A cytometric bead assay for sensitive DNA detection based on enzyme-free signal amplification of hybridization chain reaction

Recent Trends and Innovations in Bead-Based Biosensors for Cancer Detection

Demand is strong for sensitive, reliable, and cost-effective diagnostic tools for cancer detection. Accordingly, bead-based biosensors have emerged in recent years as promising diagnostic platforms based on wide-ranging cancer biomarkers owing to the versatility, high sensitivity, and flexibility to perform the multiplexing of beads. This comprehensive review highlights recent trends and innovations in the development of bead-based biosensors for cancer-biomarker detection. We introduce various types of bead-based biosensors such as optical, electrochemical, and magnetic biosensors, along with their respective advantages and limitations. Moreover, the review summarizes the latest advancements, including fabrication techniques, signal-amplification strategies, and integration with microfluidics and nanotechnology. Additionally, the challenges and future perspectives in the field of bead-based biosensors for cancer-biomarker detection are discussed. Understanding these innovations in bead-based biosensors can greatly contribute to improvements in cancer diagnostics, thereby facilitating early detection and personalized treatments.

In situ imaging miRNAs using multifunctional linear DNA nanostructure

The microRNAs (miRNAs) play a critical role in many biological processes and are essential biomarkers for diagnosing disease. However, the sensitive and specific quantification of microRNAs (miRNAs) expression in living cells still faces a huge challenge. Our study designed a multifunctional linear DNA nanostructure (MLN) as a carrier of molecular beacons (MB-21) for detecting and intracellular imaging miRNA-21. The MLN-MB consists of three parts: aptamer, MLN, and MB-21. The aptamer (AS1411) could media MLN-MB enter live cells without additional transfection reagents. Once inside the cells, the intracellular miRNA-21 could hybridize the MB-21s, resulting in significantly enhanced fluorescence signals. The whole process was enzyme-free, autonomous, and continuous, which avoided the necessity of adding external fuel strands or enzymes. We demonstrated that the MLN-MB could be used to screen the miRNA-21 with a detection limit of 320 pM in a short time (10 min) and show high specificity toward miRNA-21 against other miRNAs. Moreover, the proposed MLN-MB could detect the miRNA-21 in complex matrixes stably. With its outstanding stability, dual recognition, and biocompatibility, MLN-MB is capable of delivering into living cells to identify specific cancer cells. Therefore, our sensing approach, with high sensitivity, specificity, and simplicity advantages, holds great potential for early cancer diagnosis.

Advances in optical counting and imaging of micro/nano single-entity reactors for biomolecular analysis

Ultrasensitive detection of biomarkers is of paramount importance in various fields. Superior to the conventional ensemble measurement-based assays, single-entity assays, especially single-entity detection-based digital assays, not only can reach ultrahigh sensitivity, but also possess the potential to examine the heterogeneities among the individual target molecules within a population. In this review, we summarized the current biomolecular analysis methods that based on optical counting and imaging of the micro/nano-sized single entities that act as the individual reactors (e.g., micro-/nanoparticles, microemulsions, and microwells). We categorize the corresponding techniques as analog and digital single-entity assays and provide detailed information such as the design principles, the analytical performance, and their implementation in biomarker analysis in this work. We have also set critical comments on each technique from these aspects. At last, we reflect on the advantages and limitations of the optical single-entity counting and imaging methods for biomolecular assay and highlight future opportunities in this field.

Lateral flow colorimetric biosensor for detection of Vibrio parahaemolyticus based on hybridization chain reaction and aptamer

Vibrio parahaemolyticus (V. parahaemolyticus) is the causative agent for acute hepatopancreatic necrosis disease (AHPND) of shrimp, and it is also a common seafood-borne pathogen for humans. Rapid and accurate identification of V. parahaemolyticus is helpful to diagnose the AHPND and ensure food safety. Common detection methods suffer the deficiency of time-consuming and complexed operation. Based on the increased development of aptamer and our previous study, a new detection assay of V. parahaemolyticus was introduced, in which the aptamer combined with magnetic nanoparticles (MNPs) was the recognizer, hybridization chain reaction (HCR) was the signal amplifier, and lateral flow nucleotide biosensor (LFNB) was the signal exporter. The assay possessed high specificity of distinguishing the target with other bacteria, and the calculated limit of detection was 2.6 × 10³ cells. Furthermore, the whole process just needs 67 min, free of thermocycle instruments and signal readout instruments, which means it is suitable for low-resource laboratories or districts.

Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing

Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.

Cationic Single-Chained Surfactants with a Functional Group at the End of the Hydrophobic Tail DNA Compacting Efficiency

The interaction between calf-thymus DNA, ctDNA, and various single-chained surfactants with different functional groups at the end of hydrophobic tail was studied with the goal of investigating the influence of the functional group nature on surfactant DNA compacting efficiency. The surfactants investigated were dodecyltriethylammonium bromide (DTEABr), triethyl(1-phenoxydodecyl)ammonium bromide (12PhBr), triethyl(2-naphthoxydodecyl)ammonium bromide (12NBr) and 11-(isonicotinoyloxy)-N,N,N-triethyl-1-undecanaminium bromide (11PyBr). Results made evident that the surfactants' tendencies to self-aggregation is the key factor determining their efficiency to compact the nucleic acid. Subsequently, DOPE/12NBr/pEGFP-C1 lipoplexes, with different cationic surfactant molar fractions (α) and mass ratios (L/D), were prepared and characterized. DOPE is a zwitterionic phospholipid 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, and the plasmid pEGFP-C1 carries a GFP coding sequence with the necessary regulatory elements for constitutive expression of the gene in human cells. 12NBr was chosen because it was the most efficient DNA compacting agent among the surfactants investigated. Finally, the cytotoxicity and transfection efficiency (TE) of DOPE/12NBr/pDNA lipoplexes, with different compositions, were investigated.

Development of a two-in-one integrated assay for the analysis of circRNA-microRNA interactions

The competitive endogenous RNA hypothesis is a new mechanism of RNA dialogue, in which circRNA-miRNA interaction (cmRRI) is found to be widely involved in the regulation of gene expression in tumors and other diseases. It is urgent but challenging to develop a convenient and efficient method to study the interaction between target circRNA and the candidate miRNAs. In this work, a biosensing method that allows directly analyzing cmRRI has been developed, so as to reveal the RNA dialogue strategy. The sensing system uses a bifunctional magnetic bead for the capture of target circRNA/miRNA complex as well as the signal amplification. Based on the nature of circRNA as a miRNA sponge, only if the target circRNAs and its regulatory miRNAs coexist as a complex, can the rolling circle amplification reaction be initiated to give a fluorescent signal as the output. Compared with traditional methods where the circRNA and its regulatory miRNAs have been separately analyzed, our design allows the integrated profiling of specific cmRRI by correlation characterization of two correlative RNAs, which represents a function-oriented method. The presented method also shows the analysis of the potential binding affinity of candidate miRNAs to target circRNAs. Furthermore, we have verified the ability of the sensor to directly detect cmRRI in biological samples, which reveals the promising applicability of this method for biomedical and clinical researches in the future.

Trends of Bead Counting-Based Technologies Toward the Detection of Disease-Related Biomarkers

Nowadays, the biomolecular assay platforms built-up based on bead counting technologies have emerged to be powerful tools for the sensitive and high-throughput detection of disease biomarkers. In this mini-review, we classified the bead counting technologies into statistical counting platforms and digital counting platforms. The design principles, the readout strategies, as well as the pros and cons of these platforms are introduced in detail. Finally, we point out that the digital bead counting technologies will lead the future trend for the absolute quantification of critical biomarkers, and the integration of new signal amplification approaches and routine optical/clinical instruments may provide new opportunities in building-up easily accessible digital assay platforms.

Highly sensitive SERS assay of genetically modified organisms in maize via a nanoflower substrate coupled with hybridization chain reaction amplification

A novel biosensor based on a high-density “hot spot” SERS substrate coupled with HCR amplification strategy was developed for the ultrasensitive detection of genetically modified organisms in maize.

