Manganese porphyrin-double stranded DNA complex guided in situ deposition of polyaniline for electrochemical thrombin detection

Nucleic Acid Tests for Clinical Translation

Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.

Surface-Guided Chemical Processes on Self-Assembled DNA Nanostructures

Solid-liquid interfaces have been of great significance in the activation of chemical reactions via restricting the conformation or orientation of the reactants. Self-assembled DNA nanostructures encoded with tremendous chemical and physical information provide an efficient platform to unravel and regulate mechanisms of surface chemical processes. In this review, we discuss the surface addressability, morphological features, and charged properties of DNA nanostructures as well as the recognition, catalytic, and dynamic properties of DNA molecules. We highlight the synergies between the surface properties of DNA nanostructures and the molecular features of DNA strands, which is a key to the synthesis of conductive polymer nanomaterials with well-defined shapes or electronic/optical properties. We also focus on the control over the substrate channeling pathways of enzyme networks or metal nucleation on DNA nanostructures toward the production of specifically emissive metal nanoclusters. In the end, we provide an outlook of future possible directions based on the rational design of DNA-based self-assembly, including dynamic energy transfer, stimuli-responsive synthesis, and programmable activation of the mechanophores on the surfaces of DNA nanostructures.

Multipedal DNA Walker Biosensors Based on Catalyzed Hairpin Assembly and Isothermal Strand-Displacement Polymerase Reaction for the Chemiluminescent Detection of Proteins

In this study, two kinds of sensitive biosensors based on a multipedal DNA walker along a three-dimensional DNA functional magnet particles track for the chemiluminescent detection of streptavidin (SA) are constructed and compared. In the presence of SA, a multipedal DNA walker was constructed by a biotin-modified catalyst as a result of the terminal protection to avoid being digested by exonuclease I. Then, through a toehold-mediated strand exchange, a "leg" of a multipedal DNA walker interacted with a toehold of a catalyzed hairpin assembly (CHA)-H1 coupled with magnetic microparticles (MMPs) and opened its hairpin structure. The newly open stem in CHA-H1 was hybridized with a toehold of biotin-labeled H2. Via the strand displacement process, H2 displaced one "leg" of a multipedal DNA walker, and the other "leg" continued to interact with the neighboring H1 to initiate the next cycle. In order to solve the high background caused by the hybridization between CHA-H1 and H2 without a CHA-catalyst, the other model was designed. The principle of the other model (isothermal strand-displacement polymerase reaction (ISDPR)-DNA walker) was similar to that of the above one. After the terminal protection of SA, a "leg" of a multipedal DNA walker was triggered to open the hairpin of the ISDPR-H1 conjugated with MMPs. Then, the biotin-modified primer hybridized with the newly exposed DNA segment, triggering the polymerization reaction with the assistance of dNTPs/polymerase. As for the extension of the primer, the "leg" of a multipedal DNA walker was displaced so that the other "leg" could trigger the proximal H1 to go onto the next cycle. Due to its lower background and stronger signal, a multipedal DNA walker based on an ISDPR had a lower limit of detection for SA. The limit of detection for SA was 6.5 pM, and for expanding the application of the method, the detections of the folate receptor and thrombin were explored. In addition, these DNA walker methods were applied in complex samples successfully.

An ultrasensitive "on-off-on" photoelectrochemical aptasensor based on signal amplification of a fullerene/CdTe quantum dots sensitized structure and efficient quenching by manganese porphyrin

In this work, an ultrasensitive "on-off-on" photoelectrochemical (PEC) aptasensor was proposed based on the signal amplification of a fullerene/CdTe quantum dot (nano-C60/CdTe QDs) sensitized structure and efficient signal quenching of nano-C60/CdTe QDs by a manganese porphyrin (MnPP).

Manganese porphyrin decorated on DNA networks as quencher and mimicking enzyme for construction of ultrasensitive photoelectrochemistry aptasensor

In this work, the manganese porphyrin (MnPP) decorated on DNA networks could serve as quencher and mimicking enzyme to efficiently reduce the photocurrent of photoactive material 3,4,9,10-perylene tetracarboxylic acid (PTCA), which was elaborately used to construct a novel label-free aptasensor for ultrasensitive detection of thrombin (TB) in a signal-off manner. The Au-doped PTCA (PTCA-PEI-Au) with outstanding membrane-forming and photoelectric property was modified on electrode to acquire a strong initial photoelectrochemistry (PEC) signal. Afterward, target binding aptamer Ι (TBAΙ) was modified on electrode to specially recognize target TB, which could further combine with TBAII and single-stranded DNA P1-modified platinum nanoparticles (TBAII-PtNPs-P1) for immobilizing DNA networks with abundant MnPP. Ingeniously, the MnPP could not only directly quench the photocurrent of PTCA, but also acted as hydrogen peroxide (HRP) mimicking enzyme to remarkably stimulate the deposition of benzo-4-chlorhexidine (4-CD) on electrode for further decreasing the photocurrent of PTCA, thereby obtaining a definitely low photocurrent for detection of TB. As a result, the proposed PEC aptasensor illustrated excellent sensitivity with a low detection limit down to 3 fM, exploiting a new avenue about intergrating two functions in one substance for ultrasensitive biological monitoring.

