Single molecule detection; from microscopy to sensors

Single molecule detection is necessary to find out physical, chemical properties and their mechanism involved in the normal functioning of body cells. In this way, they can provide a new direction to the healthcare system. Various techniques have been developed and employed for their successful detection. Herein, we have emphasized various traditional methods as well as biosensing technology which offer single molecule sensitivity. The various methods including plasmonic resonance, nanopores, whispering gallery mode, Simoa assay and recognition tunneling are discussed in the initial part which has been followed by a discussion about biosensor-based detection. Plasmonic, SERS, CRISPR/Cas, and other types of biosensors are focused in this review and found to be highly sensitive for single molecule detection. This review provides an overview of progression in different techniques employed for single molecule detection.

Heterogeneous sensing of post-translational modification enzymes by integrating the advantage of homogeneous analysis

Heterogeneous analysis has great application prospects in the detection of post-translational modification (PTM) enzymes with the advantages of signal enhancement, less sample demand, and high sensitivity and selectivity. Nevertheless, once the substrate was fixed on a solid interface, the steric hindrance might limit the approaching of catalytic center to the substrate, thus reducing the efficiency of PTM. Herein, we suggested that the avidin-modified interface could be used to develop heterogeneous sensing platforms with biotin-labeled substrates as the probes, in which the enzymatic PTM was performed in solution and the heterogeneous assay was conducted on a solid surface. The sensing strategy integrates the advantages but overcomes the defects of both homogeneous and heterogeneous assays. Protein kinase A (PKA) and histone acetyltransferase (HAT) were determined as the examples by using sequence-specific peptide substrates. The signal changes were monitored by HRP-based colorimetric assay and antibody-amplified surface plasmon resonance (SPR). The methods were used for analysis of cell lysates and evaluation of inhibition efficiency with satisfactory results. The strategy can be used for the detection of a variety of biological enzymes and provide a new idea for the design of various heterogeneous biosensors. Thus, this work should be of great significance to the popularization and practical application of biosensors.

Simultaneous single-molecule detection of the acetyltransferase and crotonyltransferase activities of histone acetylation writer p300

We demonstrate for the first time the simultaneous measurement of the acetyltransferase (HAT) and crotonyltransferase (HCT) activities of histone acetylation writer p300 by integrating antibody-based fluorescence labeling with single molecule detection. This methods exhibits good specificity and high sensitivity. Moreover, it can accurately evaluate the kinetic parameters of both the HAT and HCT activities of p300 and screen inhibitors.

Aptamer-mediated rolling circle amplification for label-free and sensitive detection of histone acetyltransferase activity

We develop for the first time an aptamer-mediated rolling circle amplification approach for label-free and sensitive detection of histone-modifying enzyme (HME) activity. This method can achieve femtomolar sensitivity for histone acetyltransferase Tip60 assay, which is the most sensitive HME assay reported so far. It can be further applied for inhibitor screening, enzyme kinetic analysis, and endogenous Tip60 measurement in cancer cells.

In situ exploring Chidamide, a histone deacetylase inhibitor, induces molecular changes of leukemic T-lymphocyte apoptosis using Raman spectroscopy