A versatile magnetic bead-based flow cytometric assay for the detection of thyroid cancer related hsa-miR-221-3p in blood and tissues

In vitro detection of low abundance biomolecules including microRNAs (miRNAs) is essential to biological research and early clinical diagnosis. In this work, a versatile magnetic bead (MB)-based flow cytometric assay was developed for the detection of hsa-miR-221-3p, which is strongly associated with papillary thyroid carcinoma (PTC). In the presence of hsa-miR-221-3p, the complementary DNA probe attached to the surface of MBs is hybridized with the target to form DNA/RNA heteroduplexes. After the recognition of the DNA/RNA heteroduplexes by PicoGreen, the fluorescence signals of each MB were readily detected using a flow cytometer. This assay can selectively detect hsa-miR-221-3p with a detection limit of 2.1 pM. The practicality of the assay is demonstrated by the discrimination of thyroid cancer tissues from normal tissues, and a satisfactory result is obtained. Moreover, this assay can be rapidly carried out in one step at room temperature, providing a generic method for the sensitive detection of miRNAs in molecular diagnosis.

CRISPR-Assisted DNA Detection: A Novel dCas9-Based DNA Detection Technique

Nucleic acid detection techniques are always critical to diagnosis, especially in the background of the present coronavirus disease 2019 pandemic. Simple and rapid detection techniques with high sensitivity and specificity are always urgently needed. However, current nucleic acid detection techniques are still limited by traditional amplification and hybridization. To overcome this limitation, here we developed CRISPR-Cas9-assisted DNA detection (CADD). In this detection, a DNA sample is incubated with a pair of capture single guide RNAs (sgRNAs; sgRNAa and sgRNAb) specific to a target DNA, dCas9, a signal readout-related probe, and an oligo-coated solid support beads or microplate at room temperature (RT) for 15 min. During this incubation, the dCas9-sgRNA-DNA complex is formed and captured on solid support by the capture sequence of sgRNAa, and the signal readout-related probe is captured by the capture sequence of sgRNAb. Finally, the detection result is reported by a fluorescent or colorimetric signal readout. This detection was verified by detecting DNA of bacteria, cancer cells, and viruses. In particular, by designing a set of sgRNAs specific to 15 high-risk human papillomaviruses (HPVs), the HPV infection in 64 clinical cervical samples was successfully detected by the method. All detections can be finished in 30 min at RT. This detection holds promise for rapid on-the-spot detection or point-of-care testing.

Label-Free Detecting of the Compaction and Decompaction of ctDNA Molecules Induced by Surfactants with SERS Based on a nanoPAA-ZnCl2-AuLs Solid Substrate

DNA molecular compaction/decompaction is of great significance for the exploration of basic life processes, the research of biomedical and genetic engineering, and so forth. However, the detailed mechanism of DNA compaction/decompaction caused by surfactants remains an open and challenging problem that has not been fully solved so far. In this paper, a sort of novel solid substrate, nanoPAA-ZnCl₂-AuLs, with good stability and high sensitivity, was prepared by a self-assembly method. Based on this substrate, the surface-enhanced Raman scattering (SERS) technology was employed to investigate characteristics of interactions between DNA molecules and surfactants at a single molecular level. SERS spectra of calf thymus DNA (ctDNA), cetyl trimethyl ammonium bromide (CTAB), and sodium dodecyl sulfate (SDS) with a concentration as low as 10^-9 M, and SERS spectra of ctDNA-CTAB and ctDNA-CTAB-SDS composites were collected, respectively. The interactions between ctDNA and surfactants were analyzed by changes in SERS spectra, for example, disappearances and appearances of SERS bands and relative changes of peak intensity, in which CTAB resulted in the compaction of the DNA molecule while SDS induced the decompaction of the ctDNA-CTAB complex. Moreover, UV-visible spectrophotometry was employed to demonstrate the compaction/decompaction of ctDNA molecules caused by surfactants. The local binding modes of ctDNA molecules and surfactant molecules were expounded. This work will be helpful for understanding biological processes such as DNA compaction and recombination within nucleus or/and cells and for the development of gene therapy technologies.

On-bead enzyme-catalyzed signal amplification for the high-sensitive detection of disease biomarkers

The high-sensitive and rapid detection of critical biomarkers, e.g., disease-related nucleic acids and proteins, is always desired. Compared with the routine homogenous detection strategies, the on-bead flow cytometry (FCM)-based assays have drawn a lot of interests owing to their unique advantages. On one hand, microbeads (MBs) are employed for the enrichment of fluorescent signals, allowing the size encoding for multiplexed detection of biomarkers. On the other hand, FCM enables the fast read-out of the total fluorescent signals enriched on the MBs and the decoding of MBs' size information. For an improved sensitivity and versatile application scenarios, the signal amplification on MBs is required. However, the enzyme-catalyzed on-bead reactions remain challenging owing to the critical reaction conditions on the MBs/solution interface. Toward the high-sensitive detection of target biomolecules in real-samples, a series of on-bead enzyme-catalyzed signal amplification strategies have been developed. After careful optimization of the reaction conditions, the proposed sensors are proven to have ultra-high sensitivities to fulfill the requirement of real-sample detection.