Enzymatic oligomerization and polymerization of arylamines: state of the art and perspectives

The literature concerning the oxidative oligomerization and polymerization of various arylamines, e.g., aniline, substituted anilines, aminonaphthalene and its derivatives, catalyzed by oxidoreductases, such as laccases and peroxidases, in aqueous, organic, and mixed aqueous organic monophasic or biphasic media, is reviewed. An overview of template-free as well as template-assisted enzymatic syntheses of oligomers and polymers of arylamines is given. Special attention is paid to mechanistic aspects of these biocatalytic processes. Because of the nontoxicity of oxidoreductases and their high catalytic efficiency, as well as high selectivity of enzymatic oligomerizations/polymerizations under mild conditions-using mainly water as a solvent and often resulting in minimal byproduct formation-enzymatic oligomerizations and polymerizations of arylamines are environmentally friendly and significantly contribute to a "green" chemistry of conducting and redox-active oligomers and polymers. Current and potential future applications of enzymatic polymerization processes and enzymatically synthesized oligo/polyarylamines are discussed.

Highly sensitive chemiluminescence biosensor for protein detection based on the functionalized magnetic microparticles and the hybridization chain reaction

An ultrasensitive chemiluminescence (CL) biosensor for the detection of protein is developed in this study based on the functionalized magnetic microparticles (MMPs) and the hybridization chain reaction (HCR). First, the primer hybridized with the thrombin aptamer conjugated on the surface of MMPs. Then the HCR was triggered by part of the primer and its products were assembled on the surface of the MMPs. Through the interaction between streptavidin and biotin, the streptavidin-horseradish peroxidase (SA-HRP) was coupled with the HCR products. In the presence of thrombin, the HCR products conjugating with SA-HRP were released from the surface of MMPs after the aptamer recognized and bound to its target molecule. So the released SA-HRP in the supernatant produced a significant chemiluminescence imaging signal after the addition of H₂O₂-luminol. The detection limit of thrombin with this method could be as low as 9.7fM. Besides, the sensing strategy was modified by changing the adding order of reagents that was then successfully applied in the detection of thrombin in complex sample. What's more, the DNA detection also could be carried out with this method, which demonstrated the universality of the proposed sensing strategy.

Dendritic structure DNA for specific metal ion biosensor based on catalytic hairpin assembly and a sensitive synergistic amplification strategy

In this work, a sensitive electrochemical biosensing to Pb²⁺ was proposed based on the high specificity of DNAzymes to Pb²⁺. The response signal was efficiently amplified by the catalytic hairpin assembly induced by strand replacement reaction and the formation of dendritic structure DNA (DSDNA) by layer-by-layer assembly. Firstly, in the presence of Pb²⁺, the substrate strand (S1) of the Pb²⁺-specific DNAzymes was specifically cleaved by Pb²⁺. Secondly, one of the two fragments (rS1) introduced into the electrode surface was hybridized with a hairpin DNA (H1) and further replaced by another hairpin DNA (H2) by the hybridization reaction of H1 with H2. The released rS1 then induced the next hybridization with H1. After repeated cycles, the catalytic recycling assembly of H2 with H1 was completed. Thirdly, two bioconjugates of Pt@Pd nanocages (Pt@PdNCs) labeled with DNA S3/S4 and electroactive toluidine blue (Tb) (Tb-S3-Pt@PdNCs and Tb-S4-Pt@PdNCs) were captured onto the resultant electrode surface through the hybridization of S3 and H2, S3 and S4, resulting in the formation of DSDNA triggered by layer-by-layer assembly. This formed DSDNA greatly facilitated the immobilization of manganese(III) meso-tetrakis (4-N-methylpyridiniumyl)-porphyrin (MnTMPyP) as mimicking enzyme. Under the synergistic catalysis of Pt@PdNCs and MnTMPyP to H₂O₂ reduction, the effective signal amplification of the developed Pb²⁺ biosensor was achieved. As a result, the sensitive detection of the proposed electrochemical strategy for Pb²⁺ was greatly improved in the range of 0.1pM-200nM with a detection limit of 0.033pM.

