A fluorescent biosensing platform based on the polydopamine nanospheres intergrating with Exonuclease III-assisted target recycling amplification

Highly sensitive and stable fluorescent aptasensor based on an exonuclease III-assisted amplification strategy for ATP detection

Fluctuations in intracellular adenosine triphosphate (ATP) concentration are closely associated with some cancer diseases. Thus, it is a worthwhile undertaking to predict sickness by monitoring changes in ATP levels. However, the detection limits of current fluorescent aptamer sensors for ATP detection are in the range of nmol L^-1 to μmol L^-1. It has become crucial to employ amplification strategies to increase the sensitivity of fluorescent aptamer sensors. In the current paper, a duplex hybrid aptamer probe was developed based on exonuclease III (Exo III)-catalyzed target recycling amplification for ATP detection. The target ATP forced the duplex probe configuration to change into a molecular beacon that can be hydrolyzed with Exo III to achieve the target ATP cycling to amplify the fluorescence signal. Significantly, many researchers ignore that FAM is a pH-sensitive fluorophore, leading to the fluorescence instability of FAM-modified probes in different pH buffers. The negatively charged ions on the surface of AuNPs were replaced by new ligands bis(p-sulfonatophenyl)phenylphosphine dihydrate dipotassium salt (BSPP) to improve the drawback of FAM instability in alkaline solutions in this work. The aptamer probe was designed to eliminate the interference of other similar small molecules, showing specific selectivity and providing ultra-sensitive detection of ATP with detection limits (3σ) as low as 3.35 nM. Such detection limit exhibited about 4-500-fold better than that of the other amplification strategies for ATP detection. Thus, a relatively general high sensitivity detection system can be established according to the wide target adaptability of aptamers, which can form specific binding with different types of targets.

Application of a Dual-Probe Coloading Nanodetection System in the Process Monitoring and Efficacy Assessment of Photodynamic Therapy: An In Vitro Study

The oxygen-consuming property of photodynamic therapy (PDT) affects its effects and aggravates tumor hypoxia, thus upregulating the vascular endothelial growth factor (VEGF) to exacerbate tumor metastasis and lead to treatment failure. Therefore, it is necessary to monitor the dynamic changes in the factors related to PDT and tumor development trends in real time, thus helping to improve PDT efficiency. This study fabricated a fluorescent probe, TPE-2HPro, and a fluorescein-labeled aptamer probe, FAM-Aptamer_VEGF, to detect hydrogen peroxide (H₂O₂) and VEGF through the photoinduced electron-transfer effect and the specific affinity of the aptamer to VEGF, respectively. The two probes were loaded into the inner pores and absorbed on the surface of polydopamine coating-wrapped mesoporous silica nanoparticles (MSN@PDA) to construct the dual-probe-loaded system, MSN_TH@PDA_Apt, which was kept stable in fetal bovine serum (FBS) solution and achieved pH-responsive release behavior, thus helping to increase the accumulation of the two probes in tumor cells. The dichloroacetic acid-mediated in vitro antitumor tests showed that the changing trends of H₂O₂ and VEGF levels were consistent with the results of related mechanism studies and could be monitored by MSN_TH@PDA_Apt. The in vitro chlorin e6 (Ce6)-mediated PDT treatment demonstrated that when the illumination condition was 650 nm, 50 mW/cm² for 10 min, cells were more inclined to metastasis and invasion rather than death due to a substantial increase in VEGF expression at the low Ce6 concentrations. With the increase of the Ce6 concentration, the growth of the H₂O₂ level gradually exceeded that of VEGF, and the reactive oxygen species (ROS)-mediated cell death dominated when the Ce6 concentration was about 2 times its IC₅₀ values. Besides, hypoxia also affected the H₂O₂ and VEGF changes. These results demonstrated that MSN_TH@PDA_Apt could precisely monitor and assess the tumor development trends during PDT treatment, thus helping improve the treatment effect.

Nucleic Acid Nanotechnology for Diagnostics and Therapeutics in Acute Kidney Injury

Acute kidney injury (AKI) has impacted a heavy burden on global healthcare system with a high morbidity and mortality in both hospitalized and critically ill patients. However, there are still some shortcomings in clinical approaches for the disease to date, appealing for an earlier recognition and specific intervention to improve long-term outcomes. In the past decades, owing to the predictable base-pairing rule and highly modifiable characteristics, nucleic acids have already become significant biomaterials for nanostructure and nanodevice fabrication, which is known as nucleic acid nanotechnology. In particular, its excellent programmability and biocompatibility have further promoted its intersection with medical challenges. Lately, there have been an influx of research connecting nucleic acid nanotechnology with the clinical needs for renal diseases, especially AKI. In this review, we begin with the diagnostics of AKI based on nucleic acid nanotechnology with a highlight on aptamer- and probe-functionalized detection. Then, recently developed nanoscale nucleic acid therapeutics towards AKI will be fully elucidated. Furthermore, the strengths and limitations will be summarized, envisioning a wiser and wider application of nucleic acid nanotechnology in the future of AKI.