A signal-flexible gene diagnostic strategy coupling loop-mediated isothermal amplification with hybridization chain reaction

Recent study proves that the combination of loop mediated isothermal nucleic acid amplification (LAMP) with one-step strand displacement (OSD) is of great help to improve the sequence specificity during genetic detection. However, because OSD is incapable of signal amplification, the signal-to-noise ratio or the observable signal change may be usually not significant enough to satisfy practical usage. With the purpose to overcome this challenge, herein a more advanced and practical sensing principle is developed with the OSD replaced by an amplifiable nucleic acid circuit, hybridization chain reaction (HCR). The very contagious norovirus (NoV) was employed as the model target. Compared with LAMP-OSD, the LAMP-HCR can detect as few as 30 copies of NoV gene in 2% fecal samples with significantly enlarged signal change and signal-to-background ratio. Therefore, more reliable detection is achieved. Moreover, due to the high compatibility of HCR, the final LAMP-HCR products can be flexibly transduced into different types of readouts, including fluorescence, flow cytometer (FCM) and even a personal glucose meter (PGM). This further enlarges the operating environments for the detection from hospital labs, bedsides, to potential off-the-shelf devices in local pharmacies. Especially when using FCM or PGM, with the assistance of magnetic beads (MBs), the detection shows even higher tolerance capability to complicated biological matrices.

Fluorometric determination of ssDNA based on functionalized magnetic microparticles and DNA supersandwich self-assemblies

A method is described for the determination of DNA via nucleic acid amplification by using nucleic acid concatemers that result from DNA supersandwich self-assemblies (SSAs). The method employs two auxiliary probes to form self-assembled biotin SSAs. These exhibit strong fluorescence if labeled with intercalator SYBR Green I. In the presence of the target (as exemplified for a 30-mer), streptavidin is released from the surface of the functionalized magnetic microparticles (FMMPs) by competitive hybridization on the surface. However, the SSA products do not conjugate to the FMMPs. This leads to a large amount of SYBR Green I intercalated into the concatemers and eventually results in amplified fluorescence in the supernate. The SSA products can be prepared beforehand, and amplification therefore can be completed within 50 min. The method is more efficient than any other conventional amplification. The detection limit for the 30-mer is 26.4 fM which is better by a factor of 10 compared to other amplification methods. Conceivably, the method can be further extended to the determination of a wide variety of targets simply by replacing the sequences of the probes. Finally, this rapid and highly sensitive method was employed for detection of Ebola virus gene (≈30-mer) and ATP in spiked serum with satisfactory results. Graphical abstract A high sensitivity and efficiency bioassay is described based on functionalized magnetic microparticles and DNA supersandwich self-assemblies.

Preparation of Fluorescence-Encoded Microspheres Based on Hydrophobic Conjugated Polymer-Dye Combination and the Immunoassay

Fluorescent microspheres are greatly demanded in many applications based on high-throughput suspension array technology. To realize the multiplexed assay, microspheres should be encoded to identify the interaction between analytes and spheres. This study advanced a strategy for preparing fluorescence-encoded microspheres, employing two hydrophobic fluorophores, poly(p-phenyleneethylene) (PPE), and Nile Red (NR), as well as the monodisperse amino-modified porous substrate polymeric spheres, poly(glycidyl methacrylate) microspheres (APGMA). Loading the fluorophores sequentially onto the substrate spheres via adsorption by immersing the spheres in the dipping solution of fluorophores resulted in the APGMA-PPE-NR spheres. By varying the concentration and combination of fluorophores in the solution, an array of 64-code APGMA-PPE-NR spheres was obtained and could be easily individually decoded via flow cytometry. A 2D dot plot from the flow cytometry of a set of mixed spheres with four different codes could also be differentiated, coincident with the overlaid plots of the spheres' corresponding codes but measured individually. These spheres were found to have good stability against washing, photobleaching, and thermal treatment. In addition, a sandwich immunoassay for the detection of goat IgG was performed, and the capability of the encoded spheres to be used in suspension array technology was demonstrated.

