Switching binary states of nanoparticle superlattices and dimer clusters by DNA strands.

Nanoscale components can be self-assembled into static three-dimensional structures, arrays and clusters using biomolecular motifs. The structural plasticity of biomolecules and the reversibility of their interactions can also be used to make nanostructures that are dynamic, reconfigurable and responsive. DNA has emerged as an ideal biomolecular motif for making such nanostructures, partly because its versatile morphology permits in situ conformational changes using molecular stimuli. This has allowed DNA nanostructures to exhibit reconfigurable topologies and mechanical movement. Recently, researchers have begun to translate this approach to nanoparticle interfaces, where, for example, the distances between nanoparticles can be modulated, resulting in a distance-dependent plasmonic response. Here, we report the assembly of nanoparticles into three-dimensional superlattices and dimer clusters, using a reconfigurable DNA device that acts as an interparticle linkage. The interparticle distances in the superlattices and clusters can be modified, while preserving structural integrity, by adding molecular stimuli (simple DNA strands) after the self-assembly processes has been completed. Both systems were found to switch between two distinct rigid states, but a transition to a flexible device configuration within a superlattice showed a significant hysteresis.

Assembly pathway analysis of DNA nanostructures and the construction of parallel motifs.

We present a system for analyzing the assembly pathway of DNA nanostructures. This enables the identification, explanation, and avoidance of obstacles to proper structure formation. Potential problems include strand end-pinning and misfolding caused by the structural bias of nominally flexible junctions. We have used this system to guide the construction of parallel motifs that had previously, for unknown reasons, resisted assembly.

Inhibition of carbonic anhydrase II by thioxolone: a mechanistic and structural study.

This paper examines the functional mechanism of thioxolone, a compound recently identified as a weak inhibitor of human carbonic anhydrase II by Iyer et al. (2006) J. Biomol. Screening 11, 782-791 . Thioxolone lacks sulfonamide, sulfamate, or hydroxamate functional groups that are typically found in therapeutic carbonic anhydrase (CA) inhibitors, such as acetazolamide. Analytical chemistry and biochemical methods were used to investigate the fate of thioxolone upon binding to CA II, including Michaelis-Menten kinetics of 4-nitrophenyl acetate esterase cleavage, liquid chromatography-mass spectrometry (LC-MS), oxygen-18 isotope exchange studies, and X-ray crystallography. Thioxolone is proposed to be a prodrug inhibitor that is cleaved via a CA II zinc-hydroxide mechanism known to catalyze the hydrolysis of esters. When thioxolone binds in the active site of CA II, it is cleaved and forms 4-mercaptobenzene-1,3-diol via the intermediate S-(2,4-thiophenyl)hydrogen thiocarbonate. The esterase cleavage product binds to the zinc active site via the thiol group and is therefore the active CA inhibitor, while the intermediate is located at the rim of the active-site cavity. The time-dependence of this inhibition reaction was investigated in detail. Because this type of prodrug inhibitor mechanism depends on cleavage of ester bonds, this class of inhibitors may have advantages over sulfonamides in determining isozyme specificity. A preliminary structure-activity relationship study with a series of structural analogues of thioxolone yielded similar estimates of inhibition constants for most compounds, although two compounds with bromine groups at the C1 carbon of thioxolone were not inhibitory, suggesting a possible steric effect.

Layer-by-layer assembly of bioengineered flagella protein nanotubes.

Flagella nanotubes present on the surface of E. coli bacteria were bioengineered to display arginine-lysine and glutamic acid-aspartic acid peptide loops. These protein bionanotubes were demonstrated to self-assemble, layer-by-layer, by atomic force microscopy (AFM) on gold-coated mica and quartz surfaces. Flagella with arginine-lysine loops were assembled in a bottom-up manner on a gold-coated mica surface by employing the molecular complementarity of the biotin-streptavidin interaction. Self-assembled monolayers of alkylamines on the gold surface were derivatized with biotin, followed by binding of streptavidin to the biotinylated surface. The amine groups of the flagella peptide loops were chemically attached to biotin through a polyethyleneoxide spacer and paired with streptavidin on the gold surface. This process could be repeated to generate multiple layers of flagella. Flagella with glutamic acid-aspartic acid peptide loops were self-assembled on quartz surfaces by electrostatic attraction to protonated amine groups. The quartz surface was silanized to obtain amine groups, which were used to assemble the first layer of glutamic acid-aspartic acid peptide loop flagella nanotubes. This layer was covered with polyethyleneimine through electrostatic attraction and employed to assemble a second layer of flagella. The self-assembled glutamic acid-aspartic acid flagella were also used to demonstrate the biomineralization of CaCO 3. The layer-by-layer self-assembly employing electrostatic attraction yielded a more uniform layer of flagella than the one obtained with the molecular complementarity of the biotin-streptavidin pair.

Generation and characterization of inorganic and organic nanotubes on bioengineered flagella of mesophilic bacteria.

Three types of rationally designed peptide loops were genetically engineered for display on the surface of the FliTrx E. coil flagella scaffold, a type of bacterial bionanotube adapted for the multivalent display of peptide loops. The resulting three types of loop flagella fibers were used to demonstrate the feasibility of templating synthesis of inorganic nanotubes and nanoparticles and organic nanotubes. Purified flagella fibers displaying a cationic arginine-lysine loop peptide with three guanidine and three amine functional groups were used to form silica bionanotubes, using two types of silicate ion precursors. Purified flagella fibers displaying a tyrosine-serine-glycine loop peptide with six phenolic and three aliphatic hydroxyl groups were used to initiate formation of titania bionanotubes. Purified flagella fibers displaying an anionic aspartate-glutamate loop peptide with 18 carboxylate groups were used to initiate formation of polyaniline nanotubes and hydroxyapatite nanoparticles, a key component of bones. The resulting nanomaterials were mainly characterized by transmission electron microscopy and additionally by scanning electron microscopy, in the case of polyaniline nanotubes. The studies demonstrate the versatility of employing bioengineered flagella for the generation of a variety of nanoparticle arrays and nanotubes.

Bioengineered flagella protein nanotubes with cysteine loops: self-assembly and manipulation in an optical trap.

An E. coli flagellin protein, termed FliTrx, was investigated for use as a novel form of self-assembling protein nanotube. This protein was genetically engineered to display constrained peptide loops with a series of different thiol, cationic, anionic, and imidazole functional groups. "Cys-loop" thiol variants consisting of 6 and 12 cysteine residues were isolated in the form of disulfide-linked nanotube bundles, a novel nanomaterial. Bundles were characterized by fluorescence microscopy, transmission electron microscopy, and optical trapping.