Though it has been demonstrated that Chidamide (CS055/HBI-8000), a novel benzamide class of histone deacetylase (HDAC) subtype-selectively inhibitor, reveals better anticancer effect in acute leukemia, but it remains unknown about the precise mechanism of Chidamide-induced acute leukemia cell apoptosis due to the lack of in situ molecular changes information. Based on Raman spectral analysis, we find that the action of Chidamide on Jurkat cell will lead to an addition of an acetyl group to a specific lysine residue at the end of histone amino acid, and greatly enhance the acetylation of histones H1, H2A, H2B, H3, and H4, and then destroy the electrostatic force between the alkaline terminal of the positive charged arginine side chain and the negative charged DNA of phosphate group, finally cause the depolymerization of DNA and histone octamer in chromatin nucleosome depolymerization and the relaxation of chromatin. Accordingly, the accumulation of reactive oxygen species (ROS) and the decreasing of mitochondrial membrane potential (MMP) are observed. For comparison, we also present the corresponding results of suberoylanilide hydroxamic acid (SAHA) and MS-275 inhibitors. The achieved results show that proliferation of Chidamide-treated Jurkat cells is low relative to MS-275 or SAHA, and the action of Chidamide or MS-275 on Jurkat cells lead to obvious increasing in histones H1, H2A, H2B, H3, and H4, whereas the action effect of SAHA is mainly observed in histones H1, H2A, H2B, H3 but weak in histone H4. Moreover, it is found that Chidamide-induced histone H3 acetylation in Jurkat cells is stronger than MS-275 and SAHA. Collectively, by Raman spectral analysis, we achieve the dynamic behavior of biochemical components, molecular conformation and morphological changes of HDAC inhibitors-treated Jurkat cells. Importantly, our research is the first to demonstrate that the action site of HDAC inhibitors on Jurkat cell is located in the DNA minor groove. Most importantly, the application of Raman spectrum in exploring in-situ molecular changes information, histone acetylation modification in epigenetics, drug action sites and cell cycle affected by HDAC inhibitors will supply new idea and reference for the design and modification of HDAC inhibitors.

Recent advances in biosensors for in vitro detection and in vivo imaging of DNA methylation

DNA methylation is the predominant epigenetic modification that participates in many fundamental cellular processes through posttranscriptional regulation of gene expression. Aberrant DNA methylation is closely associated with a variety of human diseases including cancers. Therefore, accurate and sensitive detection of DNA methylation may greatly facilitate the epigenetic biological researches and disease diagnosis. In recent years, a series of novel biosensors have been developed for highly sensitive detection of DNA methylation, but an overview of recent advances in biosensors for in vitro detection and especially live-cell imaging of DNA methylation is absent. In this review, we summarize the emerging biosensors for in vitro and in vivo DNA methylation assays in the past five years (2015-2020). Based on the signal types, the biosensors for in vitro DNA methylation assay are classified into five categories including fluorescent, electrochemical, colorimetric, surface enhanced Raman spectroscopy, mass spectrometry, and surface plasmon resonance biosensors, while the biosensors for in vivo DNA methylation assay mainly rely on fluorescent imaging. We review the strategies, features and applications of these biosensors, and provide a new insight into the challenges and future directions in this area.

A sensitive homogeneous enzyme assay for euchromatic histone-lysine-N-methyltransferase 2 (G9a) based on terbium-to-quantum dot time-resolved FRET

Introduction: Histone modifying enzymes include several classes of enzymes that are responsible for various post-translational modifications of histones such as methylation and acetylation. They are important epigenetic factors, which may involve several diseases and so their assay, as well as screening of their inhibitors, are of great importance. Herein, a bioassay based on terbium-to-quantum dot (Tb-to-QD) time-resolved Förster resonance energy transfer (TR-FRET) was developed for monitoring the activity of G9a, the euchromatic histone-lysine N-methyltransferase 2. Overexpression of G9a has been reported in some cancers such as ovarian carcinoma, lung cancer, multiple myeloma and brain cancer. Thus, inhibition of this enzyme is important for therapeutic purposes.

Methods: In this assay, a biotinylated peptide was used as a G9a substrate in conjugation with streptavidin-coated ZnS/CdSe QD as FRET acceptor, and an anti-mark antibody labeled with Tb as a donor. Time-resolved fluorescence was used for measuring FRET ratios.

Results: We examined three QDs, with emission wavelengths of 605, 655 and 705 nm, as FRET acceptors and investigated FRET efficiency between the Tb complex and each of them. Since the maximum FRET efficiency was obtained for Tb to QD705 (more than 50%), this pair was exploited for designing the enzyme assay. We showed that the method has excellent sensitivity and selectivity for the determination of G9a at concentrations as low as 20 pM. Furthermore, the designed assay was applied for screening of an enzyme inhibitor, S-(5’-Adenosyl)-L-homocysteine (SAH).