Principles and Applications of Nucleic Acid Strand Displacement Reactions

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.

An innovative "unlocked mechanism" by a double key avenue for one-pot detection of microRNA-21 and microRNA-141

The accurate and quantitative detection of microRNAs (miRNAs) as next-generation, reliable biomarkers will provide vital information for cancer research and treatment. However, their unique, intrinsic features pose quite a challenge for miRNA profiling, especially for multiplexed detection. Thus, there is a strong and an ever-growing need to develop an accurate, simple, sensitive and specific miRNA sensing method. Methods: In this study, a simple and novel sensor is presented that uses a flow cytometry (FCM) method based on the double key "unlocked mechanism" and a fluorescence enrichment signal amplification strategy. The "unlocked mechanism" was cleverly designed via using hairpin DNA probes (HDs) labeled by fluorescent particles (FS) as the lock to block part of them, which can specifically hybridize with the probe on polystyrene microparticles (PS). The target miRNA and duplex-specific nuclease (DSN) forming the double key can specifically open the HDs and cleave a single-stranded DNA (ssDNA) into DNA/RNA dimers circularly in order to unlock the special part of the HDs to be specially enriched further on the PS. Results: The designed sensor with a hairpin structure and DSN special performance was found to have a high specificity. The circularly unlocking fluorescent probes and fluorescent signal enrichment can be beneficial for achieving a high sensitivity with a detection limit of 3.39 fM for miRNA-21. Meanwhile, the performance of multiplexing was estimated by simultaneous detection of miR-21 and miR-141, and the method also allowed for miR-21 detection in breast cancer blood samples. Conclusion: The designed sensor based on an "unlocked mechanism" and a signal enrichment strategy resulted in a one-pot, highly specific and sensitive detection of multiplex miRNAs. The whole detection without the need for a complex purification process is based on a FCM and is expected to have a great value in cancer diagnosis and biomedical research.

Biotin-exposure-based immunomagnetic separation coupled with nucleic acid lateral flow biosensor for visibly detecting viable Listeria monocytogenes

Infectious diseases caused by Listeria monocytogenes pose a great threat to public health worldwide. Therefore, a rapid and efficient method for L. monocytogenes detection is needed. In this study, a biotin-exposure-based immunomagnetic separation (IMS) method was developed. That is, biotinylated antibody was first targeted to L. monocytogenes. Then, streptavidin-functionalized magnetic nanoparticles were added and anchored onto L. monocytogenes cells indirectly through the strong noncovalent interaction between streptavidin and biotin. Biotin-exposure-based IMS exhibited an excellent capability to enrich L. monocytogenes. Specifically, more than 90% of L. monocytogenes was captured when the bacterial concentration was lower than 10⁴ colony-forming units (CFU)/mL. Importantly, the antibody dosage was reduced by 10 times of that in our previous study, which used antibody direct-conjugated magnetic nanoparticles. Propidium monoazide (PMA) treatment prior to PCR amplification could eliminate the false-positive results from dead bacteria and detected viable L. monocytogenes sensitively and specifically. For viable L.monocytogenes detection, enriched L. monocytogenes was treated with PMA prior to asymmetric PCR amplification. The detection limits of the combined IMS with nucleic acid lateral flow (NALF) biosensor for viable L. monocytogenes detection were 3.5 × 10³ CFU/mL in phosphate buffer solution and 3.5 × 10⁴ CFU/g in lettuce samples. The whole assay process of recognizing viable L. monocytogenes was completed within 6 h. The proposed biotin-exposure-mediated IMS combined with a disposable NALF biosensor platform posed no health risk to the end user, and possessed potential applications in the rapid screening and identification of foodborne pathogens.

