Freezing Directed Construction of Bio/Nano Interfaces: Reagentless Conjugation, Denser Spherical Nucleic Acids, and Better Nanoflares

A flash signal amplification approach for ultrasensitive and rapid detection of single nucleotide polymorphisms in tuberculosis

In recent years, the demand for rapid, sensitive, and simple methods for diagnosing deoxyribonucleic acid (DNA) has grown due to the increase in the variation of infectious diseases. This work aimed to develop a flash signal amplification method coupled with electrochemical detection for polymerase chain reaction (PCR)-free tuberculosis (TB) molecular diagnosis. We exploited the slightly miscible properties of butanol and water to instantly concentrate a capture probe DNA, a single-stranded mismatch DNA, and gold nanoparticles (AuNPs) to a small volume to reduce the diffusion and reaction time in the solution. In addition, the electrochemical signal was enhanced once two strands of DNA were hybridized and bound to the surface of the gold nanoparticle at an ultra-high density. To eliminate non-specific adsorption and identify mismatched DNA, the self-assembled monolayers (SAMs) and Muts proteins were sequentially modified on the working electrode. This sensitive and specific approach can detect as low as attomolar levels of DNA targets (18 aM) and is successfully applied to detecting tuberculosis-associated single nucleotide polymorphisms (SNPs) in synovial fluid. More importantly, as this biosensing strategy can amplify the signal in only a few seconds, it possesses a great potential for point-of-care and molecular diagnosis applications.

Accelerated Hybridization Chain Reaction Kinetics Using Poly DNA Tetrahedrons and Its Application in Detection of Aflatoxin B1

Traditional hybridization chain reaction (HCR) as a popular isothermal amplification technique shows some inevitable disadvantages in bioanalysis due to its relatively slow kinetics, which could be markedly promoted when the HCR initiator occurs under tension. Herein, a poly DNA tetrahedrons (pTDNs)-mediated HCR was successfully constructed to make its initiator in a stretched state by long-range electrostatic forces owing to the superimposed electrostatic interactions derived from the synthesized pTDNs, and it was hypothesized that it could remarkably enhance HCR performance, which was testified by theoretical simulations and experimental studies. Consequently, pTDNs-mediated HCR was applied to develop a novel immunoassay for rapid and sensitive detection of aflatoxin B1 as a proof-of-concept, and its signal amplification was attributed to the increased G4 DNAzyme that loaded on the second antibody. Our work paves a promising way using simple DNA frameworks alone to heighten HCR kinetics for reaction speed improvement and signal amplification in bioanalysis.

Engineering Biomimetic Biosensor Using Dual-Targeting Multivalent Aptamer Regulated 3D DNA Walker Enables High-Performance Detection of Heterogeneous Circulating Tumor Cells

The phenotypic heterogeneity of circulating tumor cells (CTCs) and the nonspecific adsorption of background cells impede the effective and sensitive detection of rare CTCs. Although leukocyte membrane coating approach has a good antileukocyte adhesion ability and holds great promise for addressing the challenge of capture purity, its limited specificity and sensitivity prevent its use in the detection of heterogeneous CTCs. To overcome these obstacles, a biomimetic biosensor that integrated dual-targeting multivalent aptamer/walker duplex functionalized biomimetic magnetic beads and an enzyme-powered DNA walker signal amplification strategy is designed. As compared to conventional leukocyte membrane coating, the biomimetic biosensor achieves efficient and high purity enrichment of heterogeneous CTCs with different epithelial cell adhesion molecule (EpCAM) expression while minimizing the interference of leukocytes. Meanwhile, the capture of target cells can trigger the release of walker strands to activate an enzyme-powered DNA walker, resulting in cascade signal amplification and the ultrasensitive and accurate detection of rare heterogeneous CTCs. Importantly, the captured CTCs remained viable and can be recultured in vitro with success. Overall, this work provides a new perspective for the efficient detection of heterogeneous CTCs by biomimetic membrane coating and paves the way for early cancer diagnosis.

Methods to functionalize gold nanoparticles with tandem-phosphorothioate DNA: role of physicochemical properties of the phosphorothioate backbone in DNA adsorption to gold nanoparticles

Perception of the differences in the physicochemical properties of phosphorothioate DNA (PS-DNA) and phosphodiester DNA (PO-DNA) greatly aids in understanding the AuNP-DNA binding process. Replacing one non-bridging oxygen atom of the anionic phosphodiester backbone with a sulfur atom leads to a major change in the DNA adsorption mechanism of AuNPs. In this work, we investigated and compared salt-aging, low pH-assisted, and freeze-thaw methods for conjugating phosphorothioate-modified oligonucleotides to AuNPs. The results obtained clearly demonstrate that only the pH-assisted method can successfully bind tandem phosphorothioate DNA to gold nanoparticles and sufficiently maintain the colloidal stability of AuNPs. When a phosphate group is converted to a phosphorothioate group, the negative charge of the phosphate group is located on the sulfur atom. Due to the soft nature of sulfur (a very weak H-bond acceptor), the negative charge on the sulfur atom cannot be shielded even with the gradual addition of salt to increase the ionic strength, so, the pH-assisted based method is the best for the functionalization of AuNPs with tandem-PS DNA.