Sensitive and selective detection of Mucin1 in pancreatic cancer using hybridization chain reaction with the assistance of Fe3O4@polydopamine nanocomposites

Pancreatic cancer is characterized as the worst for diagnosis lacking symptoms at the early stage, which results in a low overall survival rate. The frequently used techniques for pancreatic cancer diagnosis rely on imaging and biopsy, which have limitations in requiring experienced personnel to operate the expensive instruments and analyze the results. Therefore, there is a high demand to develop alternative tools or methods to detect pancreatic cancer. Herein, we propose a new strategy to enhance the detection sensitivity of pancreatic cancer cells both in biofluids and on tissues by combining the unique property of dopamine coated Fe₃O₄ nanoparticles (Fe₃O₄@DOP NPs) to specifically quench and separate free 6-carboxyfluorescein (FAM) labeled DNA (H₁-FAM/H₂-FAM), and the key feature of hybridization chain reaction (HCR) amplification. We have determined the limit of detection (LOD) to be 21 ~ 41 cells/mL for three different pancreatic cancer cell lines. It was also discovered that the fluorescence intensity of pancreatic cancer cells was significantly higher than that of HPDE-C7 and HepG-2 cells (control cell lines), which express lower MUC1 protein. Moreover, the HCR amplification system was used to identify the cancer cells on pancreatic tissue, which indicated the versatility of our strategy in clinical application. Therefore, the presented detection strategy shows good sensitivity, specificity and has great potential for the diagnosis of pancreatic cancer.

Application of Nanomaterials in Isothermal Nucleic Acid Amplification

Because of high sensitivity and specificity, isothermal nucleic acid amplification are widely applied in many fields. To facilitate and improve their performance, various nanomaterials, like nanoparticles, nanowires, nanosheets, nanotubes, and nanoporous films are introduced in isothermal nucleic acid amplification. However, the specific application, roles, and prospect of nanomaterials in isothermal nucleic acid amplification have not been comprehensively reviewed. Here, the application of different nanomaterials (0D, 1D, 2D, and 3D) in isothermal nucleic acid amplification is comprehensively discussed and recent progress in the field is summarized. The nanomaterials are mainly used for reaction enhancer, signal generation/amplification, or surface loading carriers. In addition, 3D nanomaterials can be also functioned as isolated chambers for digital nucleic acid amplification and the tools for DNA sequencing of amplified products. Challenges and future recommendations are also proposed to be better used for recent covid-19 detection, point-of-care diagnostic, food safety, and other fields.

Recent advances in the exonuclease III-assisted target signal amplification strategy for nucleic acid detection

The detection of nucleic acids has become significantly important in molecular diagnostics, gene therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease III (Exo III) as an enzyme in the 3'-5' exonuclease family has evolved as a frequently used technique for signal amplification of low level DNA target detection. Different from the traditional target amplification strategies, the Exo III-assisted amplification strategy has been used for target DNA detection through directly amplifying the amounts of signal reagents. The Exo III-assisted amplification strategy has its unique advantages and characters, because the character of non-specific recognition of Exo III can overcome the limitation of a target-to-probe ratio of 1 : 1 in the traditional nucleic acid hybridization assay and acquire higher sensitivity. In this review, we selectively discuss the recent advances in the Exo III-assisted amplification strategy, including the amplification strategy integrated with nanomaterials, biosensors, hairpin probes and other nucleic acid detection methods. We also discuss the strengths and limitations of each strategy and methods to overcome the limitations.

A magnified aptamer fluorescence sensor based on the metal organic frameworks adsorbed DNA with enzyme catalysis amplification for ultra-sensitive determination of ATP and its logic gate operation

With the development of frame materials, metal organic frameworks (MOFs) have been successfully applied in the fields of biological small molecule analysis and fluorescent DNA detection. In this work, in view of the good adsorption characteristics of MIL-101(Cr), the highly sensitive detection of adenosine triphosphate (ATP) assisted nucleic acid exonuclease amplification by MIL-101(Cr) on the different affinity of single stranded DNA and double stranded DNA was investigated. The detection limit of ATP reaches 1.7 μM, and the platform has good applicability in biological samples. On this basis, an "AND" logic gate was successfully constructed. Superior sensitivity to ATP in the presence of exonuclease was reflected, which greatly enhanced the system's fluorescence. Importantly, the fluorescence sensing application of this nanomaterial inspired other target detection and enriched the building blocks of fluorescence sensing platform.