Conclusion: It was shown that Tb-to-QD FRET is an outstanding platform for developing a homogenous assay for the G9a enzyme and its inhibitors. The obtained results confirmed that this assay was quite sensitive and could be used in the field of inhibitor screening.

Integration of Enzymatic Labeling with Single-Molecule Detection for Sensitive Quantification of Diverse DNA Damages

DNA damage plays an important role in the regulation of gene expression and disease processes. The accurate measurement of DNA damage is essential to the discovery of potential disease biomarkers for risk assessment, early clinical diagnosis, and therapy monitoring. However, the low abundance, random location in genomic elements, diversity, and the incapability to specifically amplify the DNA damages hinder the accurate quantification of various DNA damages within human genomes. Herein, we demonstrate the integration of enzymatic labeling with single-molecule detection for sensitive quantification of diverse DNA damages. A significant advantage of our method is that only the damaged base-containing DNA sequence can be labeled by the biotin-conjugated deoxynucleotide triphosphate (biotin-dNTP) and separated from the normal DNAs, which greatly improves the detection specificity. In addition, high sensitivity can be achieved by the terminal deoxynucleotidyl transferase (TdT)-induced polymerization of multiple Alexa Fluor 488-labeled-deoxyuridine triphosphates (AF488-dUTPs) and the introduction of single-molecule detection. This method can measure DNA damage with a detection limit as low as 1.1 × 10^-16 M, and it can distinguish DNA damage at low abundance down to 1.3 × 10^-4%. Importantly, it can provide information about the occurrence of DNA damage in a specific gene and ascertain the DNA damage level in different cancer cell lines, offering a new approach for studying the physiological function of various DNA damages in human diseases.

Peptide-templated gold nanoparticle nanosensor for simultaneous detection of multiple posttranslational modification enzymes

We developed a peptide-templated gold nanoparticle (AuNP) nanosensor for simultaneous detection of multiple posttranslational modification (PTM) enzymes with a detection limit of 28 pM for histone deacetylase (HDAC) and 0.8 pM for protein tyrosine phosphatase 1B (PTP1B), and it can be further applied for the screening of PTM enzyme inhibitors and the measurement of PTM enzymes in cancer cells.

Label-free and amplified detection of apoptosis-associated caspase activity using branched rolling circle amplification

We develop a label-free fluorescence method for ultrasensitive detection of apoptosis-associated caspase activity based on branched rolling circle amplification.

Single-molecule biosensors: Recent advances and applications

Single-molecule biosensors serve the unmet need for real time detection of individual biological molecules in the molecular crowd with high specificity and accuracy, uncovering unique properties of individual molecules which are hidden when measured using ensemble averaging methods. Measuring a signal generated by an individual molecule or its interaction with biological partners is not only crucial for early diagnosis of various diseases such as cancer and to follow medical treatments but also offers a great potential for future point-of-care devices and personalized medicine. This review summarizes and discusses recent advances in nanosensors for both in vitro and in vivo detection of biological molecules offering single-molecule sensitivity. In the first part, we focus on label-free platforms, including electrochemical, plasmonic, SERS-based and spectroelectrochemical biosensors. We review fluorescent single-molecule biosensors in the second part, highlighting nanoparticle-amplified assays, digital platforms and the utilization of CRISPR technology. We finally discuss recent advances in the emerging nanosensor technology of important biological species as well as future perspectives of these sensors.

A versatile single-molecule counting-based platform by generation of fluorescent silver nanoclusters for sensitive detection of multiple nucleic acids

