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

Interactions of Melanin with Electromagnetic Radiation: From Fundamentals to Applications

Melanin, especially integumentary melanin, interacts in numerous ways with electromagnetic radiation, leading to a set of critical functions, including radiation protection, UV-protection, pigmentary and structural color productions, and thermoregulation. By harnessing these functions, melanin and melanin-like materials can be widely applied to diverse applications with extraordinary performance. Here we provide a unified overview of the melanin family (all melanin and melanin-like materials) and their interactions with the complete electromagnetic radiation spectrum (X-ray, Gamma-ray, UV, visible, near-infrared), which until now has been absent from the literature and is needed to establish a solid fundamental base to facilitate their future investigation and development. We begin by discussing the chemistries and morphologies of both natural and artificial melanin, then the fundamentals of melanin-radiation interactions, and finally the exciting new developments in high-performance melanin-based functional materials that exploit these interactions. This Review provides both a comprehensive overview and a discussion of future perspectives for each subfield of melanin that will help direct the future development of melanin from both fundamental and applied perspectives.

Fluorescent DNA-Silver nanoclusters in food safety detection: From synthesis to application

In recent years, the conventional preparation of silver nanoclusters (AgNCs) has attracted much attention due to their ultra-small size, tunable fluorescence, easy-to-engineer, as well as biocompatible material. Moreover, its great affinity towards cytosine bases on single-stranded DNA has led to the construction of biosensors, especially aptamers, for a broad variety of applications in food safety and environmental protection. In past years, numerous researchers paid attention to the construction of AgNCs aptasensor. Therefore, this review will be an effort to summarize the synthetic strategy along with the influences of factors on synthesis, categorize the sensing mechanism of aptamer-functionalized AgNCs biosensors, as well as their specific applications in food safety detection including heavy metal, toxin, and foodborne pathogenic bacteria. Furthermore, a brief conclusion and outlook regarding the prospects and challenges of their applications in food safety were drawn in line with the developments in DNA-AgNCs.

A cost-effective, "mix & act" G-quadruplex/Cu (II) metal-nanozyme-based ratiometric fluorescent platform for highly sensitive and selective cysteine/bleomycin detection and multilevel contrary logic computing

Versatile nanozymes with fascinating catalytic properties provide inspiring and effective options for biosensing and pharmaceutical analysis. Herein, we report the first nanozyme-based ratiometric fluorescent platform for cysteine (Cys) and bleomycin (BLM) detection by harnessing the cost-effective and "mix & act" G-quadruplex/Cu(II) (G4/Cu) metal-nanozyme with satisfactory peroxidase-like activity, which was fully proven by circular dichroism (CD), electron paramagnetic resonance (EPR) spectra and reactive oxygen species (ROS) scavenging experiments. Based on the catalytic oxidation of G4/Cu metal-nanozyme toward two fluorescent substrates (Amplex Ultrared, AU; Scopoletin, Sc) with opposite responses in the presence of H2O2, and the specific interaction between Cu2+ and targets, we achieved the highly sensitive detection of Cys and BLM. Through recording the fluorescence changes of AU (emission at 590 nm, F590) and Sc (emission at 465 nm, F465), we obtained good linear relationships between ratiometric fluorescence values (F590/F465) and variable contents of targets, resulting in the competitive LODs of Cys (6.7 nM) and BLM (10 nM), respectively. Moreover, this platform presented high selectivity (without the need for masking agent) and acceptable performance in human serum samples. Furthermore, a library of DNA contrary logic pairs (CLPs) and multilevel concatenated circuits were fabricated based on the reverse dual-output of the above platform, enriching the building blocks of biocomputing. This work not only enlightened the design of affordable, "mix & act" type nanozyme-based ratiometric biosensors with high reliability, but also facilitated the pluralistic application of nucleic acid-templated nanozymes to innovative biocomputing.

Toward Minute-Level DNA Computing: An Ultrafast, Cost-Effective, and Universal System for Lighting Up Various Concurrent DNA Logic Nanodevices (CDLNs) and Concatenated Circuits

DNA logic nanodevices are powerful tools for both molecular computing tasks and smart bioanalytical applications. Nevertheless, the hour-level operation time and high cost caused by the frequent redesign/reconstruction of gates, tedious strand-displacement reaction, and expensive labeled probes (or tool enzymes) in previous works are ineluctable drawbacks. Herein, we report an ultrafast and cost-effective system for engineering concurrent DNA logic nanodevices (CDLNs) by combining polythymine CuNCs with SYBR Green I (SG I) as universal dual-output producers. Particularly, benefiting from the concomitant minute-level quick response of both unlabeled illuminators and the exquisite strand-displacement-free design, all CDLNs including contrary logic pairs (YES∧NOT, OR∧NOR, and Even∧Odd number classifier), noncontrary ones (IDE∧IMP, OR∧NAND), and concatenated circuits are implemented in just 10 min via a "one-stone-two-birds" method, resulting in only 1/12 the operation time and 1/4 the cost needed in previous works, respectively. Moreover, all of them share the same threshold value, and the dual output can be easily visualized by the naked eye under a portable UV lamp, indicating the universality and practicality of this system. Furthermore, by exploiting the "positive/negative cross-verification" advantages of concurrent contrary logic, the smart in vitro analysis of the polyadenine strand and its polymerase is realized, providing novel molecular tools for the early diagnosis of cancer-related diseases.