A new fluorescence sensor developed with polydopamine nanospheres for the detection of anti-PLA2R antibody biomarkers of idiopathic membranous nephropathy

Anti-PLA2R antibody is only expressed in podocytes from patients with idiopathic membranous nephropathy (IMN). The detection of anti-PLA2R antibody in serum is therefore able to obtain essential information for rapid diagnosis and evaluation of the disease activity of IMN. In the present study, a polydopamine nanosphere-based fluorescent sensor was constructed for direct detection of anti-PLA2R antibodies in human serum. In this sensing system, the double-stranded DNA was phosphorylated under the action of anti-PLA2R antibody and the single-stranded DNA was cut by exonuclease. The single-stranded DNA was then adsorbed on polydopamine microspheres. The fluorescent groups labeled on the DNA were quenched, and the concentration of anti-PLA2R antibody was detected quantitatively by measuring the fluorescence signal changes before and after the reaction. The experimental results show that the method has a good linear detection range between 0.05 and 10 μg/mL for anti-PLA2R antibody and the detection limit is 0.02 μg/mL. Graphical abstract.

Transition Metal-Mediated DNA Adsorption on Polydopamine Nanoparticles

Polydopamine (PDA) is a widely used universal coating for a broad range of materials. Interfacing PDA with various biomolecules, such as DNA, is critical for applications such as sensing, intracellular delivery, and material fabrication. Because of the negative surface charge of PDA at neutral pH, electrostatic repulsion exists between PDA and DNA. In previous studies, modified DNA or low pH was used to overcome this repulsion for DNA adsorption. More recently, divalent Ca²⁺ was found to bridge DNA and PDA. Herein, we studied four transition metals (Mn²⁺, Co²⁺, Zn²⁺, and Ni²⁺) and compared their efficiencies with Ca²⁺ for promoting DNA adsorption. These transition metals induced a more efficient and tighter DNA binding compared to Ca²⁺. In all these cases, the DNA phosphate backbone played a dominant role in adsorption, although DNA bases might also interact with strong binding metals such as Ni²⁺. Moreover, when the adsorption affinity was stronger, sensing was more selective to complementary DNA. Finally, aging of PDA appeared to be detrimental for DNA adsorption, which could be due to further oxidation of PDA. We showed that using Zn²⁺ or Ni²⁺ could considerably relieve the aging effect, while storing PDA at 4 °C could slow down aging.

Ultrasensitive and label-free detection of ATP by using gold nanorods coupled with enzyme assisted target recycling amplification

Abnormal concentration of adenosine triphosphate (ATP) is directly asscociate with several diseases. Thus, sensitive detection of ATP is essential to early diagnosis of disease. Herein, we described an ultrasensitive strategy for ATP detection by using positively charged gold nanorods ((+)AuNRs) as an efficient fluorescence quenching platform, coupled with exonuclease Ⅲ (Exo Ⅲ) assisted target recycling amplification. To construct the sensor, DNA template that contained ATP aptamer was used for the formation of Ag nanoclusters signal probe (DNA/AgNCs), the structure of it could change to duplex after the interaction of it with ATP. Such DNA template or duplex DNA product could electrostatically adsorb onto (+)AuNRs surface, resulting in the quenching of the fluorescence signal due to the vicinity of AgNCs to (+)AuNRs. With the addition of Exo Ⅲ, DNA duplex could be hydrolyzed and released from (+)AuNRs surface, leading to the recovery of a strong fluorescent signal, while ATP could be regenerated for next target recycling. Combing the good fluorescence quenching ability of (+)AuNRs and the Exo Ⅲ assisted signal amplification, a low detection limit of 26 pM was achieved for ATP detection. Notably, the proposed method can be successfully applied for detecting ATP in serum samples, indicating a potential application value in early cancer diagnosis.