High-Throughput Effect-Directed Monitoring Platform for Specific Toxicity Quantification of Unknown Waters: Lead-Caused Cell Damage as a Model Using a DNA Hybrid Chain-Reaction-Induced AuNPs@aptamer Self-Assembly Assay

A high-throughput cell-based monitoring platform was fabricated to rapidly measure the specific toxicity of unknown waters, based on AuNPs@aptamer fluorescence bioassays. The aptamer is employed in the platform for capturing the toxicity indicator, wherein hybrid chain-reaction (HCR)-induced DNA functional gold nanoparticle (AuNPs) self-assembly was carried out for signal amplification, which is essential for sensitively measuring the sub-lethal effects caused by target compounds. Moreover, the excellent stability given by the synthesized DNA nanostructure provides mild conditions for the aptamer thus used to bind the analyte. Herein, ATP was treated as a toxicity indicator and verified using lead-caused cell damage as a model. Under optimized conditions, excellent performance for water sample measurement was observed, yielding satisfactory accuracy (recovery rate: 82.69-114.20%; CV, 2.57%-4.65%) and sensitivity (LOD, 0.26 µM) without sample pretreatment other than filtration, indicating the method's simplicity, high efficiency, and reliability. Most importantly, this bioassay could be used as a universal platform to encourage its application in the rapid quantification of specific toxicity in varied sources of samples, ranging from drinking water to highly contaminated wastewater.

Bio-barcode assay: A useful technology for ultrasensitive and logic-controlled specific detection in food safety: A review

Food safety is one of the greatest public health challenges. Developing ultrasensitive detection methods for analytes at ultra-trace levels is, therefore, essential. In recent years, the bio-barcode assay (BCA) has emerged as an effective ultrasensitive detection strategy that is based on the indirect amplification of various DNA probes. This review systematically summarizes the progress of fluorescence, PCR, and colorimetry-based BCA methods for the detection of various contaminants, including pathogenic bacteria, toxins, pesticides, antibiotics, and other chemical substances in food in over 120 research papers. Current challenges, including long experimental times and strict storage conditions, and the prospects for the application of BCA in biomedicine and environmental analyses, have also been discussed herein.

Ultrasensitive and Specific Clustered Regularly Interspaced Short Palindromic Repeats Empowered a Plasmonic Fiber Tip System for Amplification-Free Monkeypox Virus Detection and Genotyping

The urgent necessity for highly sensitive diagnostic tools has been accentuated by the ongoing mpox (monkeypox) virus pandemic due to the complexity in identifying asymptomatic and presymptomatic carriers. Traditional polymerase chain reaction-based tests, despite their effectiveness, are hampered by limited specificity, expensive and bulky equipment, labor-intensive operations, and time-consuming procedures. In this study, we present a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a-based diagnostic platform with a surface plasmon resonance-based fiber tip (CRISPR-SPR-FT) biosensor. The compact CRISPR-SPR-FT biosensor, with a 125 μm diameter, offers high stability and portability, enabling exceptional specificity for mpox diagnosis and precise identification of samples with a fatal mutation site (L108F) in the F8L gene. The CRISPR-SPR-FT system can analyze viral double-stranded DNA from mpox virus without amplification in under 1.5 h with a limit of detection below 5 aM in plasmids and about 59.5 copies/μL when in pseudovirus-spiked blood samples. Our CRISPR-SPR-FT biosensor thus offers fast, sensitive, portable, and accurate target nucleic acid sequence detection.

Butanol accelerated entropy-driven DNA walking machine for rapid and ultrasensitive determination of alkaline phosphatase activity

Alkaline phosphatase (ALP) as an important biomarker as well as an index for the pasteurization degree of dairy food. However, there is a dilemma between the sensitivity and time-cost of ALP determination based on nucleic acid amplification approach. Herein, an ultrasensitive and rapid detection method for the ALP assay was developed based on entropy-driven DNA machine. In our design, the ALP catalyzed dephosphorylation of detection probe, which inhibited the digestion effect of lambda exonuclease. The remaining probe as a linker to tether the walking strand proximity to the surface of track strand modified gold nanoparticle, activating entropy-driven DNA machine. Accompany with walking strand moving, a large amount of assembled dye-labelled strand dissociated from gold nanoparticle with fluorescence recovery. More importantly, to further improve the walking efficiency, butanol was introduced to accelerated the signal amplification at interface, which short the incubation time from several hours to 5 min. Under the optimum condition, the change of fluorescence intensity was proportion to the concentration of ALP in the range from 0.05 U L^-1 to 5 U L^-1 with an ultralow limit of detection of 2.07 × 10^-3 U L^-1 was achieved, which is superior to other reported methods. Furthermore, the proposed method also successfully applied for the spiked milk sample assay with satisfactory recovery in the range of 98.83%-103.00%. This work proposed a new strategy for the application of entropy-driven DNA machine in the field of rapid and ultrasensitive detection.

Comparison of DNA-Gold Nanoparticle Conjugation Methods: Application in Lateral Flow Nucleic Acid Biosensors

Lateral flow nucleic acid biosensors (LFNABs) have attracted extensive attention due to their rapid turnaround time, low cost, and results that are visible to the naked eye. One of the key steps to develop LFNABs is to prepare DNA-gold nanoparticle (DNA-AuNP) conjugates, which affect the sensitivity of LFNABs significantly. To date, various conjugation methods-including the salt-aging method, microwave-assisted dry heating method, freeze-thaw method, low-pH method, and butanol dehydration method-have been reported to prepare DNA-AuNP conjugates. In this study, we conducted a comparative analysis of the analytical performances of LFNABs prepared with the above five conjugation methods, and we found that the butanol dehydration method gave the lowest detection limit. After systematic optimization, the LFNAB prepared with the butanol dehydration method had a detection limit of 5 pM for single-strand DNA, which is 100 times lower than that of the salt-aging method. The as-prepared LFNAB was applied to detect miRNA-21 in human serum, with satisfactory results. The butanol dehydration method thus offers a rapid conjugation approach to prepare DNA-AuNP conjugates for LFNABs, and it can also be extended to other types of DNA biosensors and biomedical applications.