Preparation of Ultrathin and Degradable Polymeric Films by Electropolymerization of 3-Amino-l-tyrosine

Bioderived polymers are one of many current research areas that promise a sustainable future. Due to their unique properties, the bioderived polymer polydopamine has been in the spotlight over the last decades. Its ability to adhere to virtually any surface and its stability over a wide pH range as well as in several organic solvents make it a suitable candidate for various applications like coatings and biosensors. However, strong light absorption over a broad range of wavelengths and high quenching efficiency limit its uses. Therefore, new bioderived polymers with similar features to polydopamine but without fluorescence quenching properties are highly desirable. Herein, the electropolymerization of a bioderived analog of dopamine, 3-amino-l-tyrosine, is demonstrated. The resulting polymer, poly(amino-l-tyrosine), exhibits several characteristics complementary to or even exceeding those of polydopamine and its analog, polynorepinephrine, rendering poly(amino-l-tyrosine) attractive for the development of sensors and photoactive devices. Cyclic voltammetry, spectro-electrochemistry, and electrochemical quartz crystal microbalance measurements are applied to study the electrodeposition of this material, and the resulting films are compared to polydopamine and polynorepinephrine. Impedance spectroscopy reveals increased ion permeability of poly(amino-l-tyrosine) compared to polydopamine and polynorepinephrine. Moreover, the reduced fluorescence quenching of poly(amino-l-tyrosine) supports its use as coating for biosensors and organic semiconductors.

Stimulus-Responsive Metal-Organic Framework Signal-Reporting System for Photoelectrochemical and Fluorescent Dual-Mode Detection of ATP

Dual-mode bioanalysis integrating photoelectrochemical (PEC) and other modes is emerging and allows signal cross-checking for more reliable results. Metal-organic frameworks (MOFs) have been shown to be attractive materials in various biological applications. This work presents the utilization of MOF encapsulation and stimuli-responsive decapsulation for dual-mode PEC and fluorescence (FL) bioanalysis. Photoactive dye methylene violet (MV) was encapsulated in zeolitic imidazolate framework-90 (ZIF-90) to form an MV@ZIF-90 hybrid material, and MV could be released by adenosine triphosphate (ATP)-induced ZIF-90 disintegration. The released MV not only had FL emission but also had a sensitization effect on the ZnIn₂S₄ (ZnInS) photoanode. Based on the MV-dependent sensitization effect and FL emission characteristic, a dual-mode PEC-FL strategy was established for ATP detection with low detection limits, that is, 3.2 and 4.1 pM for PEC and FL detection, respectively. This study features and will inspire the construction and implementation of smart MOF materials for dual-mode bioanalysis.

Multi-Stimuli-Responsive Janus Hollow Polydopamine Nanotubes

A tubular-shaped Janus nanoparticle based on polydopamine that responds to near-infrared, magnetic, and pH stimuli is reported. The robust tubular polydopamine structure was obtained by optimizing the halloysite template-to-dopamine ratio during synthesis. The inner and outer surfaces of the tube were exposed at different steps of the template-sonication--etching process, enabling the differential surface modification of these surfaces. Poly(ethylene glycol) (PEG) and poly(N-isopropylacrylamide) (PNIPAM) were grafted to the outer and inner surface of the nanotube, respectively. The PEG-coated surface limited aggregation of the nanoparticles at elevated temperatures. The PNIPAM-coated interior enhanced doxorubicin loading and endowed the nanoparticle with temperature-responsive behavior. The deposition of precipitated Fe₃O₄ nanoparticles further modified the nanoparticles. The resulting magnetic Janus nanoparticles responded to pH, temperature, and magnetic fields. Temperature changes could be induced by near-infrared laser, and all three stimuli were found to influence release rates of adsorbed doxorubicin from the nanoparticles. The interaction of the stimuli on release kinetics was elucidated using a linear mixed model; reduced pH and NIR irradiation enhanced release while applying a static magnetic field retarded release. Furthermore, the mechanism was shifted toward Fickian behavior by applying a static magnetic field and low pH conditions. However, NIR irradiation only shifted the behavior toward Fickian behavior at low pH.