The good photostability and strong brightness of individual DNA-templated silver nanoclusters (DNA-AgNCs) have been confirmed by single-molecule imaging in this work and DNA-AgNCs as a new class of outstanding fluorophores are applied in the construction of single-molecule counting-based probes for the first time. Based on the fluorescent AgNC-generating molecular beacons (AgNC-MBs), we present a versatile method for simultaneous analysis of multiple nucleic acids. Distinct from previous designs in which a AgNC stabilizing sequence is incorporated into the stem of a hairpin DNA to form the AgNC-MB, we prepared a nicked MB in which the AgNC stabilizing sequence is hybridized with the longer stem of a single-stranded DNA (ssDNA) with a stem-loop structure. Our proposed AgNC-MB is activated by probe-target hybridization then releasing the AgNC stabilizing sequence via a toehold-mediated strand displacement reaction, the versatility of which has been greatly improved because bases in the target-binding region are not involved in the formation of DNA-AgNCs. As a proof of concept, the simultaneous detection of two breast cancer-related MicroRNAs (miR-21 and let-7a miRNA) has been achieved with total internal reflection fluorescence (TIRF)-based imaging and the detection sensitivity of our method has been demonstrated to be improved by at least two orders of magnitude compared with conventional AgNC-MBs. Furthermore, in the single-nucleotide mutation identification assay, the simultaneous detection strategy introduces a competitive reaction between the two probe-target hybridizations, resulting in the excellent discrimination ability of the AgNC-MB sensing platform and the mutant-type targets can be successfully detected at low abundance. The new AgNC-MB sensing platform demonstrated potential to make AgNCs an attractive alternative to conventional organic dyes for single-molecule studies.

Biosensors for epigenetic biomarkers detection: A review

Epigenetic inheritance is a heritable change in gene function independent of alterations in nucleotide sequence. It regulates the normal cellular activities of the organisms by affecting gene expression and transcription, and its abnormal expression may lead to the developmental disorder, senile dementia, and carcinogenesis progression. Thus, epigenetic inheritance is recognized as an important biomarker, and the accurate quantification of epigenetic inheritance is crucial to clinical diagnosis, drug development and cancer treatment. Noncoding RNA, DNA methylation and histone modification are the most common epigenetic biomarkers. The conventional biosensors (e.g., northern blotting, radiometric, mass spectrometry and immunosorbent biosensors) for epigenetic biomarkers assay usually suffer from hazardous radiation, complicated manipulation, and time-consuming procedures. To facilitate the practical applications, some new biosensors including colorimetric, luminescent, Raman scattering spectroscopy, electrochemical and fluorescent biosensors have been developed for the detection of epigenetic biomarkers with simplicity, rapidity, high throughput and high sensitivity. In this review, we summarize the recent advances in epigenetic biomarkers assay. We classify the biosensors into the direct amplification-free and the nucleotide amplification-assisted ones, and describe the principles of various biosensors, and further compare their performance for epigenetic biomarkers detection. Moreover, we discuss the emerging trends and challenges in the future development of epigenetic biomarkers biosensors.

Chalcone-analogue fluorescent probes for detecting thiophenols in seawater samples

Two efficient chalcone fluorescent probes (probe-KCN1 and probe-KCN2) were developed for the detection of thiophenols. Upon gradual addition of thiophenols to the fluorescent probes, the fluorescence intensity of the emission band at 550 nm is enhanced about 40-fold, with a large Stokes shift (130 nm). Probe-KCN1 responds to thiophenols with a good range of linearity and a detection limit of 79 nΜ (R² = 0.9915), and Probe-KCN2 responds selectively to thiophenols over other amino acids, common metal ions and other potential interferents with a detection limit of 96 nM (R² = 0.9978). The low-toxicity probe has been successfully used to detect thiophenols in samples of seawater. These results demonstrate that Probe-KCN is a class of specific probes that might provide a simple way to monitor changes in thiophenols at low concentrations in seawater samples.

An Enzyme-Free MicroRNA Assay Based On Fluorescence Counting of Click Chemical Ligation-Illuminated Magnetic Nanoparticles with Total Internal Reflection Fluorescence Microscopy