RNA-cleaving deoxyribozyme-linked immunosorbent assay for the ultrasensitive detection of chloramphenicol in milk

In this presented work, an artificial deoxyribozyme was employed as the substitute for horseradish peroxidase (or alkaline phosphatase) in ELISA for generating amplified signals. The feasibility of the proposed deoxyribozyme-based ELISA (DLISA) was demonstrated in the detection of a forbidden veterinary drug, chloramphenicol. And its efficiency was praised since that ultrahigh sensitivity was accomplished with a detection limit of 0.1 ng/L. The wide linear range from 0.000001 μg/mL to 1.0 μg/mL, as well as good recoveries from 86 % to 104 % in whole milk samples showed its excellent practical performances. Besides, the DLISA was worth popularizing due to the easy connection of antibody and DNAzyme through a facile functionalization process of gold nanoparticles. These advantages showed the possibility of DLISA for developing commercial kits, and the utilization of flexible DNA fluorescent probes in DLISA would inspire more work on innovations.

Size-controllable colloidal Ag nano-aggregates with long-time SERS detection window for on-line high-throughput detection

Making metal nanoparticle aggregates is a common way to improve surface-enhanced Raman scattering (SERS) enhancement via the formation of hot spots between nanoparticles. Here, we propose a "freeze-thaw-ultrasonication" method to obtain stable colloidal Ag nano-aggregates (AgNAs) with controllable sizes, which can remain stable for a few days. Compared with other method using aggregation reagents (e.g., organic molecules and salt), this method can maintain metal surface charges and adsorption affinity, which ensures the excellent SERS stability and sensitivity. The SERS detection window during the experiment can reach more than 25 min, which makes it a prerequisite for accurate SERS detection during a long-time range. Combining the obtained stable AgNAs with microfluidic devices, we established a sequential SERS on-line continuous detection method for the high-throughput detection of multiplex samples. The UV-Fenton degradation process of methylene blue (MB) is continuously on-line monitored through this platform, which is more sensitive than the UV-Vis Spectrum. Moreover, we have realized the sensitive and accurate detection of 5-nitro-8-hydroxyquinoline (5-NQ) with antibacterial and anticancer activities based on chloride-functionalized silver, which paved a way for SERS high-throughput analysis in bioanalysis and other fields.

Nanoparticle Spikes Enhance Cellular Uptake via Regulating Myosin IIA Recruitment

Spike-like nanostructures are omnipresent in natural and artificial systems. Although biorecognition of nanostructures to cellular receptors has been indicated as the primary factor for virus infection pathways, how the spiky morphology of DNA-modified nanoparticles affects their cellular uptake and intracellular fate remains to be explored. Here, we design dually emissive gold nanoparticles with varied spikiness (from 0 to 2) to probe the interactions of spiky nanoparticles with cells. We discovered that nanospikes at the nanoparticle regulated myosin IIA recruitment at the cell membrane during cellular uptake, thereby enhancing cellular uptake efficiency, as revealed by dual-modality (plasmonic and fluorescence) imaging. Furthermore, the spiky nanoparticles also exhibited facilitated endocytosis dynamics, as revealed by real-time dark-field microscopy (DFM) imaging and colorimetry-based classification algorithms. These findings highlight the crucial role of the spiky morphology in regulating the intracellular fate of nanoparticles, which may shed light on engineering theranostic nanocarriers.

One-step multiplex analysis of breast cancer exosomes using an electrochemical strategy assisted by gold nanoparticles

Exosomes, as a non-invasive biomarker, perform an important role in breast cancer screening and prognosis monitoring. However, establishing a simple, sensitive, and reliable exosome analysis technique remains challenging. Herein, a one-step multiplex analysis electrochemical aptasensor based on a multi-probe recognition strategy was constructed to analyze breast cancer exosomes. HER2-positive breast cancer cell (SK-BR-3) exosomes were selected as the model targets and three aptamers including CD63, HER2 and EpCAM aptamers were used as the capture units. Methylene blue (MB) functionalized HER2 aptamer and ferrocene (Fc) functionalized EpCAM aptamer, which were modified on gold nanoparticles (Au NPs), i.e. MB-HER2-Au NPs and Fc-EpCAM-Au NPs, were used as signal units. When the mixture of target exosomes, MB-HER2-Au NPs and Fc-EpCAM-Au NPs were added on the CD63 aptamer modified gold electrode, two Au NPs modified by MB and Fc could be specifically captured on the electrode by the recognition of three aptamers with target exosomes. Then one-step multiplex analysis of exosomes was achieved by detecting two independent electrochemical signals. This strategy can not only distinguish breast cancer exosomes from other exosomes (including normal exosomes and other tumor exosomes) but also HER2-positive breast cancer exosomes and HER2-negative breast cancer exosomes. Besides, it had high sensitivity and can detect SK-BR-3 exosomes with a concentration as low as 3.4 × 10³ particles mL^-1. Crucially, this method can be applicable to the examination of exosomes in complicated samples, which is anticipated to afford assistance for the screening and prognosis of breast cancer.

A novel nanoparticle surface-constrained CRISPR-Cas12a 3D DNA walker-like nanomachines for sensitive and stable miRNAs detection

The CRISPR-Cas system has broad prospects as a new type of nucleic acid signal amplification technology based on the trans-cleavage activity of Cas12a to single-stranded DNA, but the trans-cleavage reaction efficiency is relatively low in solution. In order to overcome this negative factor, a new 3D DNA nanomachine whose CRISPR-Cas12a is limited to the surface of nanoparticles is used for sensitive and stable detection of miRNA. By loading Cas12a activator onto spherical nucleic acid (SNA), the CRISPR-Cas12a activator system on the surface of Au nanoparticles (AuNPs) acts as a walker to carry out continuous recognition-walking-cutting reaction on the surface of AuNPs, which enhances the trans-cleavage activity of Cas12a to SNAs. Benefiting from the confinement effect of spherical nucleic acids surface, a 3D DNA nanomachine has been developed for the detection of miRNA-21, which has achieved high sensitivity and accuracy, and the detection limit is able to reach 8.0 pM. This new 3D DNA walker-like nanomachine provided another insight for future bioanalysis and early clinical diagnoses of disease and liquid biopsy.