A handheld multifunctional smartphone platform integrated with 3D printing portable device: On-site evaluation for glutathione and azodicarbonamide with machine learning

Azodicarbonamide (ADA) in flour can be easily decomposed to semi-carbazide and biuret, exhibiting strong genotoxicity in vitro and carcinogenicity. Glutathione (GSH) can be conjugated with some ketone-containing compounds and unsaturated aldehydes to form toxic metabolites. Here, a novel ratio fluorescence probe based on blue emitting biomass-derived carbon dots (BCDs) and yellow emitting 2,3-diaminophenazine (OxOPD) was prepared for the bifunctional determination of glutathione (GSH) and ADA. This strategy includes three processes: (1) Ag⁺ oxidizes o-phenylenediamine (OPD) to produce OxOPD. The peak at 562 nm was enhanced, and the peak at 442 nm was reduced due to fluorescence resonance energy transfer (FRET), (2) glutathione binds Ag⁺ and inhibits the production of OxOPD, (3) ADA oxidizes GSH to form GSSG, resulting in the release of Ag⁺ by GSH. Therefore, the newly designed ratio fluorescence probe can be based on the intensity ratio (I₄₄₂/I₅₆₂) changes and significant fluorescent color changes to detect GSH and ADA. Moreover, a smartphone WeChat applet and a yolov3-assisted deep learning classification model have been developed to quickly detect GSH and ADA on-site based on an image processing algorithm. These results indicate that smartphone ratiometric fluorescence sensing combined with machine learning has broad prospects for biomedical analysis.

A highly sensitive fluorescence method for the detection of T4 polynucleotide kinase phosphatase based on polydopamine nanotubes

T4 polynucleotide kinase phosphatase (T4 PNKP) plays a critical role in various cellular events, such as DNA damage repair, replication, and recombination. Here, we have described a novel biosensor to detect the activity of T4 PNKP based on polydopamine nanotubes (PDANTs) mediated fluorescence resonance energy transfer (FRET). A FAM-labelled (6-carboxyl-fluorescein) hairpin DNA probe with 3'-phosphoryl terminal was designed as the substrate for T4 PNKP. With the addition of PDANTs, the fluorescence of FAM-labelled hairpin DNA probe could be quenched because of the high adsorption of hairpin DNA on PDANTs. When T4 PNKP dephosphorylated the DNA probe, a double-stranded DNA (dsDNA) product was obtained by Klenow fragment polymerase (KF polymerase) on its 3'-hydroxyl terminal, which could retain most of the fluorescence due to the week adsorption of dsDNA on PDANTs. The developed method demonstrates the sensitivity for T4 PNKP assay in the range from 0.05 to 1.5 U mL^-1 with the detection limit of 0.005 U mL^-1, which endows the proposed strategy with high enough sensitivity for practical detection in cell lysates. With the advantages mentioned above, this novel sensitive strategy has the potential in the study of DNA damage repair mechanisms.

Polydopamine-Induced Modification on the Highly Charged Surface of Asymmetric Nanofluidics: A Strategy for Adjustable Ion Current Rectification Properties

Surface charge effects in nanoconfines is one of the fundamentals in the ion current rectification (ICR) of nanofluidics, which provides entropic driving force by asymmetric surface charges and causes ion enrichment/depletion by the electrostatic interaction of fixed surface charges. However, the surface charge effect causes a significant electrostatic repulsion in nanoconfines, restricting additional like charge or elaborate chemistry on the highly charged confined surface, which limits ICR manipulation. Here, we use polydopamine (PDA), a nearly universal adhesive, that adheres to the highly positive-charged poly(ethyleneimine) (PEI) gel network in a nanochannel array. PDA enhances the ICR effect from a low rectification ratio of 9.5 to 92.6 by increasing the surface charge and hydrophobicity of the PEI gel network and, meanwhile, shrinking its gap spacing. Theoretical and experimental results demonstrate the determinants of the fixed surface charge in the enrichment/depletion region on ICR properties, which is adjustable by PDA-induced change in a nanoconfined environment. Chemically active PDA brings Au nanoparticles by chloroauric reduction for further hydrophobization and the modification of negative-charged DNA complexes in nanochannels, whereby ICR effects can be manipulated in versatile means. The results describe an adjustable and versatile strategy for adjusting the ICR behaviors of nanofluidics by manipulating local surface charge effects using PDA.