MicroRNAs (miRNAs) have been considered as promising cancer biomarkers. However, the simple but sensitive detection of low levels of miRNAs in biological samples still remains challenging. Herein, we wish to report an entirely enzyme-free, simple, and highly sensitive miRNA assay based on the counting of cycling click chemical ligation (3CL)-illuminated fluorescent magnetic nanoparticles (MNPs) with a total internal reflection fluorescence microscopy (TIRFM). In this strategy, each miRNA molecule can trigger many cycles of click chemical ligation reactions to produce plentiful ligated oligonucleotides (ODNs) with both 5'-biotin and 3'-fluorophore, resulting in efficient signal amplification. It is worth noting that only the ligated ODNs can bring fluorophores onto streptavidin-functionalized MNPs (STV-MNPs). Notably, merely 10 fluorescent molecules on each 50 nm MNP can make it bright enough to be clearly visualized by the TIRFM, which can significantly improve the detection sensitivity for miRNA. Through fluorescence counting of individual MNPs and integrating their fluorescence intensities, the amount of target miRNA can be quantitatively determined. This miRNA assay can be accomplished in a mix-and-read manner just by simply mixing the enzyme-free 3CL reaction system with the MNPs before TIRFM imaging, which avoids tedious immobilization, washing, and purification steps. Despite the extremely simple operation, this strategy exhibits high sensitivity with a quite low detection limit of 50 fM target miRNA as well as high specificity to well discriminate miRNA sequences with a single-base variation. Furthermore, the applicability of this method in real biological samples is also verified through the accurate detection of the miRNA target in cancer cells.

A Single-Molecule Homogeneous Immunoassay by Counting Spatially "Overlapping" Two-Color Quantum Dots with Wide-Field Fluorescence Microscopy

We developed a single-molecule homogeneous immunoassay by counting spatially "overlapping" two-color quantum dots (QD) under a wide-field fluorescence microscope. QD 655 with red fluorescence and QD 565 with green fluorescence were modified with capture and detection antibodies, respectively. A capture antibody-modified QD 655 and a detection antibody-modified QD 565 were conjugated by a corresponding antigen molecule to form a "sandwich" immunocomplex. The conjugated QD 655 could not be distinguished from the conjugated QD 565 by fluorescent microscopy because the distance between them was smaller than the resolution of an optical microscope (approximately 200 nm). The immunocomplex color became yellow because of the spatial "overlap" of the red and green fluorescence. The number of the yellow spots was equal to the number of immunocomplex molecules, while the concentration of the antigen was related to the ratio of the yellow dots to the red dots. The successful quantification of two model proteins in the human plasma, namely, alpha-fetoprotein and carcinoembryonic antigen, demonstrated the accuracy and reliability of our approach.

Development of dual-color total internal reflection fluorescence biosensor for simultaneous quantitation of two small molecules and their affinity constants with antibodies

A novel dual-color total internal reflection fluorescence biosensor (DTB) was successfully developed for the simultaneous detection of two small molecules based on a simple optical structure and the time resolved effect of fiber optic switch. The DTB employed a single-multi mode fiber optic coupler instead of a sophisticated confocal optical system for the transmission of two excitation lights and dual-color fluorescence, and a photodiode detector instead of photomultiplier for the simultaneous detection of dual-color fluorescence. The compact optical design of DTB improved its optical transmission efficiency and detection sensitivity because of no requirement of numerous optical separation elements and rigorous optical alignment. The DTB was applied for the simultaneous detection of 2,4-Bisphenol-A (BPA) and 2,4-Dichlorophenoxyacetic acid (2,4-D) using one bifunctional fiber optic bio-probe modified by two hapten-protein conjugates. When the mixture of Cy5.5 labeled anti-2,4-D antibody and Pacific Blue dye labeled anti-BPA antibody was introduced over the surface of the bio-probe, they bound with their respective hapten-protein conjugate immobilized onto the bio-probe. Based on the time-resolved effect of fiber optic switch, two fluorescence dyes were alternatively excited by 635 nm and 405 nm laser lights and simultaneously detected by one photodiode detector. Taking indirect competitive immunoassay principle, BPA and 2,4-D were simultaneously detected using the DTB with high sensitivity, accuracy, and rapidity. The quantitation of affinity constants between small molecules and their antibodies was also achieved based on the proposed theory. The DTB provides a flexible and powerful platform for simultaneously sensitive quantitation of multiple targets and the affinity constants of biomolecular interactions.