Challenges and opportunities for SERS in the infrared: materials and methods

In the wake of a global, heightened interest towards biomarker and disease detection prompted by the SARS-CoV-2 pandemic, surface enhanced Raman spectroscopy (SERS) positions itself again at the forefront of biosensing innovation. But is it ready to move from the laboratory to the clinic? This review presents the challenges associated with the application of SERS to the biomedical field, and thus, to the use of excitation sources in the near infrared, where biological windows allow for cell and through-tissue measurements. Two main tackling strategies will be discussed: (1) acting on the design of the enhancing substrate, which includes manipulation of nanoparticle shape, material, and supramolecular architecture, and (2) acting on the spectral collection set-up. A final perspective highlights the upcoming scientific and technological bets that need to be won in order for SERS to stably transition from benchtop to bedside.

Spherical DNA for Probing Wettability of Microplastics

Wettability of microplastics may change due to chemical or physical transformations at their surface. In this work, we studied the adsorption of spherical nucleic acids (SNAs) with a gold nanoparticle core and linear DNA of the same sequence to probe the wettability of microplastics. Soaking microplastics in water at room temperature for 3 months resulted in the enhancement of SNA adsorption capacity and affinity, whereas linear DNA adsorption was the same on the fresh and soaked microplastics. Drying of the soaked microplastics followed by rehydration decreased the adsorption of the SNA, suggesting that the effect of soaking was reversible and related to physical changes instead of chemical changes of the microplastics. Raman spectroscopy data also revealed no chemical transformations of the soaked microplastics. Heating of microplastics over a short period induced a similar effect to long-term soaking. We propose that soaking or heating removes air entrapped in the nanosized pores at the water-plastic interface, increasing the contact surface area of the SNA to afford stronger adsorption. However, such wetted porosity would not change the adsorption of linear DNA because of its much smaller size.

Surface engineering of colloidal nanoparticles

Synthesis of engineered colloidal nanoparticles (NPs) with delicate surface characteristics leads to well-defined physicochemical properties and contributes to multifunctional applications. Surface engineering of colloidal NPs can improve their stability in diverse solvents by inhibiting the interparticle attractive forces, thus providing a prerequisite for further particle manipulation, fabrication of the following materials and biological applications. During the last decades, surface engineering methods for colloidal NPs have been well-developed by numerous researchers. However, accurate control of surface properties is still an important topic. The emerging DNA/protein nanotechnology offers additional possibility of surface modification of NPs and programmable particle self-assembly. Here, we first briefly review the recent progress in surface engineering of colloidal NPs, focusing on the improved stability by grafting suitable small molecules, polymers or biological macromolecules. We then present the practical strategies for nucleic acid surface encoding of NPs and subsequent programmable assembly. Various exciting applications of these unique materials are summarized with a specific focus on the cellular uptake, bio-toxicity, imaging and diagnosis of colloidal NPs in vivo. With the growing interest in colloidal NPs in nano-biological research, we expect that this review can play an instructive role in engineering the surface properties for desired applications.

Targeted degradation of ABCG2 for reversing multidrug resistance by hypervalent bispecific gold nanoparticle-anchored aptamer chimeras

Hypervalent bispecific gold nanoparticle-anchored aptamer chimeras (AuNP-APTACs) were designed as a new tool of lysosome-targeting chimeras (LYTACs) for efficient degradation of the ATP-binding cassette, subfamily G, isoform 2 protein (ABCG2) to reverse multidrug resistance (MDR) of cancer cells. The AuNP-APTACs could effectively increase the accumulation of drugs in drug-resistant cancer cells and provide comparable efficacy to small-molecule inhibitors. Thus, this new strategy provides a new way to reverse MDR, holding great promise in cancer therapy.

Irregular DNA Triangular Prism/Triplex Assembly for Duplicate MiRNA Analysis with Nicking Endonuclease-Mediated Amplification

Highly sensitive and selective detection of microRNA (miRNA) is becoming more and more important in the discovery, diagnosis, and prognosis of various diseases. Herein, we develop a three-dimensional DNA nanostructure based electrochemical platform for duplicate detection of miRNA amplified by nicking endonuclease. Target miRNA first helps construction of three-way junction structures on the surfaces of gold nanoparticles. After nicking endonuclease-powered cleavage reactions, single-stranded DNAs labeled with electrochemical species are released. These strands can be facilely immobilized at four edges of the irregular triangular prism DNA (iTPDNA) nanostructure via triplex assembly. By evaluating the electrochemical response, target miRNA levels can be determined. In addition, the triplexes can be disassociated by simply changing pH conditions, and the iTPDNA biointerface can be regenerated for duplicate analyses. The developed electrochemical method not only exhibits an excellent prospect in the detection of miRNA but also may inspire the engineering of recyclable biointerfaces for biosensing platforms.

A novel ultrasensitive and fast aptamer biosensor of SEB based on AuNPs-assisted metal-enhanced fluorescence

A fluorescent biosensor strategy was developed in combination with immunomagnetic separation for rapid and sensitive detection of staphylococcal enterotoxin B (SEB). Magnetic nanoparticles (MNPs) modified with aptamer of SEB could capture the SEB. Then the gold nanoparticles (AuNPs) fluorescent probe was added and a "sandwich structure" was formed between AuNPs, SEB and MNPs. The MNPs-SEB-AuNPs structure could be separated with an additional magnetic field, which resulted the lower signals of AuNPs fluorescent probe. In optimal conditions, the current method displayed a broad quantitative range from 100 to 10⁷ fg/mL and the limit of detection was 3.43 fg/mL. The recovery of SEB-spiked milk samples ranged from 92.00 to 119.00 %, which revealed that the developed method had great accuracy. Furthermore, the method was fast and economical for ultrasensitive detection. Therefore, the fluorescent biosensor based on MNPs-AuNPs is promising for the detection of other environmental and food pollutants.