Development and Applications of Quantum Dot-based Molecularly Imprinted Polymer Composites for Optosensing of Carbofuran in Water

In this paper, quantum dot (QD)-based molecularly imprinted polymer (MIP) was fabricated and successfully utilized as a fluorescent probe for highly selective and sensitive detection of carbofuran in water samples. The MIPs were synthesized followed by a multi-step swelling and polymerization method, and then labeled with CdSe/ZnS QDs via gradual solvent evaporation. Then the prepared QDs-MIP microspheres were introduced to flow cytometry by virtue of their good dispersibility in water, and fast adsorption and desorption. Under optimized conditions, the fluorescence intensity of QDs-MIP decreased linearly with the increasing of carbofuran in the concentration range of 1 - 20 μg L^-1 (R² > 0.99) and it can detect down to 0.2 μg L^-1 of carbofuran. This method was simple, selective and applied successfully to the optosensing of trace carbofuran in water samples with good recoveries ranging from 94.1 ± 3.7 to 98.4 ± 4.5%.

An enzyme-free flow cytometric bead assay for the sensitive detection of microRNAs based on click nucleic acid ligation-mediated signal amplification

An enzyme-free flow cytometric assay is developed for the sensitive detection of microRNAs based on click nucleic acid ligation-mediated signal amplification.

Hybridization chain reactions on silica coated Qbeads for the colorimetric detection of multiplex microRNAs

An array of Qbead@SiO₂ integrated with target binding, hybridization chain reaction and staining achieved colorimetric detection of multiplex miRNAs.

Enzyme-free, signal-amplified nucleic acid circuits for biosensing and bioimaging analysis

Enzyme-free, signal-amplified nucleic acid circuits utilize programmed assembly reactions between nucleic acid substrates to transduce a chemical input into an amplified detection signal.

Rational design of hybridization chain reaction monomers for robust signal amplification

We established four-point guidelines for the sequence design of hairpin monomers in hybridization chain reaction (HCR). This enabled greater flexibility to customize specific hairpin sequences for use with the readout platform of interest. Using shorter hairpin stem length, a one-pot signal amplification system was demonstrated by incorporating distance-sensitive Förster resonance energy transfer (FRET) readout.

Label-free electrochemiluminescent detection of transcription factors with hybridization chain reaction amplification

Label-free and efficient ECL strategy for detection of NF-κB based on the HCR signal amplification.

Rapid and enzyme-free nucleic acid detection based on exponential hairpin assembly in complex biological fluids

Herein, we have developed a rapid and enzyme-free nucleic acid amplification detection method that combined the exponential self-assembly of four DNA hairpins and the FRET pair Cy3 and Cy5.

Lab on a single microbead: an ultrasensitive detection strategy enabling microRNA analysis at the single-molecule level

A single microbead-based sensing platform has been developed, which enables the detection of microRNA at the single-molecule level.

Detection of a single nucleic acid molecule is of great significance for both fundamental biochemistry studies and clinical diagnostics. By using microRNA (miRNA) as a model target, herein, we have developed a single-microbead-based sensing (SMBS) platform, which simply enables the detection of miRNA at the single-molecule level. In this strategy, an isothermal exponential amplification reaction (EXPAR) is rationally designed towards specific miRNAs and all products of the EXPAR are integrated onto a single microbead for signal amplification and fluorescence enrichment. This pushes the detection of miRNAs down to 1 aM in a 5 μL sample, corresponding to 3 copies of the miRNA molecule. This new strategy also affords high selectivity and it is capable of distinguishing among homologous miRNA family members even with a single-base difference. Due to its ultrahigh sensitivity and selectivity, the proposed SMBS platform has been successfully applied to the detection of miRNA extracted from a single cell.

Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection

Spectrometrically or optically encoded microsphere based suspension array technology (SAT) is applicable to the high-throughput, simultaneous detection of multiple analytes within a small, single sample volume. Thanks to the rapid development of nanotechnology, tremendous progress has been made in the multiplexed detecting capability, sensitivity, and photostability of suspension arrays. In this review, we first focus on the current stock of nanoparticle-based barcodes as well as the manufacturing technologies required for their production. We then move on to discuss all existing barcode-based bioanalysis patterns, including the various labels used in suspension arrays, label-free platforms, signal amplification methods, and fluorescence resonance energy transfer (FRET)-based platforms. We then introduce automatic platforms for suspension arrays that use superparamagnetic nanoparticle-based microspheres. Finally, we summarize the current challenges and their proposed solutions, which are centered on improving encoding capacities, alternative probe possibilities, nonspecificity suppression, directional immobilization, and "point of care" platforms. Throughout this review, we aim to provide a comprehensive guide for the design of suspension arrays, with the goal of improving their performance in areas such as multiplexing capacity, throughput, sensitivity, and cost effectiveness. We hope that our summary on the state-of-the-art development of these arrays, our commentary on future challenges, and some proposed avenues for further advances will help drive the development of suspension array technology and its related fields.