A highly selective colorimetric and ratiometric fluorescent probe for instantaneous sensing of Hg2+ in water, soil and seafood and its application on test strips

A new simple and efficient oligothiophene-based colorimetric and ratiometric fluorescent probe has been developed for highly sensitive and fast detection of Hg2+ in water, soil and seafood. The probe 5-(1,3-dithiolan-2-yl)-2,2':5',2″-terthiophene 3 TS can selectively detect Hg2+ via the Hg2+-promoted deprotection reaction of thioacetals, which caused a remarkable color change from colorless to yellow and a strong fluorescence enhancement with emission color varying from blue to yellow, enabling naked-eye detection of Hg2+. The probe shows high sensitivity with the detection limit down to 1.03 × 10-8 M. Visual color changes of 3 TS were observed on filter paper and TLC testing strips when they were impregnated on testing strips and immersed in Hg2+ solution. Moreover, the probe 3 TS has been successfully used to rapidly detect trace amounts of hazardous Hg2+ ions in tap, distilled, river and lake water, cropland soil, fish, shrimp and kelp samples with acceptable results and good recoveries.

Advances in the integration of quantum dots with various nanomaterials for biomedical and environmental applications

Quantum dots (QDs) are semiconductor nanocrystals with distinct characteristics of high brightness, large Stokes shift and broad absorption spectra, large molar extinction coefficients, high quantum yield, good photostability and long fluorescence lifetime. The QDs have replaced the conventional fluorophores with wide applications in immunoassays, microarrays, fluorescence imaging, targeted drug delivery and therapy. The integration of QDs with various nanomaterials such as noble metal nanoparticles, carbon allotropes, upconversion nanoparticles (UCNPs), metal oxides and metal-organic frameworks (MOFs) brings new opportunities and possibilities in nanoscience and nanotechnology. In this review, we summarize the recent advances in the integration of QDs with various nanomaterials for biomedical and environmental applications including sensing, bioimaging, theranostics and cancer therapy. We highlight the involved interactions such as fluorescence resonance energy transfer (FRET), plasmon enhanced fluorescence (PEF), and nanometal surface energy transfer (NSET) as well as the synergistic effect resulting from the integration of QDs with nanomaterials. In addition, we discuss the sensing and imaging mechanisms of different strategies and give new insight into the challenges and future direction as well.

Development of quantum dot-based biosensors: principles and applications

We review the recent advances in quantum dot-based biosensors and focus on quantum dot-based fluorescent, bioluminescent, chemiluminescent, and photoelectrochemical biosensors.

Simultaneous sensitive detection of multiple DNA glycosylases from lung cancer cells at the single-molecule level

We demonstrate the simultaneous detection of human 8-oxoguanine DNA glycosylase 1 and human alkyladenine DNA glycosylase at the single-molecule level.

DNA glycosylases are involved in the base excision repair pathway, and all mammals express multiple DNA glycosylases to maintain genome stability. However, the simultaneous detection of multiple DNA glycosylase still remains a great challenge. Here, we develop a single-molecule detection method for the simultaneous detection of human 8-oxoguanine DNA glycosylase 1 (hOGG1) and human alkyladenine DNA glycosylase (hAAG) on the basis of DNA glycosylase-mediated cleavage of molecular beacons. We designed a Cy3-labeled molecular beacon modified with 8-oxoguanine (8-oxoG) for a hOGG1 assay and a Cy5-labeled molecular beacon modified with deoxyinosine for a hAAG assay. hOGG1 may catalyze the removal of 8-oxoG from 8-oxoG/C base pairs to generate an apurinic/apyrimidinic (AP) site, and hAAG may catalyze the removal of deoxyinosine from deoxyinosine/T base pairs to generate an AP site. With the assistance of apurinic/apyrimidinic endonuclease (APE1), the cleavage of AP sites results in the cleavage of molecular beacons, with Cy3 indicating the presence of hOGG1 and Cy5 indicating the presence of hAAG. Both of the Cy3 and Cy5 signals can be simply quantified by total internal reflection fluorescence-based single-molecule detection. This method can simultaneously detect multiple DNA glycosylases with a detection limit of 2.23 × 10^–6 U μL^–1 for hOGG1 and 8.69 × 10^–7 U μL^–1 for hAAG without the involvement of any target amplification. Moreover, this method can be used for the screening of enzyme inhibitors and the simultaneous detection of hOGG1 and hAAG from lung cancer cells, having great potential for further application in early clinical diagnosis.