MnO2@Au nanostructures supported colorimetric biosensing with duplex-specific nuclease-assisted DNA structural transition

Manganese dioxide (MnO₂) nanosheets are regarded as a new class of two-dimensional nanomaterials with several attractive properties with enormous progress in biomedical fields. Gold nanoparticles (AuNPs) are also important biocompatible nanomaterials with unusual optical properties. Hetero-nanostructure of MnO₂ and AuNPs with the medium of DNA is an interesting topic. In this work, the protection of the hetero-nanostructure from salt-induced aggregation is systematically investigated including the effects of sequence length, reagents concentrations, incubation time and temperature. The MnO₂@Au nanostructures are thus applied for the analysis of miRNA. Duplex-specific nuclease (DSN) catalyzed digestion, hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) are utilized for signal amplification. By finally analyzing the optical responses of the nanocomponents, highly sensitive analysis of target miRNA can be achieved. Excellent analytical performances are attributed to the unique features of MnO₂@Au nanostructures and signal amplification designs. They are promising basis for the construction of novel biosensors for clinical applications.

A DNA walker triggered isothermal amplification method based on freezing construction of AuNP probes and its application in ricin detection

DNA molecular machines are widely used in the fields of biosensors and biological detection. Among them, DNA walkers have attracted much attention due to their simple design and controllability. Herein, we attempt to develop a DNA walker triggered exponential amplification method and explore its application. The AuNP probes in the DNA walker are constructed by a freezing technology, instead of the time-consuming and complex synthesis process of the traditional method. Meanwhile, after the "recognition-cleavage-relative motion" cycle of this DNA walker reaction, the exponential amplification reaction is initiated, and leads to the fluorescence recovery of the molecular beacon. Taking ricin as a target, this new method shows a limit of detection of 2.25 pM by selecting aptamers with strong binding affinity, and exhibits a wide detection range, satisfactory specificity, and excellent stability in practical application. Therefore, our method provides a universal sensing platform and has great prospects in the fields of biosensors, food safety detection, and clinical diagnostics.

Ultrasensitive detection of SARS-CoV-2 S protein with aptamers biosensor based on surface-enhanced Raman scattering

A rapid and accurate diagnostic modality is essential to prevent the spread of SARS-CoV-2. In this study, we proposed a SARS-CoV-2 detection sensor based on surface-enhanced Raman scattering (SERS) to achieve rapid and ultrasensitive detection. The sensor utilized spike protein deoxyribonucleic acid aptamers with strong affinity as the recognition entity to achieve high specificity. The spherical cocktail aptamers-gold nanoparticles (SCAP) SERS substrate was used as the base and Au nanoparticles modified with the Raman reporter molecule that resonates with the excitation light and spike protein aptamers were used as the SERS nanoprobe. The SCAP substrate and SERS nanoprobes were used to target and capture the SARS-CoV-2 S protein to form a sandwich structure on the Au film substrate, which can generate ultra-strong "hot spots" to achieve ultrasensitive detection. Analysis of SARS-CoV-2 S protein was performed by monitoring changes in SERS peak intensity on a SCAP SERS substrate-based detection platform. This assay detects S protein with a LOD of less than 0.7 fg mL^-1 and pseudovirus as low as 0.8 TU mL^-1 in about 12 min. The results of the simulated oropharyngeal swab system in this study indicated the possibility of it being used for clinical detection, providing a potential option for rapid and accurate diagnosis and more effective control of SARS-CoV-2 transmission.

Non-Invasive, Reliable, and Fast Quantification of DNA Loading on Gold Nanoparticles by a One-Step Optical Measurement

An exquisite, versatile, and reproducible quantification of DNA loading on gold nanoparticles (Au NPs) has long been pursued because this loading influences the analytical, therapeutic, and self-assembly behaviors of DNA-Au NPs. Nevertheless, the existing methods used thus far rely solely on the invasive detachment and subsequent spectroscopic quantification of DNA, which are error-prone and highly dependent on trained personnel. Here, we present a non-invasive optical framework that can determine the number of DNA strands on Au NPs by versatile one-step measurement of the visible absorption spectra of DNA-Au NP solutions without any invasive modifications or downstream processes. Using effective medium theory in conjunction with electromagnetic numerical calculation, the change in DNA loading density, resulting from varying the ion concentration, Au NP size, DNA strand length, and surrounding temperature, can be tracked in situ merely by the one-step measurement of visible absorption spectra, which is otherwise impossible to achieve. Moreover, the simplicity and robustness of this method promote reproducible DNA loading quantification regardless of experimental adeptness, which is in stark contrast with existing invasive and multistep methods. Overall, the optical framework outlined in this work can contribute to democratizing research on DNA-Au NPs and facilitating their rapid adoption in transformative applications.

A Label-Free, Mix-and-Detect ssDNA-Binding Assay Based on Cationic Conjugated Polymers

The accurate, simple, and efficient measurement of the concentration of single-stranded DNA (ssDNA) is important for many analytical applications, such as DNA adsorption, biosensor design, and disease diagnosis, but it is still a challenge. Herein, we studied a cationic conjugated polymer (CCP)-based ssDNA assay taking advantage of the obvious fluorescence change of CCPs upon binding ssDNA. Poly(3-(3'-N,N,N-triethylamino-1'-propyloxy)-4-methyl-2,5-thiophene hydrochloride) (PMNT) achieved an apparent dissociation constant (K_d) of 57 ± 4 nM for ssDNA, indicating a very high binding affinity between PMNT and ssDNA. This allowed us to develop a CCP-based ssDNA biosensor with a detection limit of 0.6 nM, similar to the fluorescence-dye-based method using SYBR Green I and SYBR Gold. Our CCP-based biosensor produced smaller differences among ssDNA samples with different base compositions. In addition, the existence of double-stranded DNA (dsDNA) at different concentrations did not interfere with the fluorescence of PMNT, indicating that our CCP-based biosensor was more suitable for the measurement of ssDNA. Compared with fluorescence-intensity-based quantification, our CCP system allowed ratiometric quantification, which made the calibration easier and more robust. We then applied our method to the quantification of ssDNA on AuNPs using both unmodified and thiolated ssDNA, and the accurate quantification of ssDNA was achieved without any fluorophore modification. This method provides an alternative approach for the measurement of ssDNA.