Influence of a Polyneurotransmitter on DNA-Mediated Förster-Based Resonance Energy Transfer: A Path Leading to White Light Generation

The physiologically important biomolecule, dopamine (DA), shows strong self-oxidation and aggregation behaviors, which have been controlled and modulated to result in fluorescent polydopamine (F-PDA) nanoparticles. On the other hand, the simultaneous binding of two diverse deoxyribonucleic acid (DNA) binding probes, 4',6-diamidino-2-phenylindole dihydrochloride (DAPI) and ethidium bromide (EtBr), has been elaborately established to follow the Förster-based resonance energy transfer (FRET) pathway. The comparative understanding of this DNA-mediated FRET in three media, phosphate buffer saline (PBS) of pH 7.4, DA, and F-PDA, has concluded that the FRET efficiency in the three media follows the order: PBS > DA > F-PDA. This controlled FRET in the fluorescent F-PDA matrix serves a pivotal role for efficient white light (WL) generation with excellent Commission Internationale de l'Eclairage (CIE) parameters that match well with that of pure WL emission. The obtained WL emission has been shown to be very specific with respect to concentrations of different participating components and the excitation wavelength of the illuminating source. Furthermore, the optical properties of the WL emitting solution have been observed to be retained excellently inside the well-known agarose gel matrix. Finally, the mechanistic pathway behind such a FRET-based WL generation has been established in detail, and to the best of our knowledge, the current study offers the first and only report that discloses the influence of a fluorescent polyneurotransmitter matrix for successful generation of WL emission.

Intrinsically conductive polymers hybrid bilayer films for the fluorescence molecular diagnosis of the Zika virus

In 2016, the Zika virus (ZIKV) infection became a major public health problem, after the discovery that an alarming increase in the number of Brazilian newborns with microcephaly could be associated with the occurrence of this viral disease during the pregnancy of their mothers. The urgent need for simple diagnostic methods that allow rapid screening of suspected cases has stimulated the search for low-cost devices capable of detecting specific sequences of nucleic acids. The present work describes the development of nanostructured films formed by bilayers of conjugated polymers for rapid detection of the presence of Zika virus DNA, via fluorescence methods. For this, we initially deposited alternating layers of polyaniline (PANI) and polypyrrole (PPY) on the surface of polyethylene terephthalate (PET) sheets. The films obtained were then characterized by SEM, UV-Vis, ATR-FTIR, and contact angle measurements. For their use as quenchers for the diagnosis of Zika, a single DNA strand-specific for ZIKV was labeled with a fluorophore (FAM-ssDNA). We determined the time required for the saturation of the interaction between probe FAM-ssDNA and the film (180 min) and the time for the maximal hybridization between FAM-ssDNA and target DNA to occur (60 min). The detection limits were estimated as 345 pM and 278 pM for the PET/PPY-PANI and PET/PANI-PPY hybrid films, respectively. The simplicity of the procedure, coupled with the fact that a positive/negative response can be obtained in less than 60 min, suggests that the proposal of using these polymeric bilayer films is a promising methodology for the development of rapid molecular diagnostic tests.

Interfacial Engineering of Hybrid Polydopamine/Polypyrrole Nanosheets with Narrow Band Gaps for Fluorescence Sensing of MicroRNA

Nanoquencher-based biosensors have emerged as powerful tools for the detection of tumor markers, where challenges in efficiently docking the π-electron interaction interface toward nucleic acid probes containing π-electron-rich units of bases and fluorescent dyes still remain. Herein, we present hybrid polydopamine/polypyrrole nanosheets (PDA-PPy-NS) with π electron coupling and ultranarrow band gap (0.29 eV) by interfacial engineering of polymer hybrids at the nanoscale. PDA-PPy-NS were first prepared through oxidant-induced polymerization of pyrrole on PDA nanosheets. By utilizing fluorescent-dye-labeled single-stranded DNA as a probe, the hybrid nanoquencher showed ultrahigh fluorescence quenching ability, i.e., a Cy5-ssDNA/nanoquencher mass ratio of 36.9 under the complete quenching condition, which is comparable to that of graphene oxide. It was demonstrated that the energy level coupling of nanosheets and nucleic acid dye (Cy5) was the key factor contributing to the efficient photoinduced electron transfer (PET). Subsequently, the nanoquencher/DNA probe was proved to possess superior sensitivity and selectivity for efficient and reliable detection of miRNA-21 with a detection limit of 23.1 pM. Our work proves that the π-electron-rich biosensor interface can significantly enhance the PET efficiency, providing a theoretical basis for developing novel high-performance sensors.

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.

