Self-assembly of chiral DNA nanotubes

A system of DNA "tiles" that is designed to assemble to form two-dimensional arrays is observed to form narrow ribbons several micrometers in length. The uniform width of the ribbons and lack of frayed edges lead us to propose that they are arrays that have curled and closed on themselves to form tubes. This proposal is confirmed by the observation of tubes with helical order.     

Similarity searching in databases of three-dimensional molecules and macromolecules.

This paper discusses algorithmic techniques for measuring the degree of similarity between pairs of three-dimensional (3-D) chemical molecules represented by interatomic distance matrices. A comparison of four methods for the calculation of 3-D structural similarity suggests that the most effective one is a procedure that identifies pairs of atoms, one from each of the molecules that are being compared, that lie at the center of geometrically-related volumes of 3-D space. This atom mapping method enables the calculation of a wide range of types of intermolecular similarity coefficient, including measures that are based on physicochemical data. Massively-parallel implementations of the method are discussed, using the AMT Distributed Array Processor, that achieve a substantial increase in performance when compared with a sequential implementation on a UNIX workstation. Current work involves the use of angular information and the extension of the method to field-based similarity searching. Similarity searching in 3-D macromolecules is effected by the use of a maximal common subgraph (MCS) isomorphism algorithm with a novel, graph-based representation of the tertiary structures of proteins. This algorithm is being used to identify similarities between the 3-D structures of proteins in the Brookhaven Protein Data Bank; its use is exemplified by searches involving the NAD-binding fold motif.     

Investigation of Ig.G adsorption and the effect on electrochemical responses at titanium dioxide electrode

The adsorption of Immunoglobulin G on a titanium dioxide (TiO(2)) electrode surface was investigated using (125)I radiolabeling and electrochemical impedance spectroscopy (EIS). (125)I radiolabeling was used to determine the extent of protein adsorption, while EIS was used to ascertain the effect of the adsorbed protein layer on the electrode double layer capacitance and electron transfer between the TiO(2) electrode and the electrolyte. The adsorbed amounts of Ig.G agreed well with previous results and showed approximately monolayer coverage. The amount of adsorbed protein increased when a positive potential was applied to the electrode, while the application of a negative potential resulted in a decrease. Exposure to solutions of Ig.G resulted in a decrease of the double layer capacitance (C) and an increase in the charge-transfer resistance (R(2)) at the electrode solution interface. As more Ig.G adsorbed onto the electrode surface, the extent of C and R(2) variation increased. These capacitance and charge-transfer resistance variations were attributed to the formation of a proteinaceous layer on the electrode surface during exposure.     

Reconfigurable T-junction DNA Origami

DNA self-assembly allows the construction of nanometre-scale structures and devices. Structures with thousands of unique components are routinely assembled in good yield. Experimental progress has been rapid, based largely on empirical design rules. Herein, we demonstrate a DNA origami technique designed as a model system with which to explore the mechanism of assembly. The origami fold is controlled through single-stranded loops embedded in a double-stranded DNA template and is programmed by a set of double-stranded linkers that specify pairwise interactions between loop sequences. Assembly is via T-junctions formed by hybridization of single-stranded overhangs on the linkers with the loops. The sequence of loops on the template and the set of interaction rules embodied in the linkers can be reconfigured with ease. We show that a set of just two interaction rules can be used to assemble simple T-junction origami motifs and that assembly can be performed at room temperature.     

Investigation of protein adsorption and electrochemical behavior at a gold electrode

The adsorption of two model proteins, human serum albumin and immunoglobulin G, on a gold electrode surface was investigated using 125I radiolabeling and cyclic voltammetry (CV). 125I radiolabeling was used to determine the extent of protein adsorption, while CV was used to ascertain the effect of the adsorbed protein layer on the electron transfer between the gold electrode and an electroactive moiety in solution, namely, K3Fe(CN)6. The adsorbed amounts of HSA and IgG agreed well with previous results and showed approximately monolayer coverage. The amount of adsorbed protein increased when a positive potential (700 mV) was applied to the electrode, while the application of a negative potential (-800 mV) resulted in a decrease. When the solution pH was varied to alter the charge on the protein, the adsorption trends appeared to follow electrostatic interaction, namely, greater adsorption when the electrode and the protein possessed opposite charge and vice versa. The adsorbed protein layer had the effect of blocking the electron transfer. It was possible to correlate the degree of electron blocking with the amount of adsorbed protein to show that the greater the adsorption, the larger the blocking effect. Of the two proteins used, HSA proved to be more efficient at blocking the electron transfer.     

Electrical resistivity of ZnSb and CdSb liquid alloys in the compound-forming concentration range

The electrical resistivities ? and their temperature dependences $\text{d}\text{?}\text{dT}$ of liquid ZSb and CSb alloys have been determined experimentally between 40 and 52 at% Sb, corresponding to the compound-forming range. The resistivity isotherms of the two systems show one maximum at about 47 at% Sb. The electrical behaviour of the melts is related to the tendency towards compound formation.     

Reconfigurable T‐junction DNA Origami

DNA self‐assembly allows the construction of nanometre‐scale structures and devices. Structures with thousands of unique components are routinely assembled in good yield. Experimental progress has been rapid, based largely on empirical design rules. Herein, we demonstrate a DNA origami technique designed as a model system with which to explore the mechanism of assembly. The origami fold is controlled through single‐stranded loops embedded in a double‐stranded DNA template and is programmed by a set of double‐stranded linkers that specify pairwise interactions between loop sequences. Assembly is via T‐junctions formed by hybridization of single‐stranded overhangs on the linkers with the loops. The sequence of loops on the template and the set of interaction rules embodied in the linkers can be reconfigured with ease. We show that a set of just two interaction rules can be used to assemble simple T‐junction origami motifs and that assembly can be performed at room temperature.