescence emission were prepared from hyperbranched poly(ethylenimine) (PEI) and d-glucose via Schiff base reaction and self-assembly in aqueous phase. Preparation of the PEI-d-glucose (PEI-G) PNPs was facile (one-pot reaction) and environmentally friendly under mild conditions. Also, PEI-G PNPs showed a high fluorescence quantum yield in aqueous solution, and the fluorescence properties (such as concentration- and solvent-dependent fluorescence) and origin of intrinsic fluorescence were investigated and discussed. PEI-G PNPs were then used to develop a fluorescent probe for fast, selective, and sensitive detection of nitro-explosive picric acid (PA) in aqueous medium, because the fluorescence can be easily quenched by PA whereas other nitro-explosives and structurally similar compounds only caused negligible quenching. A wide linear range (0.05-70 μM) and a low detection limit (26 nM) were obtained. The fluorescence quenching mechanism was carefully explored, and it was due to a combined effect of electron transfer, resonance energy transfer, and inner filter effect between PA and PEI-G PNPs, which resulted in good selectivity and sensitivity for PA. Finally, the developed sensor was successfully applied to detection of PA in environmental water samples.

Silver enhanced ratiometric nanosensor based on two adjustable Fluorescence Resonance Energy Transfer modes for quantitative protein sensing

We developed a silver decahedral nanoparticles (Ag₁₀NPs)-enhanced ratiometric Fluorescence Resonance Energy Transfer (FRET) nanosensor based on two adjustable FRET modes. Alexa Fluor 488 (Alexa) and Cyanine3 (Cy3)-aptamer-Black hole quencher-2 (BHQ-2) were bound with Ag₁₀NPs to form the ratiometric FRET nanosensor (Ag-Alexa/Cy3/BHQ-2). Alexa act as donor and Cy3 as acceptor in the FRET mode 1 while Cy3 was donor and BHQ-2 was acceptor in the FRET mode 2. In the absence of platelet-derived growth factor (PDGF-BB), the fluorescence intensity of Alexa was lowest while that of Cy3 was highest. Upon the addition of PDGF-BB, Cy3-aptamer-BHQ-2 binds with PDGF-BB resulting in the change of structure of aptamer. The fluorescence intensity of Alexa increased while that of Cy3 decreased. In addition, the fluorescence intensity ratio of Alexa to Cy3 increased remarkably with PDGF-BB concentration in the range of 0.4-400ng/mL. A good linear response was obtained when the PDGF-BB concentrations were in the range of 3.1-200ng/mL, with the limit of detection at 0.4ng/mL. When compared to sensors without Ag₁₀NPs (Alexa/Cy3/BHQ-2) and one without BHQ-2 (Ag-Alexa/Cy3), the new nanosensor Ag-Alexa/Cy3/BHQ-2 showed remarkable increase in sensitivity.

Fluorescence resonance energy transfer-based hybridization chain reaction for in situ visualization of tumor-related mRNA

The ability to visualize tumor-related mRNA in situ in single cells would distinguish whether they are cancer cells or normal cells, which holds great promise for cancer diagnosis at an early stage. Fluorescence resonance energy transfer (FRET) and hybridization chain reactions (HCRs) were combined with amplified sense tumor-related mRNA (TK1 mRNA) in situ with high sensitivity in single cells and tissue sections. Using this strategy, each copy of the target mRNA can propagate a chain reaction of hybridization events between two alternating hairpins to form a nicked duplex that contains repeated FRET units, amplifying the fluorescent signal. The detection limit of 18 pM is about three orders of magnitude lower than that of a non-HCR method (such as the binary-probe-system). Meanwhile, due to the FRET strategy, complicated washing steps are not necessary and experimental time is sharply reduced. As far as we know, this is the first report of a fluorescence in situ hybridization (FISH) strategy that can simultaneously fulfil signal amplification and is wash-free. We believe that this FRET-based HCR strategy has great potential as a powerful tool in basic research and clinical diagnosis.