Enzyme-free and label-free signal amplification for monitoring endonuclease activity and inhibition via hybridization chain reaction

A facile and sensitive method for studying EcoRI activity and inhibition had been developed based on EcoRI-triggered hybridization chain reaction.

Sensitive mutant DNA biomarker detection based on magnetic nanoparticles and nicking endonuclease assisted fluorescence signal amplification

Amplified fluorescence target DNA detection was developed combining nicking endonuclease assisted target recycling and magnetic nanoparticles with low background signal.

Phosphorylation-induced hybridization chain reaction on beads: an ultrasensitive flow cytometric assay for the detection of T4 polynucleotide kinase activity

A versatile flow cytometric bead assay (FCBA) has been developed for an ultrasensitive detection of T4 PNK activity.

Highly sensitive DNA detection using cascade amplification strategy based on hybridization chain reaction and enzyme-induced metallization

A novel highly sensitive colorimetric assay for DNA detection using cascade amplification strategy based on hybridization chain reaction and enzyme-induced metallization was established. The DNA modified superparamagnetic beads were demonstrated to capture and enrich the target DNA in the hybridization buffer or human plasma. The hybridization chain reaction and enzyme-induced silver metallization on the gold nanoparticles were used as cascade signal amplification for the detection of target DNA. The metalization of silver on the gold nanoparticles induced a significant color change from red to yellow until black depending on the concentration of the target DNA, which could be recognized by naked eyes. This method showed a good specificity for the target DNA detection, with the capabilty to discriminate single-base-pair mismatched DNA mutation (single nucleotide polymorphism). Meanwhile, this approach exhibited an excellent anti-interference capability with the convenience of the magentic seperation and washing, which enabled its usage in complex biological systems such as human blood plasma. As an added benefit, the utilization of hybridization chain reaction and enzyme-induced metallization improved detection sensitivity down to 10pM, which is about 100-fold lower than that of traditional unamplified homogeneous assays.

Label-free and enzyme-free sensitive fluorescent detection of human immunodeficiency virus deoxyribonucleic acid based on hybridization chain reaction

A label-free and enzyme-free sensitive fluorescent detection of human immunodeficiency virus (HIV) deoxyribonucleic acid (DNA) based on isothermal hybridization chain reaction (HCR) was developed. A G-quadruplex sequence which was incorporated into one of the two hairpin probes was inactive in the absence of target DNA. However, at the presence of target DNA numerous G-quadruplexes along DNA nanowires were self-assembled through HCR. Using N-methyl mesoporphyrin IX (NMM) as the fluorophore, a "turn-on" fluorescent response would be achieved and detected as low as 0.5 nmol L(-1) of HIV DNA. This proposed method was applied to detect HIV DNA in biologic samples with satisfactory results.

Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability

Hybridization chain reaction (HCR) provides multiplexed, isothermal, enzyme-free, molecular signal amplification in diverse settings. Within intact vertebrate embryos, where signal-to-background is at a premium, HCR in situ amplification enables simultaneous mapping of multiple target mRNAs, addressing a longstanding challenge in the biological sciences. With this approach, RNA probes complementary to mRNA targets trigger chain reactions in which metastable fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. The properties of HCR lead to straightforward multiplexing, deep sample penetration, high signal-to-background, and sharp subcellular signal localization within fixed whole-mount zebrafish embryos, a standard model system for the study of vertebrate development. However, RNA reagents are expensive and vulnerable to enzymatic degradation. Moreover, the stringent hybridization conditions used to destabilize nonspecific hairpin binding also reduce the energetic driving force for HCR polymerization, creating a trade-off between minimization of background and maximization of signal. Here, we eliminate this trade-off by demonstrating that low background levels can be achieved using permissive in situ amplification conditions (0% formamide, room temperature) and engineer next-generation DNA HCR amplifiers that maximize the free energy benefit per polymerization step while preserving the kinetic trapping property that underlies conditional polymerization, dramatically increasing signal gain, reducing reagent cost, and improving reagent durability.