Synthesis of Polydopamine Hollow Capsules via a Polydopamine Mediated Silica Water Dissolution Process and Its Application for Enzyme Encapsulation

Herein, we present a systematic study on the preparation of polydopamine (PDA) hollow capsules by templating silica particles which were subsequently removed by a PDA mediated water dissolution process without using any harsh chemical treatment. It was found that the time required for silica removal varied depending on the PDA coating and dissolution conditions. Factors that could influence the core removal process including the PDA thickness and coating temperature, silica calcination duration and the availability of water were then examined in detail. Additionally, catalase was used as a model enzyme to be encapsulated into PDA hollow capsules and its bio-functionality was found to remain active. The bioactivity test results also indicated that the as-synthesized PDA capsules possessed a porous structure, which allows the penetration of small molecules such as H₂O₂. This study offers a better insight into silica dissolution process that mediated by PDA and contributes to the development of an eco-friendly approach for the fabrication of hollow capsules that have promising applications in drug delivery systems.

Polydopamine nanosphere@silver nanoclusters for fluorescence detection of multiplex tumor markers

There is an increasing demand to establish a convenient and stable analytical methodology for screening multiplex tumor markers in early diagnosis of cancers. In this work, an innovative fluorescence method is proposed for simultaneous detection of alpha-fetoprotein (AFP) and carcinoembryonic antigen (CEA). A polydopamine nanosphere@silver nanocluster (PDAN@AgNC) system is introduced for fluorescence quenching and recovery. The AgNCs with different emissions are synthesized using different DNA templates, which also contain aptamer sequences towards AFP and CEA, respectively. These single-stranded DNA sequences could be adsorbed on the surface of the PDAN through π-π stacking, which results in the quenching of AgNCs. However, in the presence of the corresponding tumor marker, the aptamer/target complex forms which releases AgNCs from the surface of the PDAN and the recovered fluorescence could be used to indicate the concentration of the tumor marker. This PDAN@AgNC system has been validated preliminarily to screen human serum samples with excellent results. Taking advantages of simplicity, enzyme/antibody-free nature, low cost and convenient operation, the proposed biosensor has great potential to be used in biomedical research studies and clinical diagnosis.

Polydopamine nanotube mediated fluorescent biosensor for Hg(ii) determination through exonuclease III-assisted signal amplification

We describe a highly sensitive fluorescence biosensor incorporating polydopamine nanotubes (PDNTs) based on the mechanism of exonuclease III (Exo III) assisted signal amplification for the determination of Hg2+ in aqueous solution. Fluorescent probes of FAM labeled ssDNA (FAM-ssDNA) adsorbed on the PDNTs act as an efficient quencher. In the presence of Hg2+, the FAM-ssDNA can bind to Hg2+ to form double stranded DNA (dsDNA) via the formation of T-Hg2+-T base pairs. Then, the dsDNA was removed from the surface of the PDNTs to restore the fluorescence. The release of the dsDNA was triggered by Exo III digestion. At the same time, the liberated Hg2+ mediates a new cycle of digestion. This assay is ultrasensitive for the selective recognition of Hg2+, and a detection limit as low as 10 pM was achieved. In addition, the fluorescent biosensing system also displays remarkable specificity to Hg2+ in the presence of other possible competing ions. This approach was applied to the determination of Hg2+ in real water samples with good recovery and high efficiency for practical analysis.

Single-Molecule Kinetic Fingerprinting for the Ultrasensitive Detection of Small Molecules with Aptasensors

Aptamers have emerged as promising molecular tools for small-molecule analyte sensing. However, the performance of such aptasensors is generally limited by leakage since it has been difficult to completely suppress signal in the absence of analyte, resulting in a compromise between sensitivity and specificity. Here, we describe a methodology for the ultrasensitive detection of analytes combining aptasensors with single-molecule kinetic fingerprinting. A short, fluorescently labeled DNA probe is utilized to detect the structural changes upon ligand binding to the designed hairpin-shaped aptasensor probe. The Poisson statistics of binding and dissociation events of the DNA probe to single surface-immobilized aptasensor molecules is monitored by total internal reflection fluorescence microscopy, permitting the high-accuracy discrimination of the ligand bound and ligand-free states, resulting in zero background. The programmable dynamics of the hairpin enables fine-tuning of the hybridization kinetics of the fluorescent probe, rendering the acquisition time sufficiently flexible to optimize discrimination. Remarkable detection limits are achieved for a diverse set of analytes when spiked into chicken meat extract: the nucleotide adenosine (0.3 pM), the insecticide acetamiprid (0.35 pM), and the dioxin-like toxin PCB-77 (0.72 pM), which is superior to recently reported aptasensors. Our generalizable method significantly improves the performance of aptasensors, with the potential to extend to other molecular biomarkers.