Tuning DNA-nanoparticle conjugate properties allows modulation of nuclease activity

Enzyme-nanoparticle interactions can give rise to a range of new phenomena, most notably significant enzymatic rate enhancement. Accordingly, the careful study and optimization of such systems is likely to give rise to advanced biosensing applications. Herein, we report a systematic study of the interactions between nuclease enzymes and oligonucleotide-coated gold nanoparticles (spherical nucleic acids, SNAs), with the aim of revealing phenomena worthy of evolution into functional nanosystems. Specifically, we study two nucleases, an exonuclease (ExoIII) and an endonuclease (Nt.BspQI), via fluorescence-based kinetic experiments, varying parameters including enzyme and substrate concentrations, and nanoparticle size and surface coverage in non-recycling and a recycling formats. We demonstrate the tuning of nuclease activity by SNA characteristics and show that the modular units of SNAs can be leveraged to either accelerate or suppress nuclease kinetics. Additionally, we observe that the enzymes are capable of cleaving restriction sites buried deep in the oligonucleotide surface layer and that enzymatic rate enhancement occurs in the target recycling format but not in the non-recycling format. Furthermore, we demonstrate a new SNA phenomenon, we term 'target stacking', whereby nucleic acid hybridization efficiency increases as enzyme cleavage proceeds during the beginning of a reaction. This investigation provides important data to guide the design of novel SNAs in biosensing and in vitro diagnostic applications.

Advances in fluorescent probes for detection and imaging of amyloid-β peptides in Alzheimer's disease

Amyloid plaques generated from the accumulation of amyloid-β peptides (Aβ) fibrils in the brain is one of the main hallmarks of Alzheimer's disease (AD), a most common neurodegenerative disorder. Aβ aggregation can produce neurotoxic oligomers and fibrils, which has been widely accepted as the causative factor in AD pathogenesis. Accordingly, both soluble oligomers and insoluble fibrils have been considered as diagnostic biomarkers for AD. Among the existing analytical methods, fluorometry using fluorescent probes has exhibited promising potential in quantitative detection and imaging of both soluble and insoluble Aβ species, providing a valuable approach for the diagnosis and drug development of AD. In this review, the most recent advances in the fluorescent probes for soluble or insoluble Aβ aggregates are discussed in terms of design strategy, probing mechanism, and potential applications. In the end, future research directions of fluorescent probes for Aβ species are also proposed.

Surface Modification of Fluorescent Nanodiamonds for Biological Applications

Fluorescent nanodiamonds (FNDs) are a new class of carbon nanomaterials that offer great promise for biological applications such as cell labeling, imaging, and sensing due to their exceptional optical properties and biocompatibility. Implementation of these applications requires reliable and precise surface functionalization. Although diamonds are generally considered inert, they typically possess diverse surface groups that permit a range of different functionalization strategies. This review provides an overview of nanodiamond surface functionalization methods including homogeneous surface termination approaches (hydrogenation, halogenation, amination, oxidation, and reduction), in addition to covalent and non-covalent surface modification with different functional moieties. Furthermore, the subsequent coupling of biomolecules onto functionalized nanodiamonds is reviewed. Finally, biomedical applications of nanodiamonds are discussed in the context of functionalization.

A highly sensitive fluorescent biosensor for the detection of cytochrome c based on polydopamine nanotubes and exonuclease I amplification

A novel fluorescence method for the detection of Cyt c was developed based on PDANTs and exonuclease I amplification.

Cooperative Metal Ion-Mediated Adsorption of Spherical Nucleic Acids with a Large Hysteresis

Spherical nucleic acids (SNA) refer to nanoparticles attached with a high density of oligonuleotides. Linear and spherical nucleic acids have many differences such as hybridization affinity, melting transition, and cellular uptake. In this work, these two types of DNA of the same sequence were compared for adsorption on polydopamine (PDA) nanoparticles and graphene oxide (GO). We focused on the effect of metal ions including Na⁺, Ca²⁺, and Zn²⁺ since metal ions are indispensible for DNA adsorption on PDA and GO. Gold nanoparticles (AuNPs) of various sizes were used to prepare the SNAs. For both PDA and GO, a normal binding curve of one metal ion was obtained for adsorbing the linear DNA, while the spherical DNAs larger than 5 nm showed a sigmoidal binding curve requiring multiple metal ions. Urea and EDTA were used to probe DNA adsorption affinity, where the spherical DNA showed stronger adsorption in general. In the presence of 300 mM Na⁺, 4 M urea or 4 mM EDTA failed to desorb the 13 nm spherical DNA. The spherical DNA showed a very large hysteresis of metal-dependent adsorption. This study demonstrates another unique property of SNA compared to linear DNA, revealing interesting orientation and packing of DNA on AuNPs, which has deepened our understanding of DNA interface chemistry.

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.