Peroxidase-like activity of gold nanoparticles stabilized by hyperbranched polyglycidol derivatives over a wide pH range

The aim of this work was to carry out comparative studies on the peroxidase-like activity of gold nanoparticles (AuNPs) stabilized with low molecular weight hyperbranched polyglycidol (HBPG-OH) and its derivative modified with maleic acid residues (HBPG-COOH). The influence of the stabilizer to gold precursor ratio on the size and morphology of nanoparticles obtained was checked, and prepared nanoparticles were characterized by means of transmission electron microscopy and UV-Vis spectroscopy. The results indicated the divergent effect of increasing the concentration of stabilizers (HBPG-OH or HBPG-COOH) on the size of the nanostructures obtained. The gold nanoparticles obtained were characterized as having intrinsic peroxidase-like activity and the mechanism of catalysis in acidic and alkaline mediums was consistent with the standard Michaelis-Menten kinetics, revealing a strong affinity of AuNPs with 2, 2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and 3, 3', 5, 5'-tetramethylbenzidine (TMB), and significantly lower affinity towards phenol. By comparing the kinetic parameters, a negligible effect of polymeric ligand charge on activity against various types of substrates (anionic or cationic) was indicated. The superiority of steric stabilization via the application of tested low-weight hyperbranched polymers over typical stabilizers in preventing salt-induced aggregation and maintaining high catalytic activity in time was proved. The applied hyperbranched stabilizers provide a good tool for manufacturing gold-based nanozymes, which are highly stable and active over a wide pH range.

Target catalyzed hairpin assembly for constructing a ratiometric electrochemical aptasensor

In this paper, we develop a novel dual-signaling amplified aptasensor for protein detection via target-catalyzed hairpin assembly. Thrombin was chosen as a model target. This aptasensor contains two DNA hairpins termed as H1 and H2. H1, which is modified at its 3' ends with a methylene blue (MB), consists of the aptamer sequence of human thrombin. Meanwhile, H2 which is modified at its 3' ends with a ferrocene (Fc), is partially complementary to H1. Upon the addition of target protein, it can facilitate the opening of the hairpin structure of H1 and thus accelerate the hybridization between H1 and H2, the target protein can be displaced from hairpin H1 by hairpin H2 through a process similar to DNA branch migration. The released target found another H1 to trigger the cycle, resulting in the multiplication of the Fc confined near the GE surface and MB away from the GE surface. When IFc/IMB is used as the response signal for quantitative determination of thrombin, the detection limit (41 fM) is much lower than that by using either MB or Fc alone. This new dual-signaling aptasensor is readily regenerated and shows good response toward the target. Furthermore, this amplified aptasensor shows high selectivity toward its target protein. The clever combination of the functional DNA hairpin and the novel device achieved a ratiometric electrochemical aptasensor, which could be used as a simple, sensitive high repeatability and selective platform for target protein detection.

An amplified electrochemical aptasensor based on hybridization chain reactions and catalysis of silver nanoclusters

In the present study, based on the mimic oxidase catalytic character of nucleic-acid-stabilized silver nanoclusters (DNA/AgNCs) and hybridization chain reactions for signal amplification, the fabrication of a label-free sensitive "turn-on" electrochemical aptasensor for the amplified determination of lysozyme was demonstrated. First, the designed DNA duplex was modified on the electrode. With the specific binding of the target, lysozyme and its aptamer, the lysozyme-binding DNA sequence was liberated, exposing the induced DNA sequence, which in turn triggered the formation of the supersandwich DNA structure. Because the cytosine-rich sequence was designed ingeniously on the DNA sequence, DNA/AgNCs were formed on the supersandwich DNA structure. The peroxidase-like character of DNA/AgNCs produced detectable electrochemical signals for the lysozyme aptasensor, which showed a satisfying sensitive detection of lysozyme with a low detection limit of 42 pM and a wide linear range of 10(-10) M to 10(-5) M.

3,4,9,10-Perylenetetracarboxylic acid/o-phenylenediamine nanomaterials as novel redox probes for electrochemical aptasensor systems based on an Fe3O4 magnetic bead as a nonenzymatic catalyst

A novel redox probe 3,4,9,10-perylenetetracarboxylic acid/o-phenylenediamine was applied in an electrochemical aptasensor to detect thrombin based on an Fe₃O₄ magnetic bead as a nonenzymatic catalyst.