A peptide-based four-color fluorescent polydopamine nanoprobe for multiplexed sensing and imaging of proteases in living cells

A novel peptide-based four-color fluorescent polydopamine nanoprobe has been developed for multiplexed sensing and imaging of tumor-related proteases in living cells. This nanoprobe responds rapidly and selectively, enabling accurate differentiation between cancer cells and normal cells.

Fluorescent miRNA analysis enhanced by mesopore effects of polydopamine nanoquenchers

The combination of fluorophore-labelled single-strand DNA probes and nanomaterial quenchers has shown great potential in miRNA detection. The development of advanced detection systems by understanding and controlling the fluorescence quenching/recovery via nanoquenchers' microstructures and local morphologies is an attractive area warranting further investigations. Inspired by nanopore sequencing, we present a novel miRNA sensing strategy using fluorophore-labeled DNA as probes and a type of large-pore-sized mesoporous polydopamine nanoparticles (MPDA-L, 70 nm in diameter) as fluorescence quenchers. It is revealed that the quenching efficiency of MPDA-L towards the fluorophore labelled on the probe, reached more than 99% at a relatively low particle concentration. Moreover, the mesopores effectively protected the probe DNA from cleavage by DNase I which was used for signal amplification. Sensitive detection of miRNA with a low detection limit of 32-40 pM, as well as a linear detection range of up to 5 nM, was realized by the mesopore effects via a greatly improved differential affinity of ssDNA and the probe-miRNA heteroduplex toward the surface of nanoquenchers. Interestingly, enhanced DLVO (Derjaguin-Landau-Verwey-Overbeek) repulsion generated inside the pore surface by the negative surface-curvature effect correlates with the improved duplex detachment and fluorescence recovery. The developed strategy can be successfully applied to quantify down-regulated let-7a and up-regulated miRNA-21 in different types of cancer cells by using total RNA samples from cell lysate. These findings are expected to inspire strategies and pave a way for utilizing porous nanomaterials for constructing miRNA detection systems.

A fluorometric aptasensor for patulin based on the use of magnetized graphene oxide and DNase I-assisted target recycling amplification

A fluorometric patulin (PAT) assay is presented that is based on the use of magnetic reduced graphene oxide (rGO) and DNase I. The fluorescence of the PAT aptamer labelled with 6-carboxyfluorescein (FAM) is quenched by magnetized reduced graphene oxide (rGO-Fe₃O₄) due to fluorescence resonance energy transfer (FRET). However, in the presence of PAT, the labelled aptamer is stripped off from rGO-Fe₃O₄. The rGO-Fe₃O₄ is then magnetically separated so that the fluorescence of free labelled PAT aptamer is restored. DNase I cannot hydrolyze the aptamer on rGO-Fe₃O₄, but it can cleave the free aptamer-PAT complex. This will release FAM and PAT which can undergo a number of additional cycles to trigger the cleavage of abundant aptamer. Recycling of DNase I-assisted target therefore leads to a strong amplification of fluorescence and consequently to an assay with low limit of detection. The detection limit for PAT is as low as 0.28 μg L^-1 which is about 13 times lower than that without using DNase I. The method offers a new approach towards rapid, sensitive and selective detection based on an aptamer. Conceivably, it has a wide scope in that it may be applied to numerous other analytes if appropriate aptamers are available. Abstract Schematic of a fluorometric assay based on the use of magnetic graphene oxide and DNase I. It was applied to the determination of patulin. DNase I was introduced for recycling amplification. The detection limit is about 13 times lower than that without using DNase I. Figure a contains poor quality of text in image. Otherwise, please provide replacement figure file.Thank you. I will provide the figure file.

A label-free fluorescent adenosine triphosphate biosensor via overhanging aptamer-triggered enzyme protection and target recycling amplification

Herein, a label-free fluorescent adenosine triphosphate (ATP) aptasensor is fabricated with a DNA hairpin and an overhanging aptamer. In the presence of ATP, the overhanging sequences of the aptamer may form preferred substrates of exo III, and thus trigger the enzyme-assisted amplification, which results in the release of G-rich sequences. Free G-rich sequences subsequently generate an enhanced flourescent signal by binding with thioflavin T. However, if ATP is absent, the overhanging sequence can induce steric hindrance and protect the DNA hairpin against the digestion of exo III, significantly reducing the noise of this biosensor. Accordingly, the signal-to-noise ratio of the sensing system is greatly improved, which ensures the desirable analytical performance of the proposed aptasensor both in pure samples and real samples.