Telomerase-initiated three-dimensional DNAzyme motor for monitoring of telomerase activity in living cells

Telomerase (TE) is recognized as a potential biomarker for early diagnosis, monitoring and treatment of cancer. At present, most of the methods for TE detection are only applicable to in vitro assays, and unsuitable for in vivo applications. Though a few intracellular probes have been reported to have good specificity for TE, they do not involve signal amplification, which hinders their applicability in scenarios requiring high sensitivity. It is rather challenging to develop highly sensitive biosensors for intracellular TE detection due to the difficulty in design TE probes with both high specificity and compatibility with signal amplification in living cells. Herein, a highly sensitive and selective three-dimensional DNAzyme motor for monitoring of TE activity in living cells was developed by innovatively integrating TE-mediated chain replacement reaction with a three-dimensional DNA walker. Specifically, the DNAzyme motor was constructed by assembling both DNAzyme substrates and swing arms made up of a hairpin-structured DNAzyme and a telomeric primer onto gold nanoparticles. TE in cells can activate the DNAzyme motor to carry out continuous chain replacement and substrate cutting reactions, and hence realize signal amplification in living cells. The DNAzyme motor was successfully utilized to monitor the dynamic changes of TE activity in four types of cells. Due to the advantages of simple synthesis, good biocompatibility and high sensitivity and specificity for TE, the proposed DNAzyme motor is expected to have great application potential in the early diagnosis of cancer.

Rapid Point-of-Care Assay by SERS Detection of SARS-CoV-2 Virus and Its Variants

Addressing the spread of coronavirus disease 2019 (COVID-19) has highlighted the need for rapid, accurate, and low-cost diagnostic methods that detect specific antigens for SARS-CoV-2 infection. Tests for COVID-19 are based on reverse transcription PCR (RT-PCR), which requires laboratory services and is time-consuming. Here, by targeting the SARS-CoV-2 spike protein, we present a point-of-care SERS detection platform that specifically detects SARS-CoV-2 antigen in one step by captureing substrates and detection probes based on aptamer-specific recognition. Using the pseudovirus, without any pretreatment, the SARS-CoV-2 virus and its variants were detected by a handheld Raman spectrometer within 5 min. The limit of detection (LoD) for the pseudovirus was 124 TU μL-1 (18 fM spike protein), with a linear range of 250-10,000 TU μL-1. Moreover, this assay can specifically recognize the SARS-CoV-2 antigen without cross reacting with specific antigens of other coronaviruses or influenza A. Therefore, the platform has great potential for application in rapid point-of-care diagnostic assays for SARS-CoV-2.

Isolation of Bacteria Aptamers with Non-SELEX for the Development of a Highly Sensitive Colorimetric Assay Based on Dual Signal Amplification

In this work, an aptamer against Escherichia coli is isolated via non-SELEX, which executes efficient selection by employing repetitive cycles of centrifugation-based partitioning, and the binding site of the aptamer on E. coli cell surfaces is inferred to be a membrane protein. Moreover, truncated sequence 2-17-2 with a higher affinity (K_d = 101.76 nM) is employed for highly sensitive colorimetric detection of bacteria based on the dual signal amplification strategy. When targets exist, the release of DNA 1 from the polymer activates a hybridization chain reaction (HCR) between DNA 1 and DNA 2, thereby inducing the aggregation of probe 1. Subsequently, DNA 3 dissociated from probe 1 as a linker DNA further assembles probe 2/3. In this system, two types of DNA@gold nanoparticles (AuNPs) coexist and successively aggregate AuNPs based on divergent triggering mechanisms. Under optimal conditions, the dual signal amplification strategy presents excellent sensitivity (10 CFU mL^-1) and specificity, as well as the realization of real sample analysis.

Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes

Reliable characterization of binding affinities is crucial for selected aptamers. However, the limited repertoire of universal approaches to obtain the dissociation constant (K_D) values often hinders the further development of aptamer-based applications. Herein, we present a competitive hybridization-based strategy to characterize aptamers using DNA origami-based chiral plasmonic assemblies as optical reporters. We incorporated aptamers and partial complementary strands blocking different regions of the aptamers into the reporters and measured the kinetic behaviors of the target binding to gain insights on aptamers' functional domains. We introduced a reference analyte and developed a thermodynamic model to obtain a relative dissociation constant of an aptamer-target pair. With this approach, we characterized RNA and DNA aptamers binding to small molecules with low and high affinities.

DNA-functionalized gold nanoparticles: Modification, characterization, and biomedical applications

With the development of technologies based on gold nanoparticles (AuNPs), bare AuNPs cannot meet the increasing requirements of biomedical applications. Modifications with different functional ligands are usually needed. DNA is not only the main genetic material, but also a good biological material, which has excellent biocompatibility, facile design, and accurate identification. DNA is a perfect ligand candidate for AuNPs, which can make up for the shortcoming of bare AuNPs. DNA-modified AuNPs (DNA-AuNPs) have exciting features and bright prospects in many fields, which have been intensively investigated in the past decade. In this review, we summarize the various approaches for the immobilization of DNA strands on the surface of AuNPs. Representative studies for biomedical applications based on DNA-AuNPs are also discussed. Finally, we present the challenges and future directions.