Single-Molecule Detection of Polynucleotide Kinase Based on Phosphorylation-Directed Recovery of Fluorescence Quenched by Au Nanoparticles

5'-Polynucleotide kinase such as T4 polynucleotide kinase (T4 PNK) may catalyze the phosphorylation of 5'-hydroxyl termini in nucleic acids, playing a crucial role in DNA replication, DNA recombination, and DNA damage repair. Here, we demonstrate for the first time single-molecule detection of PNK based on phosphorylation-directed recovery of fluorescence quenched by Au nanoparticle (AuNP) in combination with lambda exonuclease-mediated cleavage reaction. In the presence of PNK, the γ-phosphate group from adenosine triphosphate (ATP) is transferred to 5'-hydroxyl terminus, resulting in 5'-phosphorylation of the hairpin probe. The phosphorylated hairpin probes may function as the substrates of lambda exonuclease and enable the removal of 5' mononucleotides from the stem, leading to the unfolding of hairpin structure and the formation of binding probes. The resultant binding probes may specifically hybridize with the AuNP-modified capture probes, forming double-strand DNA (dsDNA) duplexes with 5'-phosphate groups as the substrates of lambda exonuclease and subsequently leading to the cleavage of capture probes and the liberation of Cy5 molecules and the binding probes. The released binding probes may further hybridize with new capture probes, inducing cycles of digestion-release-hybridization and consequently the release of numerous Cy5 molecules. Through simply monitoring Cy5 molecules with total internal reflection fluorescence (TIRF)-based imaging, PNK activity can be quantitatively measured. This assay is very sensitive with a limit of detection of 9.77 × 10^-8 U/μL, and it may be further used to screen the PNK inhibitors and measure PNK in cancer cell extracts.

Multifunctional nanoprobes for both fluorescence and 19F magnetic resonance imaging

Fluorescence is widely used for cell imaging due to its high sensitivity and rich color choice but limited for in vivo imaging because of its low light penetration. Meanwhile, magnetic resonance imaging (MRI) is widely applied for in vivo diagnosis but not suitable for cell imaging because of its low resolution. Compared to ¹H-MRI, ¹⁹F-MRI is more suitable for clinical application due to its high sensitivity but fabricating ¹⁹F-MRI probes is a great challenge. Therefore, it is highly desirable to develop a dual-modal imaging probe for both cell fluorescence imaging and in vivo¹⁹F-MRI with high sensitivity and deep penetration. In this study, ¹⁹F moiety loaded nanocomposites with an organic fluorescent core were successfully prepared via a facile strategy by encapsulating organic dyes with oleylamine-functionalized polysuccinimide and 1H,1H,2H,2H-perfluorodecyltriethoxysilane (PDTES). The aggregation of organic fluorescent dyes in the core results in significant fluorescence for optical imaging, while the ¹⁹F moieties on PDTES allow for simultaneous ¹⁹F MRI. Moreover, the nanocomposites exhibited high water dispersibility and excellent biocompatibility. These properties make them promising for both cell imaging and in vivo imaging applications.

Advances in single quantum dot-based nanosensors

We review the advances in single quantum dot-based nanosensors and their biomedical applications. We highlight their challenges and future direction.