Copper nanoclusters/polydopamine nanospheres based fluorescence aptasensor for protein kinase activity determination

A fluorescence aptasensor was constructed for protein kinase (PKA) activity detection by utilizing copper nanoclusters (CuNCs) and polydopamine nanospheres (PDANS). Through the π-π stacking interactions between adenosine triphosphate (ATP) aptamer and PDANS, the ATP aptamer modified CuNCs (apt-CuNCs) were absorbed onto PDANS surface, thus the fluorescence of apt-CuNCs were quenched through fluorescence resonance energy transfer (FRET) from apt-CuNCs to PDANS. In the presence of ATP, ATP specifically bound to aptamer, causing the dissociation of apt-CuNCs from PDANS surface and restoring the fluorescence of apt-CuNCs. However, PKA translated ATP into adenosine diphosphate (ADP), and ADP had no competence to combine with ATP aptamer, thus, apt-CuNCs were released and absorbed onto the PDANS surface to cause the fluorescence quenching of apt-CuNCs again. Therefore, PKA activity was conveniently detected via the fluorescence signal change. Under the optimal conditions, PKA activity was detected in the range of 0.05-4.5 U mL^-1 with a detection limit of 0.021 U mL^-1. Furthermore, the feasibility of the aptasensor for kinase inhibitor screening was explored via assessment of kinase inhibitor H-89 as one model. This aptasensor was also performed for PKA activity determination in HepG2 cell lysates with satisfactory results.

Magnetic nanoparticles and polydopamine amplified FP aptasensor for the highly sensitive detection of rHuEPO-α

In this paper, an amplified fluorescence polarization (FP) aptasensor based on magnetic nanoparticles @polydopamine (MNP@PDA) was innovatively developed for sensitive detection of recombinant human erythropoietin-alpha(rHuEPO-α). The amplified FP signal was due to the large mass of protein and MNP@PDA. And this assay can be utilized for target separation or recycling based on the magnetic property of MNP@PDA through magnetic separation. Briefly, rHuEPO-α and MNP@PDA were added successively to react with the labeled aptamer (FAM-P1), which both contributed to the increase of FP signal via the formation of FAM-P1-rHuEPO-α and particularly FAM-P1-MNP@PDA complex. The strong interaction between MNP@PDA and FAM-P1 ensured the high efficiency of mass amplification and magnetic separation. As a result, the detection limit for rHuEPO-α was 0.12 pM, 4 orders of magnitude lower than original assay. Besides, three kinds of rHuEPO-α injections, NuPIAO, Epogen and ESPO were used to evaluate the selectivity of this assay in complex matrix with reasonable standard deviation. In a word, this work provides a simple, rapid, non-modified, highly sensitive and selective sensing platform for the detection of rHuEPO-α.

A novel fluorescent biosensor for Adenosine Triphosphate detection based on the polydopamine nanospheres integrating with enzymatic recycling amplification

Based on the protective performance of polydopamine nanospheres (PDANSs) for DNA against nuclease digestion and the specific recognition characteristic of aptamer, we have developed an enzymatic recycling signal amplification method for highly sensitive and selective detection of adenosine triphosphate (ATP). Fluorescence measurements were carried out to verify the DNA polymerase and exonuclease III (Exo III) assisted target recycling process and fluorescence signal amplification. In the absence of the ATP, initially, the signal DNA-PDANSs complex was in the "off" state due to the efficient fluorescence quenching of 6-carboxyfluorescein (FAM) adjacent to the surface of PDANSs. Due to the binding of the aptamer by ATP, it trigger DNA polymerase and Exo III assisted target recycling process by the product of release, the complex would change into the "on" state as a result of the dissociation of the FAM from the surface of PDANSs, thus providing greatly enhanced fluorescence emission intensity. The method allows quantitative detection of ATP in the range of 20-600nM with a detection limit of 8.32nM. This biosensor requires no complex operations, and is a new high efficiency method for ATP detection.

Bifunctional polydopamine thin film coated zinc oxide nanorods for label-free photoelectrochemical immunoassay

