Amplified electrochemical DNA sensor using peroxidase-like DNAzyme

A novel electrochemical DNA sensor was developed here by using peroxidase-like G-quadruplex-based DNAzyme as a biocatalytic label. A hairpin structure including the G-quadruplex-based DNAzyme in a caged configuration and the target DNA probe were immobilized on Au-electrode surface. Upon hybridization with the target, the hairpin structure was opened, and the G-quadruplex-based DNAzyme was generated on the electrode surface, triggering the electrochemical oxidization of hydroquinone by H₂O₂, which provide a quantitative measure for the detection of the target DNA. The DNA target was analyzed with a detection limit of 0.6 nM. This method is simple and easy to design without direct conjugation of redox-active element.     

Enzyme-free amplified detection of DNA by an autonomous ligation DNAzyme machinery

The Zn(2+)-dependent ligation DNAzyme is implemented as a biocatalyst for the amplified detection of a target DNA by the autonomous replication of a nucleic acid reporter unit that is generated by the catalyzed ligation process. The reporter units enhance the formation of active DNAzyme units, thus leading to the isothermal autocatalytic formation of the reporter elements. The system was further developed and applied for the amplified detection of Tay-Sachs genetic disorder mutant, with a detection limit of 1.0 × 10(-11) M. Besides providing a versatile paradigm for the amplified detection of DNA, the system reveals a new, enzyme-free, isothermal, autocatalytic mechanism that introduces means for effective programmed synthesis.     

Hierarchical mesoporous silica wires by confined assembly

The assembly of silicate and surfactant confined within cylindrical alumina pore channels results in circular hexagonal, concentric lamellar and other unique mesostructures.     

Sensitive analysis of DNA methyltransferase based on a hairpin-shaped DNAzyme

The analysis of DNA methylation and MTase (methyltransferase) activity is important in epigenetic study. We have developed a novel strategy for sensitive analysis of MTase activity based on a hairpin shaped DNAzyme; 8-17 DNAzyme amplicon has been adopted and found to be very effective in such analysis.     

Switchable Enzyme/DNAzyme Cascades by the Reconfiguration of DNA Nanostructures

Mimicking cellular transformations and signal transduction pathways by means of biocatalytic cascades proceeding in organized media is a scientific challenge. We describe two DNA machines that enable the “ON/OFF” switchable activation and deactivation of three‐component biocatalytic cascades. One system consists of a reconfigurable DNA tweezers‐type structure, whereas in the second system the catalytic cascade proceeds on a switchable DNA clamp scaffold. The three‐component catalytic cascades consist of β‐galactosidase (β‐Gal), glucose oxidase (GOx), and the K⁺‐ion‐stabilized hemin‐G‐quadruplex horseradish peroxidase (HRP)‐mimicking DNAzyme. The hemin‐G‐quadruplex‐bridged closed structure of the tweezers or clamp allows the biocatalytic cascades to operate (switched “ON′′), whereas separation of the hemin‐G‐quadruplex by means of 18‐crown‐6‐ether opens the tweezers/clamp structures, thus blocking the catalytic cascade (switched ”OFF“). This study is complemented by two‐component, switchable biocatalytic cascades composed of GOx and hemin‐G‐quadruplex assembled on hairpin‐bridged DNA tweezers or clamp nanostructures.     

A novel electrochemical aptasensor for highly sensitive detection of thrombin based on the autonomous assembly of hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme nanowires

In this work, a new signal amplified strategy was constructed based on isothermal exponential amplification reaction (EXPAR) and hybridization chain reaction (HCR) generating the hemin/G-quadruplex horseradish peroxidase-mimicking DNAzyme (HRP-mimicking DNAzyme) nanowires as signal output component for the sensitive detection of thrombin (TB). We employed EXPAR’s ultra-high amplification efficiency to produce a large amount of two hairpin helper DNAs within a minutes. And then the resultant two hairpin helper DNAs could autonomously assemble the hemin/G-quadruplex HRP-mimicking DNAzymes nanowires as the redox-active reporter units on the electrode surface via hybridization chain reaction (HCR). The hemin/G-quadruplex structures simultaneously served as electron transfer medium and electrocatalyst to amplify the signal in the presence of H₂O₂. Specifically, only when the EXPAR reaction process has occurred, the HCR could be achieved and the hemin/G-quadruplex complexes could be formed on the surface of an electrode to give a detectable signal. The proposed strategy combines the amplification power of the EXPAR, HCR, and the inherent high sensitivity of the electrochemical detection. With such design, the proposed assay showed a good linear relationship within the range of 0.1 pM–50 nM with a detection limit of 33 fM (defined as S/N = 3) for TB.     

Enzyme-free signal amplification in the DNAzyme sensor via target-catalyzed hairpin assembly

A simple, highly sensitive and enzyme-free DNAzyme sensor based on target-catalyzed hairpin assembly is developed, which permits detection of 0.1 pM target DNA. Furthermore, this DNAzyme sensor is capable of detecting target DNA in real samples because of its high selectivity.     