Fluorescent Biosensors Based on Single-Molecule Counting

Biosensors for highly sensitive, selective, and rapid quantification of specific biomolecules make great contributions to biomedical research, especially molecular diagnostics. However, conventional methods for biomolecular assays often suffer from insufficient sensitivity and poor specificity. In some case (e.g., early disease diagnostics), the concentration of target biomolecules is too low to be detected by these routine approaches, and cumbersome procedures are needed to improve the detection sensitivity. Therefore, there is an urgent need for rapid and ultrasensitive analytical tools. In this respect, single-molecule fluorescence approaches may well satisfy the requirement and hold promising potential for the development of ultrasensitive biosensors. Encouragingly, owing to the advances in single-molecule microscopy and spectroscopy over past decades, the detection of single fluorescent molecule comes true, greatly boosting the development of highly sensitive biosensors. By in vitro/in vivo labeling of target biomolecules with proper fluorescent tags, the quantification of certain biomolecule at the single-molecule level is achieved. In comparison with conventional ensemble measurements, single-molecule detection-based analytical methods possess the advantages of ultrahigh sensitivity, good selectivity, rapid analysis time, and low sample consumption. Consequently, single-molecule detection may be potentially employed as an ideal analytical approach to quantify low-abundant biomolecules with rapidity and simplicity. In this Account, we will summarize our efforts for developing a series of ultrasensitive biosensors based on single-molecule counting. Single-molecule counting is a member of single-molecule detection technologies and may be used as a very simple and ultrasensitive method to quantify target molecules by simply counting the individual fluorescent bursts. In the fluorescent sensors, the signals of target biomolecules may be translated to the fluorescence signals by specific in vitro/in vivo fluorescent labeling, and consequently, the fluorescent molecules indicate the presence of target molecules. The resultant fluorescence signals may be simply counted by either microfluidic device-integrated confocal microscopy or total internal reflection fluorescence-based single-molecule imaging. We have developed a series of single-molecule counting-based biosensors which can be classified as separation-free and separation-assisted assays. As a proof-of-concept, we demonstrate the applications of single-molecule counting-based biosensors for sensitive detection of various target biomolecules such as DNAs, miRNAs, proteins, enzymes, and intact cells, which may function as the disease-related biomarkers. Moreover, we give a summary of future directions to expand the usability of single-molecule counting-based biosensors including (1) the development of more user-friendly and automated instruments, (2) the discovery of new fluorescent labels and labeling strategies, and (3) the introduction of new concepts for the design of novel biosensors. Due to their high sensitivity, good selectivity, rapidity, and simplicity, we believe that the single-molecule counting-based fluorescent biosensors will indubitably find wide applications in biological research, clinical diagnostics, and drug discovery.

Multiplexed Detection of Epigenetic Markers Using Quantum Dot (QD)-Encoded Hydrogel Microparticles

Epigenetic alterations in gene expression are influenced by experiences and environment, resulting in significant variation of epigenetic markers from individual to individual. Therefore, it is imperative to measure various epigenetic markers simultaneously from samples of individual subjects to accurately analyze the epigenetic markers in biological samples. Moreover, the individualized genome-wide analysis has become a critical technology for recent trends in clinical applications such as early diagnosis and personalized medicine screening of numerous diseases. The array-based detection of modified histones, conventionally used for multiplexed analysis of epigenetic changes, requires pooling of samples from many subjects to analyze population-wise differences in the expression of histone markers and does not permit individualized analysis. Here, we report multiplexed detection of genome-wide changes in various histone modifications at a single-residue resolution using quantum dot (QD)-encoded polyethylene glycol diacrylate (PEGDA) hydrogel microparticles. To demonstrate the potential of our methodology, we present the simultaneous detection of (1) acetylation of lysine 9 of histone 3 (Ac-H3K9), (2) dimethylation of H3K9 (2Me-H3K9), and (3) trimethylation of H3K9 (3Me-H3K9) from three distinct regions in the brain [nucleus accumbens (NAc), dorsal striatum (DSt), and cerebellum (Cbl)] of cocaine-exposed mice. Our hydrogel-based epigenetic assay enabled relative quantification of the three histone variants from only 10 μL of each brain lysate (protein content = ∼ 1 μg/μL) per mouse. We verified that the exposure to cocaine induced a significant increase of acetylation while a notable decrease in methylation in NAc.

A ratiometric fluorescent formaldehyde probe for bioimaging applications

The first ratiometric fluorescent formaldehyde probe (RFFP) has been engineered for bio-applications.

Recent advances in transcription factor assays in vitro

We review the recent advances in transcription factor assaysin vitroand highlight the emerging trends as well.