Photoelectrochemical (PEC) detection is a promising method for label-free immunoassay by reporting the specific biological recognition events with electrical signals. However, it is challenging to rationally incorporate immunosensing components with a photocurrent conversion interface, which generally necessitates multistep fabrication and careful tailoring of various components such as photoactive material and biological probe. For high detection reliability and reproducibility, it is highly desirable to rationally construct an efficient PEC interface with architecture as simple as possible. In this work, a novel yet simple PEC immunosensor based on bio-inspired polydopamine (PDA) thin film-coated zinc oxide (ZnO) nanorods was reported. In this PEC immunosensor, the PDA thin film serves simultaneously as a unique sensitizer for charge separation as well as a functional layer for probe antibody attachment. The photocurrent on this electrode under illumination decreases upon the immunoreaction on the surface, possibly due to the blocking effect of formed immunocomplexes on the access of reducing reagent to the photoelectrode, thus offering a simple and reliable platform for PEC label-free immunoassay. By using an antibody-antigen pair as a model, successful label-free immunoassay was achieved with a detection limit of 10pgmL^-1 and a dynamic range from 100pgmL^-1 to 500ngmL^-1. This work demonstrates intriguing electro-optical property and bioconjugation activity of PDA film and may pave the way toward advanced PEC immunoassays.

Polydopamine Nanotubes as an Effective Fluorescent Quencher for Highly Sensitive and Selective Detection of Biomolecules Assisted with Exonuclease III Amplification

In this work, the effective fluorescence quenching ability of polydopamine nanotubes (PDANTs) toward various fluorescent dyes was studied and further applied to fluorescent biosensing for the first time. The PDANTs could quench the fluorophores with different emission frequencies, aminomethylcoumarin acetate (AMCA), 6-carboxyfluorescein (FAM), 6-carboxytetramethylrhodamine (TAMRA), and Cy5. All the quenching efficiencies reached to more than 97%. Taking advantage of PDANTs' different affinities toward ssDNA and dsDNA and utilizing the complex of FAM-labeled ssDNA and PDANTs as a sensing platform, we achieved highly sensitive and selective detection of human immunodeficiency virus (HIV) DNA and adenosine triphosphate (ATP) assisted with Exonuclease III amplification. The limits of detection (LODs) of HIV DNA and ATP reached to 3.5 pM and 150 nM, respectively, which were all lower than that of previous nanoquenchers with Exo III amplification, and the platform also presented good applicability in biological samples. Fluorescent sensing applications of this nanotube enlightened other targets detection based upon it and enriched the building blocks of fluorescent sensing platforms. This polydopamine nanotube also possesses excellent biocompatibility and biodegradability, which is suitable for future drug delivery, cell imaging, and other biological applications.

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

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

Highly sensitive detection of lipopolysaccharides using an aptasensor based on hybridization chain reaction

Lipopolysaccharides (LPS), integral components of the outer membrane of all gram-negative bacteria, are closely associated with foodborne diseases such as fever, diarrhea and hypotension, and thus, the early and sensitive detection of LPS is necessary. In this study, an aptasensor assay based on hybridization chain reaction (HCR) was developed to detect LPS. Briefly, two complementary stable species of biotinylated DNA hairpins coexisted in solution until the introduction of a detection probe triggered a hybridization chain reaction cascade. The DNA conjugates specifically reacted with the LPS, which were captured by the ethanolamine aptamer attached to the reaction well surface. After optimizing the key reaction conditions, such as the reaction time of HCR, the amount of the capture probe and detection probes, the increase in the LPS concentration was readily measured by the optical density value, and a relatively low detection limit (1.73 ng/mL) was obtained, with a linear response range of 1–10⁵ng/mL. The approach presented herein introduced the use of an aptasensor for LPS discrimination and HCR for signal amplification, offering a promising option for detecting LPS.

Aptamer/Polydopamine Nanospheres Nanocomplex for in Situ Molecular Sensing in Living Cells

A nanocomplex was developed for molecular sensing in living cells, based on the fluorophore-labeled aptamer and the polydopamine nanospheres (PDANS). Due to the interaction between ssDNA and PDANS, the aptamer was adsorbed onto the surface of PDANS forming the aptamer/PDANS nanocomplex, and the fluorescence was quenched by PDANS through Förster resonance energy transfer (FRET). In vitro assay, the introduction of adenosine triphosphate (ATP) led to the dissociation of the aptamer from the PDANS and the recovery of the fluorescence. The retained fluorescence of the nanocomplex was found to be linear with the concentration of ATP in the range of 0.01-2 mM, and the nanocomplex was highly selective toward ATP. For the strong protecting capability to nucleic acids from enzymatic cleavage and the excellent biocompatibility of PDANS, the nanocomplex was transported into cells and successfully realized "signal on" sensing of ATP in living cells; moreover, the nanocomplex could be employed for ATP semiquantification. This design provides a strategy to develop biosensors based on the polydopamine nanomaterials for intracellular molecules analysis. For the advantages of polydopamine, it would be an excellent candidate for many biological applications, such as gene and drug delivery, intracellular imaging, and in vivo monitoring.