Double-stranded helical polymers consisting of complementary homopolymers

Two complementary homopolymers of chiral amidines and achiral carboxylic acids with m-terphenyl-based backbones were synthesized by the copolymerization of a p-diiodobenzene derivative with the diethynyl monomers bearing a chiral amidine group and a carboxyl group using the Sonogashira reaction, respectively. Upon mixing in THF, the homopolymer strands assembled into a preferred-handed double helix through interstrand amidinium-carboxylate salt bridges, as evidenced by its absorption, circular dichroism, and IR spectra. In contrast, when mixed in less polar solvents, such as chloroform, the complementary strands kinetically formed an interpolymer complex with an imperfect double helical structure containing a randomly hybridized cross-linked structure, probably because of strong salt bridge formations. This primary complex was rearranged into the fully double helical structure by treatment with a strong acid followed by neutralization with an amine. High-resolution atomic force microscopy revealed the double-stranded helical structure and enabled the determination of the helical sense.     

Amplified detection of DNA and analysis of single-base mismatches by the catalyzed deposition of gold on Au-nanoparticles

A novel amplification route for DNA detection based on the deposition of gold on a 10 nm Au-colloid/avidin conjugate label acting as a 'seeding' catalyst, is described. Microgravimetric quartz-crystal-microbalance measurements are employed to transduce the catalyzed deposition of gold on the piezoelectric crystals. Three different DNA detection schemes are described: (i) analysis of a 27-base nucleic acid fragment; (ii) analysis of the entire M13phi DNA (7229 bases); and (iii) detection of a single-base mismatch in a DNA. Ultrasensitive detection of DNA is accomplished by the catalyzed deposition of gold, detection limit approximately 1 x 10(-15) M.     

Ultrasensitive detection of DNA by the PCR-Induced generation of DNAzymes: the DNAzyme primer approach

The ultrasensitive detection of DNA is achieved by PCR-induced evolution of a DNAzyme.     

Amplified DNA sensing and immunosensing by the rotation of functional magnetic particles

Amplified chemiluminescent detection of DNA-complementary DNA or of antigen-antibody interactions is accomplished in the presence of rotating functionalized magnetic particles.     

Enhanced catalytic DNAzyme for label-free colorimetric detection of DNA

A DNAzyme-based label-free method for the colorimetric detection of DNA is introduced, with a supramolecular hemin-G-quartet complex as the sensing element and a 36-mer single-strand DNA as the analyte that is detected at 10 nM.     

Control and modeling of the dielectrophoretic assembly of on-chip nanoparticle wires

Suspensions of metallic nanoparticles in water were assembled via the action of an alternating electric field (dielectrophoresis) into wires of micrometer thickness. Two modes of microwire assembly, one through the bulk of the suspension and one as half-cylinders on the glass surface between the electrodes, were identified. The operating conditions responsible for the two assembly modes were recognized. The control of the process parameters allows making, for example, straight single connectors or massively parallel arrays of microwires on the surface of the chip, which can be extracted in dry form. The microwire assembly process was modeled using finite element electrostatic calculations. The direction of growth can be guided by introducing conductive islands or particles in the suspension. The experiments, supported by electrostatic calculations, show that the wires grow in the direction of highest field intensity, "automatically" making electrical connections to the objects between the electrodes. The results point the way to controlled dielectrophoretic assembly of nanoparticles into on-chip electrical connectors, switches, and networks.     

Noncovalent control for bottom-up assembly of functional supramolecular wires

Noncovalent bonds have been used to assemble stacks of pi-electron-rich moieties at a surface, generating a pathway for charge transport. The system is comprised of a tetrathiafulvalene (TTF) derivative incorporating two amide groups which fasten the relative orientations of the electroactive moieties in the supramolecular polymer that is formed at the surface of graphite in octanoic acid. Scanning tunneling microscopy (STM) combined with molecular mechanics calculations has been used to prove the structure of the wires, and theory, corroborated with STS experiments, predicts that they are promising superstructures for charge transport.     

DNA-templated assembly of nanoscale wires and protein-functionalized nanogap contacts

The use of DNA to template the assembly of nanoscale wires and protein-functionalized nanogap contacts is described: Specifically, the use of DNA to template the assembly of gold nanowires between conventionally patterned gold contacts on a silicon wafer substrate. Also described is the use of DNA to template the assembly of protein-functionalized nanogap gold contacts on a silicon wafer substrate. Of particular significance is the finding that suitably modified gold nanoparticles recognize and bind selectively the protein-functionalized nanogap and are localized there.     

Amplified label-free electrical detection of DNA hybridization

A new protocol is described for amplifying label-free electrochemical measurements of DNA hybridization based on the enhanced accumulation of purine nucleobases in the presence of copper ions . Such electrical DNA assays involve hybridization of the target to inosine-substituted oligonucleotide probes (captured on magnetic beads), acidic dipurinization of the hybrid DNA, and adsorptive chronopotentiometric stripping measurements of the free nucleobases in the presence of copper ions. Both amplified adenine and guanine peaks can be used for detecting the DNA hybridization. The dramatic signal amplification advantage of this type of detection has been combined with efficient magnetic removal of non-complementary DNA, use of microliter sample volumes and disposable transducers. Factors influencing the signal enhancement were assessed and optimized. A detection limit of 40 fmol (250 pg) was obtained with 10 min hybridization and 5 min adsorptive-accumulation times. The advantages of this procedure were demonstrated by its application in the detection of DNA segments related to the BRCA1 breast cancer gene. The copper enhancement holds great promise not only for the detection of DNA hybridization, but also for trace measurement of nucleic acids.