One-step and ultrasensitive ATP detection by using positively charged nano-gold@graphene oxide as a versatile nanocomposite

A versatile nanocomposite was simply prepared based upon the electrostatic adsorption of positively charged gold nanoparticles with negatively charged graphene oxide (nano-gold@GO), and utilized as a novel fluorescence quenching platform for ultrasensitive detection of adenosine triphosphate (ATP). In the designed system, DNA-stabilized Ag nanoclusters (DNA/AgNCs) were used as fluorescent probes, DNA duplex was formed in the presence of ATP, and they can electrostatically adsorb onto the surface of nano-gold@GO to quench the fluorescence signal. Upon the addition of exonuclease III (Exo III), the DNA duplex would be hydrolyzed into DNA fragments and resulted in the recovery of the fluorescence signals due to the diffusion of AgNCs away from nano-gold@GO. Based on these, sensitive detection of ATP was realized with a detection range of 5.0 pM-20 nM. Notably, a good recovery in the range of 94-104% was obtained when detecting ATP in human serum samples, indicating a promising application value in early disease diagnosis. Graphical abstract A functional positively charged nano-gold@graphene oxide was fabricated and utilized as an enhanced fluorescence quenching platform for the detection of ATP, coupled with exonuclease III-assisted signal amplification.

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.

A rapid label- and enzyme-free G-quadruplex-based fluorescence strategy for highly-sensitive detection of HIV DNA

Because rapid, convenient, and selective methods for HIV detection are urgently needed, herein, a simple label-free and enzyme-free strategy is constructed for sensitive fluorescence detection of HIV DNA using the fluorescent intercalating dye thioflavin T (THT) as the detection signal source. This strategy utilizes a hairpin DNA sequence (H1) and two assistant strands. H1 is wisely designed with a G-quadruplex sequence in the stem. Target DNA, when present in solution, will hybridize with H1 to form H1/target duplexes and release the G-quadruplexes. Additionally, the assistant probes hybridize with the unfolded H1 to form a stable DNA double strand, resulting in the displacement of the target to participate in another similar reaction cycle. Consequently, many G-quadruplex structures are generated, leading to a significantly amplified fluorescence signal of THT. The linear range is from 0.1 nM to 50.0 nM with a limit of detection of 13 pM. Results can be achieved within 40 min, because the cyclic amplification involves only one DNA hairpin and two auxiliary chains. Furthermore, this platform exhibited good selectivity with one base mismatch or other DNA sequences. This strategy could be used as a simple, sensitive, and selective tool to detect other DNA biomarkers.

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

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

Mussel-inspired functionalization of semiconducting polymer nanoparticles for amplified photoacoustic imaging and photothermal therapy

A versatile and straightforward strategy for the encapsulation of semiconducting polymer nanoparticles (SPNs) using biocompatible polydopamine (PDA) as both the protection and versatile bioconjugation layer is proposed. In addition to providing stable functionalized SPNs, this approach provides SPNs with a flexible surface for further modification with various functional ligands. In this study, three representative surface modifiers including a small molecule (folic acid, FA), a peptide (cRGD) and a stealth polymer (SH-PEG) were conjugated onto the surface of SPNs. Specifically, PDA encapsulation can reliably form SPNs that are uniform in size (∼65 nm) and facilitate the rapid purification of SPN bioconjugates by centrifugation which is difficult to achieve using traditional methods for preparing SPN bioconjugates. Compared to pristine PSBTBT NPs, the synthesized PSBTBT@PDA NPs simultaneously showed more excellent structural stability, significantly enhanced PA brightness and amplified PTT efficacy. Benefiting from the outstanding PA and PTT performances, it is possible for the PSBTBT@PDA NPs to ablate tumors more effectively compared to PSBTBT NPs. Our study thus demonstrates that the PDA encapsulated SPNs should be a promising theranostic agent for PA imaging and PTT.

An electrochemiluminescence immunosensor for the N-terminal brain natriuretic peptide based on the high quenching ability of polydopamine

A sandwich-type electrochemiluminescence (ECL) immunosensor for the N-terminal brain natriuretic peptide (NT-proBNP) is described. The assay is based on the quenching of the ECL of graphite-like carbon nitride (g-C₃N₄) by polydopamine (PDA). Two-dimensional g-C₃N₄ is grown in-situ on titanium dioxide nanoflowers (TiO₂ NFs). The macroporous structure of the NFs enhances the interfacial stability of g-C₃N₄, and also promotes the ECL reaction of g-C₃N₄ with the co-reactant. The introduction of gold nanoparticles into the matrix further enhances the ECL and facilitates the immobilization of capture antibodies. The nanoquencher used to label the secondary antibody is synthesized by catalytic polymerization of dopamine in the presence of bimetallic NiPd nanoparticles. The nanoquencher preserves the high reactivity of polydopamine and quenches the ECL of the g-C₃N₄/TiO₂ system. Compared to other methods, the detection limit for NT-proBNP is decreased to 50 fg∙mL^-1. Graphical abstract Schematic presentation of the electrochemiluminescence (ECL) process of the immunosensor: titanium dioxide nanoflowers@graphite-like carbon nitride-gold nanoparticles (TiO₂ NFs@g-C₃N₄-Au) as luminophor, and polydopamine (PDA) as nanoquencher.