A polydopamine nanosphere based highly sensitive and selective aptamer cytosensor with enzyme amplification

With CCRF-CEM as the model cell, a highly sensitive and selective cytosensor was developed by taking advantage of polydopamine nanospheres for the first time. The strategies of aptamer/membrane protein recognition and Exonuclease III assisted cycle amplification were used for improving selectivity and sensitivity. The detection of limit reached was as low as 15 cells per mL.

Enzyme-free fluorescent biosensor for the detection of DNA based on core-shell Fe3O4 polydopamine nanoparticles and hybridization chain reaction amplification

A novel, highly sensitive assay for quantitative determination of DNA is developed based on hybridization chain reaction (HCR) amplification and the separation via core-shell Fe3O4 polydopamine nanoparticles (Fe3O4@PDA NPs). In this assay, two hairpin probes are designed, one of which is labeled with a 6-carboxyfluorescein (FAM). Without target DNA, auxiliary hairpin probes are stable in solution. However, when target DNA is present, the HCR between the two hairpins is triggered. The HCR products have sticky ends of 24 nt, which are much longer than the length of sticky ends of auxiliary hairpins (6 nt) and make the adsorption much easier by Fe3O4@PDA NPs. With the addition of Fe3O4@PDA NPs, HCR products could be adsorbed because of the strong interaction between their sticky ends and Fe3O4@PDA NPs. As a result, supernatant of the solution with target DNA emits weak fluorescence after separation by magnet, which is much lower than that of the blank solution. The detection limit of the proposed method is as low as 0.05 nM. And the sensing method exhibits high selectivity for the determination between perfectly complementary sequence and target with single base-pair mismatch. Importantly, the application of the sensor for DNA detection in human serum shows that the proposed method works well for biological samples.

Fluorometric detection of mutant DNA oligonucleotide based on toehold strand displacement-driving target recycling strategy and exonuclease III-assisted suppression

We describe here a fluorometric assay for sensitive detection of oligonucleotides, based on a target recycling amplification strategy driven by toehold-mediated strand displacement reaction and on exonuclease III (Exo Ш)-assisted fluorescence background suppression strategy. The network consists of a pair of partially complementary DNA hairpins (HP1 and HP2) with 3' overhang ends, between which the spontaneous hybridization is kinetically hindered by the stems. The target DNA is repeatedly used to trigger a recycling progress between the hairpins, generating numerous HP1-HP2 duplex complexes. Exo III was then employed to digest the double strand parts of the residual hairpins and the intermediate products. The fluorescent dye, SYBR Green I, binds to the double-strand DNA products and emits strong fluorescence to achieve sensitive detection of the target DNA with the detection limit of 5.34 pM. Moreover, this proposed strategy showed high discrimination efficiency towards target DNA against mismatched DNA and was successfully applied in the analysis of human serum sample.

Exonuclease III-based target recycling for ultrasensitive homogeneous monitoring of HIV DNA using Ag(+)-coordinated hairpin probe

A new homogeneous electrochemical sensing strategy based on exonuclease III-assisted target recycling amplification was utilized for simple, rapid and highly sensitive detection of human immunodeficiency virus (HIV) DNA on an immobilization-free Ag(I)-assisted hairpin DNA through the cytosine-Ag(+)-cytosine coordination chemistry. The assay involved target-induced strand-displacement reaction accompanying dissociation of the chelated Ag(+) in the hairpins and exonuclease III-triggered target recycling. Initially, the added target DNA hybridized with hairpin DNA to disrupt the Ag(I)-coordinated hairpin probe and releases the coordinated Ag(+) ion. Then, the newly formed DNA double-stranded DNA could be cleaved by exonuclease III, and released target HIV DNA, which retriggered the strand-displacement reaction with the hairpin for target recycling, thereby resulting in formation of numerous free Ag(+) ions in the detection cell. The released Ag(+) ions can be readily captured by the negatively charged electrode, and subsequent anodic-stripping voltammetric detection of the captured Ag(+) ions are conducted to form the anodic current for the production of the electronic signal within the applied potential. Under optimal conditions, the exonuclease III-based sensing system exhibited good electrochemical responses for the detection of HIV DNA at a concentration as low as 23 fM.

Ultrasensitive biosensing platform based on layered vanadium disulfide–graphene composites coupling with tetrahedron-structured DNA probes and exonuclease III assisted signal amplification

An electrochemical aptasensor is developed to sensitively detect PDGF-BB based on vanadium disulfide–graphene composites and exonuclease III signal amplification.