Covalently linked DNA nanotubes.

The present study introduces an approach to prepare covalently linked DNA nanotubes. A circular DNA that includes at its opposite poles thiol and amine functionalities acts as the building block for the construction of the DNA nanotubes. The circular DNA is cross-linked with a bis-amide-modified nucleic acid to yield DNA nanowires, and these are subsequently cross-linked by a bis-thiolated nucleic acid to yield the DNA nanotubes.

Logic gates and antisense DNA devices operating on a translator nucleic Acid scaffold.

A series of logic gates, "AND", "OR", and "XOR", are designed using a DNA scaffold that includes four "footholds" on which the logic operations are activated. Two of the footholds represent input-recognition strands, and these are blocked by complementary nucleic acids, whereas the other two footholds are blocked by nucleic acids that include the horseradish peroxidase (HRP)-mimicking DNAzyme sequence. The logic gates are activated by either nucleic acid inputs that hybridize to the respective "footholds", or by low-molecular-weight inputs (adenosine monophosphate or cocaine) that yield the respective aptamer-substrate complexes.

Cooperative multicomponent self-assembly of nucleic acid structures for the activation of DNAzyme cascades: a paradigm for DNA sensors and aptasensors.

The activation of a DNAzyme cascade by the cooperative self-assembly of multicomponent nucleic acid structures is suggested as a method for the amplified sensing of DNA, or the specific substrates of aptamers. According to one configuration, the DNA analyte 1 is detected by two tailored nucleic acids 2 and 3 that form a multicomponent supramolecular structure with a ribonucleobase-containing quasi-circular DNA 4, but only upon the concomitant hybridization with 1. The resulting supramolecular nucleic acid structure includes the Mg(2+)-dependent DNAzyme that cleaves the ribonucleobase site of 4.

DNAzymes for sensing, nanobiotechnology and logic gate applications.

Catalytic nucleic acids (DNAzymes or ribozymes) are selected by the systematic evolution of ligands by exponential enrichment process (SELEX). The catalytic functions of DNAzymes or ribozymes allow their use as amplifying labels for the development of optical or electronic sensors. The use of catalytic nucleic acids for amplified biosensing was accomplished by designing aptamer-DNAzyme conjugates that combine recognition units and amplifying readout units as in integrated biosensing materials.

A DNAzyme cascade for the amplified detection of Pb(2+) ions or L-histidine.

DNAzyme cascades activated by Pb(2+)- or L-histidine-dependent DNAzymes yield the horseradish peroxidase-mimicking catalytic nucleic acids that enable the colorimetric or chemiluminescence detection of Pb(2+) or L-histidine.

Parallel analysis of two analytes in solutions or on surfaces by using a bifunctional aptamer: applications for biosensing and logic gate operations.

A bifunctional aptamer that includes two aptamer units for cocaine and adenosine 5'-monophosphate (AMP) is blocked by a nucleic acid to form a hybrid structure with two duplex regions. The blocked bifunctional aptamer assembly is used as a functional structure for the simultaneous sensing of cocaine or AMP. The blocked bifunctional aptamer is dissociated by either of the two analytes, and the readout of the separation of the sensing structure is accomplished by a colorimetric detection, by a released DNAzyme, or by electronic means that use Faradaic impedance spectroscopy or field-effect transistors.

Proteins modified with DNAzymes or aptamers act as biosensors or biosensor labels.

Hybrid systems composed of a glucose oxidase (GOx)/peroxidase-mimicking DNAzyme, and of microperoxidase-11 (MP-11)/anti-thrombin aptamer were synthesized. The hybrid systems were employed as amplifying labels for the colorimetric or chemiluminescence detection of an enzyme functions, and thrombin analysis, respectively. In the GOx/DNAzyme system, the GOx-mediated oxidation of glucose led to the formation of H(2)O(2), and this activated the oxidation of ABTS to a colored product, or to the generation of chemiluminescence in the presence of luminol.

Shape and color of au nanoparticles follow biocatalytic processes.

The NAD(P)H-mediated growth of Au nanoparticles (NPs) in the presence of ascorbic acid, AuCl4-, and cetyltrimethylammonium bromide leads to the formation of shaped NP structures consisting of dipods, tripods, and tetrapods. The shaped particles exhibit a red-shifted plasmon absorbance at lambda = 680 nm, consistent with the existence of a longitudinal plasmon exciton. High-resolution transmission electron microscopy analysis of the tripod and tetrapod structures reveals directional growth along the <211> and <010> directions, respectively.

Fluorescence detection of DNA by the catalytic activation of an aptamer/thrombin complex.

A conjugate consisting of a thrombin aptamer tethered to the thrombin, Th, with a sensing nucleic acid (1) is used for the optical detection of DNA. The thrombin/aptamer complex blocks the biocatalytic functions of Th. Hybridization of the analyte DNA (2) to the sensing nucleic acid 1 yields a rigid duplex that detaches the aptamer from Th, a process that activates the protein toward the hydrolysis of bis(p-tosyl-Gly-Pro-Arg)-R110 (3) to the rhodamine 110 fluorophore (4).

An Os(II)--bisbipyridine--4-picolinic acid complex mediates the biocatalytic growth of au nanoparticles: optical detection of glucose and acetylcholine esterase inhibition.

The complex Os(II)-bisbipyridine-4-picolinic acid, [Os(bpy)(2)PyCO(2)H](2+) (1), mediates the biocatalyzed growth of Au nanoparticles, Au NPs, and enables the spectroscopic assay of biocatalyzed transformations and enzyme inhibition by following the Au NP plasmon absorbance. In one system, [Os(bpy)(2)PyCO(2)H](2+) mediates the biocatalyzed oxidation of glucose and the growth of Au NPs in the presence of glucose oxidase, GOx, AuCl(4) (-), citrate and Au NP seeds. The mechanism of the Au NPs growth involves the oxidation of the [Os(bpy)(2)PyCO(2)H](2+) complex by AuCl(4) (-) to form [Os(bpy)(2)PyCO(2)H](3+) and Au(I).

Aptamer-functionalized Au nanoparticles for the amplified optical detection of thrombin.

The catalytic enlargement of aptamer-functionalized Au nanoparticles amplifies the optical detection of aptamer-thrombin complexes in solution and on surfaces.