A fluorescent aptasensor based on single oligonucleotide-mediated isothermal quadratic amplification and graphene oxide fluorescence quenching for ultrasensitive protein detection

In this work, we have developed a novel fluorescent aptasensor based on single oligonucleotide-mediated isothermal quadratic amplification (SOIQA) and graphene oxide (GO)-mediated fluorescence quenching for the ultrasensitive detection of proteins in a homogeneous solution. The SOIQA consists of a fluorophore-labeled aptamer hairpin probe containing T7 exonuclease (T7 Exo)-resistant 5'-protruding termini and a mismatch base at its 3'-end, DNA polymerase, T7 Exo and GO. The target analyte binds with the aptamer sequences and unfolds the fluorophore-labeled aptamer hairpin probe to form a new DNA hairpin, inducing the catalytic recycling of the target analyte (assisted by DNA polymerase) and DNA sequences (aided by T7 Exo) to achieve SOIQA, which results in the digestion of numerous fluorophore-labeled aptamer hairpin probes and the generation of a large amount of mononucleotides carrying the fluorophore. These mononucleotide products cannot be adsorbed onto the GO, leading to a dramatic increase in the fluorescence intensity for the amplified detection of the target molecules. In the absence of the target analyte, however, the SOIQA reaction is inhibited and the fluorophore-labeled aptamer hairpin probe is adsorbed onto the GO, leading to an extremely low fluorescence background signal. To test the feasibility of the SOIQA systems, a protein cancer marker, carcinoembryonic antigen (CEA) was used as the model analyte. The developed aptasensor could detect CEA with a detection limit of 28.5 fg mL-1 (∼142 aM), high specificity and a broad detection range of 6 orders of magnitude. And this one-step incubation can be completed in 60 min. In addition, the approach uses only one oligonucleotide strand, and is simple. Moreover, this SOIQA sensing method is suitable for rapid and direct quantification of proteins in complex biological samples such as clinical serum. Considering the simplicity and superior sensitivity/specificity, the developed sensing method provides a promising platform for the analysis of a variety of low-abundance biomolecules.

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.

Facile fabrication of polydopamine nanotubes for combined chemo-photothermal therapy

Polydopamine nanoparticles with higher drug loading capacity and enhanced photothermal behavior.

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.

Polydopamine Nanomaterials: Recent Advances in Synthesis Methods and Applications

Polydopamine (PDA), the final oxidation product of dopamine or other catecholamines, attracted much attention as versatile coatings that can be used to cover the surface of almost all materials with a conformal layer of adjustable thickness ranging from a few to about 100 nm. These PDA layers can be subsequently modified with molecules carrying nucleophilic groups or with metallic nanoparticles from solutions containing metallic cations. However, during the deposition of PDA film on the surfaces, the reaction products that are simultaneously obtained from the oxidation of catecholamines in solution precipitate. Hence, some recent effort has been devoted to produce PDA in the form of nanoparticles. The aim of this short review is to give a comprehensive description of the synthesis methods yielding of PDA nanoparticles in the absence or in the presence of templating agents (polymers, polyelectrolytes, surfactants, proteins, and even some small organic molecules). We will also describe the use of thin PDA layers to coat already synthesized nanoparticles or nanotubes. Finally, several first applications of the obtained PDA nanoparticles will be described.

Metal-Polydopamine Framework as an Effective Fluorescent Quencher for Highly Sensitive Detection of Hg(II) and Ag(I) Ions through Exonuclease III Activity

In this paper, we propose a metal-polydopamine (MPDA) framework with a specific molecular probe which appears to be the most promising approach to a strong fluorescence quencher. The MPDA framework quenching ability toward various organic fluorophore such as aminoethylcoumarin acetate, 6-carboxyfluorescein (FAM), carboxyteramethylrhodamine, and Cy5 are used to establish a fluorescent biosensor that can selectively recognize Hg²⁺ and Ag⁺ ions. The fluorescent quenching efficiency was sufficient to achieve more than 96%. The MPDA framework also exhibits different affinities with ssDNA and dsDNA. In addition, the FAM-labeled ssDNA was adsorbed onto the MPDA framework, based on their interaction with the complex formed between MPDA frameworks/ssDNA taken as a sensing platform. By taking advantage of this sensor, highly sensitive and selective determination of Hg²⁺ and Ag⁺ ions is achieved through exonuclease III signal amplification activity. The detection limits of Hg²⁺ and Ag⁺ achieved to be 1.3 and 34 pM, respectively, were compared to co-existing metal ions and graphene oxide-based sensors. Furthermore, the potential applications of this study establish the highly sensitive fluorescence detection targets in environmental and biological fields.