A label-free colorimetric aptasensor for simple, sensitive and selective detection of Pt (II) based on platinum (II)-oligonucleotide coordination induced gold nanoparticles aggregation

Herein, a gold nanoparticles (AuNPs) based label-free colorimetric aptasensor for simple, sensitive and selective detection of Pt (II) was constructed for the first time. Four bases (G-G mismatch) mismatched streptavidin aptamer (MSAA) was used to protect AuNPs from salt-induced aggregation and recognize Pt (II) specifically. Only in the presence of Pt (II), coordination occurs between G-G bases and Pt (II), leading to the activation of streptavidin aptamer. Streptavidin coated magnetic beads (MBs) were used as separation agent to separate Pt (II)-coordinated MSAA. The residual less amount of MSAA could not efficiently protect AuNPs anymore and aggregation of AuNPs will produce a colorimetric product. With the addition of Pt (II), a pale purple-to-blue color variation could be observed by the naked eye. A detection limit of 150nM and a linear range from 0.6μM to 12.5μM for Pt (II) could be achieved without any amplification.

A pH-responsive DNA nanomachine-controlled catalytic assembly of gold nanoparticles

The toehold-mediated DNA-strand-displacement reaction has unique programmable properties for driving the catalytic assembly of gold nanoparticles (AuNPs). Herein, we introduced a pH-responsive triplex structure into the DNA-strand-displacement-based catalytic assembly system of DNA-AuNPs to add an additional controlling factor, namely the pH. In this catalytic system, the aggregation rate of AuNPs could be regulated by both internal factors (concentrations of substrate, target, etc.) and an external control (pH gradient). This strategy can be used to construct pH-induced DNA logic gates and sophisticated DNA networks as well as to image instantaneous pH changes in living cells.

Aptazyme-Gold Nanoparticle Sensor for Amplified Molecular Probing in Living Cells

To date, a few of DNAzyme-based sensors have been successfully developed in living cells; however, the intracellular aptazyme sensor has remained underdeveloped. Here, the first aptazyme sensor for amplified molecular probing in living cells is developed. A gold nanoparticle (AuNP) is modified with substrate strands hybridized to aptazyme strands. Only the target molecule can activate the aptazyme and then cleave and release the fluorophore-labeled substrate strands from the AuNP, resulting in fluorescence enhancement. The process is repeated so that each copy of target can cleave multiplex fluorophore-labeled substrate strands, amplifying the fluorescence signal. Results show that the detection limit is about 200 nM, which is 2 or 3 orders of magnitude lower than that of the reported aptamer-based adenosine triphosphate (ATP) sensors used in living cells. Furthermore, it is demonstrated that the aptazyme sensor can readily enter living cells and realize intracellular target detection.

Live Cell MicroRNA Imaging Using Exonuclease III-Aided Recycling Amplification Based on Aggregation-Induced Emission Luminogens

Enzyme-assisted detection strategies of microRNAs (miRNAs) in vitro have accomplished both great sensitivity and specificity. However, low expression of miRNAs and a complex environment in cells induces big challenges for monitoring and tracking miRNAs in vivo. The work reports the attempt to carry miRNA imaging into live cells, by enzyme-aided recycling amplification. We utilize facile probes based yellow aggregation-induced emission luminogens (AIEgens) with super photostable property but without quencher, which are applied to monitor miRNAs not only from urine sample extracts (in vitro) but also in live cells (in vivo). The assay could distinguish the cancer patients' urine samples from the healthy urine due to the good specificity. Moreover, the probe showed much higher fluorescence intensity in breast cancer cells (MCF-7) (miR-21 in high expression) than that in cervical cancer cells (HeLa) and human lung fibroblast cells (HLF) (miR-21 in low expression) in more than 60 min, which showed the good performance and super photostability for the probe in vivo. As controls, another two probes with FAM/Cy3 and corresponding quenchers, respectively, could perform miRNAs detections in vitro and parts of in vivo tests but were not suitable for the long-term cell tracking due to the photobleach phenomena, which also demonstrates that the probe with AIEgens is a potential candidate for the accurate identification of cancer biomarkers.