A Sensitive and Nonoptical CRISPR Detection Mechanism by Sizing Double‐Stranded λ DNA Reporter

CRISPR-based biosensors often rely on colorimetric, fluorescent, or electrochemical signaling mechanism, which involves expensive reporters and/or sophisticated equipment. Here, we demonstrated a simple, inexpensive, nonoptical, and sensitive CRISPR-Cas12a-based sensing platform to detect ssDNA targets by sizing double-stranded λ DNA as novel report molecules. In this platform, the size reduction of λ DNA was quantified by gel electrophoresis analysis. We hypothesize that the massive trans-nuclease activity of Cas12a toward λ DNA is due to the presence of single-stranded looped structures along the λ DNA sequence. In addition, we observed a strong binding affinity between Cas12a and λ DNA, which further promotes the trans-cleavage activity and helps achieve sub-picomolar detection sensitivity, ≈100 times more sensitive than the fluorescent counterpart. The concept of utilizing the physical size change of λ DNA unlocks the possibility of using a variety of dsDNA as CRISPR reporters.

Modular nanoarray vaccine for SARS-CoV-2

The current vaccine development strategies for the COVID-19 pandemic utilize whole inactive or attenuated viruses, virus-like particles, recombinant proteins, and antigen-coding DNA and mRNA with various delivery strategies. While highly effective, these vaccine development strategies are time-consuming and often do not provide reliable protection for immunocompromised individuals, young children, and pregnant women. Here, we propose a novel modular vaccine platform to address these shortcomings using chemically synthesized peptides identified based on the validated bioinformatic data about the target. The vaccine is based on the rational design of an immunogen containing two defined B-cell epitopes from the spike glycoprotein of SARS-CoV-2 and the universal T-helper epitope PADRE. The epitopes were conjugated to short DNA probes and combined with a complementary scaffold strand, resulting in sequence-specific self-assembly. The immunogens were then formulated by conjugation to gold nanoparticles by three methods or by co-crystallization with epsilon inulin. BALB/C mice were immunized with each formulation, and the IgG immune responses and virus neutralizing titers were compared. The results demonstrate that this assembly is immunogenic and generates neutralizing antibodies against wildtype SARS-CoV-2 and the Delta variant.

Photoacoustic detection of SARS-CoV-2 spike N501Y single-nucleotide polymorphism based on branched rolling circle amplification

Rapid and accurate diagnosis of SARS-CoV-2 single-nucleotide variations is an urgent need for the initial detection of local circulation and monitoring the alternation of dominant variant. In this proof-of-concept study, a homogeneous and isothermal photoacoustic biosensor is demonstrated for rapid molecular amplification and detection of a synthetic DNA corresponding to SARS-CoV-2 spike N501Y. Branched rolling circle amplification produces single-stranded amplicons that can aggregate detection probe-modified AuNPs, which induces a strong photoacoustic signal at 640 nm due to both the surface plasmon resonance shift and the size-dependent effect of laser-induced nanobubbles, achieving a sub-femtomolar detection limit within a total assay time of 80 min. The limit of detection can be kept when measuring 5% serum samples. Moreover, the proposed biosensor is highly specific for single-nucleotide polymorphism discrimination and robust against background DNA.

Recent Advances in Detection for Breast-Cancer-Derived Exosomes

Breast cancer is the most common malignant tumor in women, its incidence is secret, and more than half of the patients are diagnosed in the middle and advanced stages, so it is necessary to develop simple and efficient detection methods for breast cancer diagnosis to improve the survival rate and quality of life of breast cancer patients. Exosomes are extracellular vesicles secreted by all kinds of living cells, and play an important role in the occurrence and development of breast cancer and the formation of the tumor microenvironment. Exosomes, as biomarkers, are an important part of breast cancer fluid biopsy and have become ideal targets for the early diagnosis, curative effect evaluation, and clinical treatment of breast cancer. In this paper, several traditional exosome detection methods, including differential centrifugation and immunoaffinity capture, were summarized, focusing on the latest research progress in breast cancer exosome detection. It was summarized from the aspects of optics, electrochemistry, electrochemiluminescence and other aspects. This review is expected to provide valuable guidance for exosome detection of clinical breast cancer and the establishment of more reliable, efficient, simple and innovative methods for exosome detection of breast cancer in the future.

Simultaneous Determination of Antibiotics, Mycotoxins, and Hormones in Milk by an 8-17 DNAzyme-Based Enzyme-Linked Immunosorbent Assay

The simultaneous detection of three kinds of small-molecule contaminants (antibiotics, mycotoxins, and hormones) in milk was realized by using an 8-17 DNAzyme-based fluorescent enzyme-linked immunosorbent assay (ELISA), in which 8-17 DNAzyme was utilized as the catalytic enzyme for amplifying the signal. Compared with the conventional ELISA in which horseradish peroxidase is used as the catalyzing factor, this 8-17 DNAzyme-based ELISA could achieve multicolor signal output with lower detection limits. The linearities for chloramphenicol, 17β-estradiol, and aflatoxin M₁ were in the range of 0.3 ng/mL-3 μg/mL, 3 ng/mL-3 μg/mL, and 3 pg/mL-3 ng/mL with quantitation limits of 0.3, 3, and 0.003 ng/mL, respectively. This proposed scheme demonstrated that the 8-17 DNAzyme might be an effective substitute for horseradish peroxidase in ELISA for the development of ultrasensitive and multicolor fluorescence immunoassay, which would stimulate the development of ELISA in a new orientation.