A Universal Upconversion Sensing Platform for the Sensitive Detection of Tumour-Related ncRNA through an Exo III-Assisted Cycling Amplification Strategy

Here, a sensitive and universal noncoding RNA (ncRNA) upconversion sensing nanoplatform is developed. Gold nanoparticles bearing one hairpin DNA (Hp) molecule are conjugated to the linker DNA modified NaYF₄ :Yb, Er@NaYF₄ upconversion nanoparticles by DNA hybridization, leading to quenching of the upconversion emission through fluorescence resonance energy transfer. A signal DNA (SDNA) sequence is designed to open Hp, recovering the upconversion emission. To achieve universality and high sensitivity of the nanoprobe, an exonuclease III (Exo III)-assisted cycling amplification strategy is introduced. A multifunctional hairpin DNA (mHp) containing ncRNA recognition sequence and SDNA sequence is designed to recognize ncRNA and trigger Exo III as a biocatalyst to stepwise disintegrate itself, releasing both ncRNA and SDNA. The released ncRNA can be reused to release more SDNA, which greatly improves the sensing sensitivity. By changing the recognition portion of mHp, various ncRNA can be detected. The sensitive detection of both homeobox (HOX) transcript antisense RNA segment and miR-21 is achieved with this novel strategy, even in human serum, indicating the universality and sensitivity of the proposed strategy. Additionally, the expression level of miR-21 in human breast cancer cell (MCF-7) lysate is successfully measured, suggesting its potential in clinical diagnosis.

Label-free and nicking enzyme-assisted fluorescence signal amplification for RNase H determination based on a G-quadruplexe/thioflavin T complex

In this paper, we describe a novel, label-free and nicking enzyme-assisted fluorescence signal amplification strategy that demonstrates to be cost efficient, sensitive, and unique for assaying the RNase H activity and inhibition based on G-quadruplex formation using a thioflavin T (ThT) dye. This novel assay method is able to detect RNase H with a detection limit of 0.03 U /mL and further exhibits a good linearity R² = 0.9923 at a concentration range of 0.03-1 U/mL under optimized conditions. Moreover, the inhibition effect of gentamycin on the RNase H activity is also studied. This strategy provides a potential tool for the biochemical enzyme analysis and inhibitor screening.

Fabrication and evaluation of hemoglobin-based polydopamine microcapsules as oxygen carriers

Polydopamine-hemoglobin (PDA-Hb) microcapsules possess a high oxygen affinity and could bind and release oxygen reversibly as demonstrated by electrochemical methods.

Exonuclease III-boosted cascade reactions for ultrasensitive SERS detection of nucleic acids

A variety of nucleic acid amplification techniques have been integrated into different detection methods to promote the development of sensitive and convenient analysis of nucleic acids. However, it is still in urgent need to develop amplified nucleic acid biosensors for the analysis of susceptible gene and even distinguishing single-base mismatched DNA in complex biological samples. Benefiting from the achieved detection strategies, here we boost isothermal nucleic acid amplification by resorting to enzyme amplification, and combine this two-stage amplification method with surface-enhanced Raman spectroscopy (SERS) to develop a signal-on nucleic acid detection platform. Due to the high cleavage efficiency of Exonuclease III (Exo III), a large amount of trigger DNA are produced to initiate multiple hybridization chain reaction circles. The product structure tagged with Tamra is then anchored onto the plasmonic SERS substrate and meanwhile enriched. It is demonstrated that this detection platform is sensitive toward the myocardial infarction disease related gene. A detection limit of 1 fM for the gene analysis in a linear relationship in the wide range from 1 fM to 10nM is achieved, better than most of previous counterparts. Meanwhile, our developed detection platform exhibits a high selectivity for the target gene over mismatched analogues. Our strategy provides a robust tool for signal amplification of gene detection even in blood samples.

Polydopamine Based Colloidal Materials: Synthesis and Applications

Polydopamine is a synthetic analogue of natural melanin (eumelanin) produced from oxidative polymerization of dopamine. Owing to its strong adhesion ability, versatile chemical reactivity, biocompatibility and biodegradation, polydopamine is commonly applied as a versatile linker to synthesize colloidal materials with diverse structures, unique physicochemical properties and tunable functions, which allow for a broad scope of applications including biomedicine, sensing, catalysis, environment and energy. In this personal account, we discuss first about the different synthetic approaches of polydopamine, as well as its polymerization mechanism, and then with a comprehensive overview of recent progress in the synthesis and applications of polydopamine-based colloidal materials. Finally, we summarize this personal account with future perspectives.