Framework and Spherical Nucleic Acids Synergistically Enhanced Electrochemiluminescence Nanosensors for Rapidly Diagnosing Acute Myocardial Infarction Based on Circulating MicroRNA Levels

Acute myocardial infarction (AMI)-related microRNAs (miRNAs) in circulating blood have been proved as promising biomarkers for AMI diagnosis. The detection of these miRNAs at ultralow levels usually requires nucleic acid amplification strategies to improve the sensitivity at the cost of time. Given that the first hour after an AMI attack is the golden time for saving AMI patients' lives, shortening the time of ultrasensitive miRNA analysis is of great significance for clinical AMI diagnosis. Toward this goal, here we present a direct electrochemiluminescence (ECL) sensing strategy for fast and ultrasensitive miRNA detection, circumventing the time-consuming signal amplification steps. Target miRNAs are directly hybridized with two probe strands that are attached to a covalently hemin-modified spherical nucleic acid enzyme (SNAzyme) and a truncated triangular pyramid DNA nanoplatform on the electrode, respectively. Both of them improve the ECL signal and meanwhile reduce the background, thereby remarkably promoting the detection sensitivity of target miRNAs. It enables the rapid detection of an AMI-related miRNA (miR-499) at 10 aM in human serum within 30 min using the SNAzyme-catalyzed luminol-H₂O₂ ECL reaction. This sensing strategy is then utilized for AMI diagnosis via probing endogenous miR-499 in patients' circulating blood with endogenous miR-16 as an intrinsic reference, showing a significant difference (P < 0.001) between the miR-499 levels of patients and the healthy.

Paper-based LRET sensor for the detection of total heavy rare-earth ions

Based on the mechanism of luminescence resonance energy transfer (LRET) and using a special single strand DNA as the recognition element, a portable paper-based sensor for the accurate detection of total heavy rare-earth ions (mainly Gd3+, Tb3+ and Dy3+) concentration was proposed. The RNA cleaving-DNAzyme should recognize rare-earth ions to cleave RNA on DNA duplexes linking UCNPs and AuNPs, causing UCNPs and AuNPs to approach each other, inducing LRET, which attenuated the green upconversion luminescence (UCL) triggered by the 980 nm laser. UCL was captured by a charge-coupled device (CCD) image sensor and processed with the red-green-blue (RGB) image to quantitatively analyze heavy rare-earth ions in the samples. In the range of 5–50 μmol·L-1, the sensor has good sensitivity, with the limit of detection of 1.26 μmol L−1.

Ratiometric Electrochemiluminescence Sensing of Carcinoembryonic Antigen Based on Luminol

Ratiometric electrochemiluminescence (ECL) sensors can efficiently remove environmental interference to attain precise detection. Nonetheless, two eligible luminophores or coreactants were usually needed, increasing the complexity and restricting their practical application. In this study, a single luminophore of luminol with a single coreactant of H₂O₂ was employed to construct a dual-potential ratiometric ECL sensor for the detection of carcinoembryonic antigen (CEA). The produced palladium nanoclusters (Pd NCs) employing a DNA duplex as a template could not only stimulate luminol to produce cathodic ECL (I_cathodic) but also quench its anodic ECL (I_anodic). During the detection process, CEA could damage the double-stranded structure and reduce the Pd NCs' amount, triggering a significant decrease in the ratio of I_cathodic to I_anodic (I_cathodic/I_anodic) and thereby achieving sensitive CEA's detection. Furthermore, the I_cathodic/I_anodic was independent of the H₂O₂ concentration, which avoided a prejudicial effect from H₂O₂ decomposition and considerably enhanced the detection's reliability. The developed ratiometric ECL sensor demonstrated a sensitive detection toward CEA with a wide linear range from 100 ag/mL to 10 ng/mL and a detection limit of 87.1 ag/mL (S/N = 3). In conclusion, this study offers a new idea for constructing ratiometric ECL sensors based on a single luminophore and technical support for cancer's early diagnosis.

An ultrasensitive fluorescence detection template of pathogenic bacteria based on dual catalytic hairpin DNA Walker@Gold nanoparticles enzyme-free amplification

Integrating the advantages of catalytic hairpin components and multi-foot DNA walker, we designed a 16S rRNA detection probe template for pathogen bacteria, which utilizes DNA ligation quencher and dual catalytic hairpin@DNA walker to induce signal recovery. The dual catalytic hairpin@DNA walker uses the walking position of the target on the AuNP as a foothold to promote the reaction, so that the biosensing of the low-abundance target sequence can induce signal recovery. During the entire experiment, no enzyme is required, which can avoid the limitation of enzyme degradation under unfavorable conditions and the inability to detect the target. Most importantly, the detection template has the advantages of high sensitivity, and its detection limit is significantly better than that of single hairpin DNA walker probe. As the detection system can sensitively and rapidly detect its targeted bacteria and not rely on any enzyme and sophisticated instrumentation, it has great potential for sensitive and specific pathogenic bacteria detection.

Sensitive colorimetric detection of miRNA-155 via G-quadruplex DNAzyme decorated spherical nucleic acid

Rapid and sensitive detection of biomarkers enables monitoring patients' health status and can enhance the early diagnosis of deadly diseases. In this work, we have developed a new colorimetric platform based on spherical nucleic acid (SNA) and G-quadruplex DNAzymes for the identification of specific miRNAs. The simple hybridization between the target miRNA and two capture probes (capture probe 1 located at AuNP surface and free capture probe 2) is the working principle of this biosensor. The hybridization and duplex formation among probes and miRNAs led to a significant decrease in the intensity of color change. A linear relationship between the decrease of colorimetric signal and the amount of target molecules was witnessed from 1 to 100 nM for miRNA-155. Using this method, we were able to detect concentrations of miRNA-155 as low as 0.7 nM. Furthermore, the proposed sensing platform can be utilized profitably to detect miRNA-155 in real human serum samples. We further investigated the applicability of the proposed method in a microfluidic system which displayed promising results. In this project, A G-quadruplex based SNAzyme was constructed to provide a fast and simple colorimetric method for miRNA detection. The SNAzyme actually employed as both target recognition element and catalytic nano labels for colorimetric detection.