Decomposition-Coordination Optimization of the Dynamic Systems with Adaptation of the Criterion

For optimization of the dynamic systems with decentralized control, a universal method based on adaptation of the performance index in the course of design was presented. For a large class of systems, computations were simplified and control noise-immunity improved.     

Fluorescence recovery assay for the detection of protein-DNA binding

We report a novel and straightforward fluorescence recovery assay which enables the detection of protein-DNA interactions and simultaneously determines relative binding affinities of sequence-specific DNA-binding proteins for a variety of DNA sequences in a multiplexed format. The detection of protein-DNA binding is accomplished by monitoring fluorescence recovery during exonuclease digestion of DNA sequences that are modified with fluorophore-quencher pairs. Retardation of fluorescence recovery occurs with binding of the protein to the putative DNA binding element, which arrests exonuclease digestion. The assay detects protein-DNA binding in a homogeneous solution simply, quickly, and reliably without using radioisotopes. Multiplexing is possible by labeling different DNA sequences with spectrally distinct dyes, allowing simultaneous analysis of experimental and control binding reactions in the same mixture.     

In Vivo Behavior of Ultrasmall Spherical Nucleic Acids

The biological properties of spherical nucleic acids (SNAs) are largely independent of nanoparticle core identity but significantly affected by oligonucleotide surface density. Additionally, the payload-to-carrier (i.e., DNA-to-nanoparticle) mass ratio of SNAs is inversely proportional to core size. While SNAs with many core types and sizes have been developed, all in vivo analyses of SNA behavior have been limited to cores >10 nm in diameter. However, “ultrasmall” nanoparticle constructs (<10 nm diameter) can exhibit increased payload-to-carrier ratios, reduced liver accumulation, renal clearance, and enhanced tumor infiltration. Therefore, we hypothesized that SNAs with ultrasmall cores exhibit SNA-like properties, but with in vivo behavior akin to traditional ultrasmall nanoparticles. To investigate, we compared the behavior of SNAs with 1.4-nm Au₁₀₂ nanocluster cores (AuNC-SNAs) and SNAs with 10-nm gold nanoparticle cores (AuNP-SNAs). Significantly, AuNC-SNAs possess SNA-like properties (e.g., high cellular uptake, low cytotoxicity) but show distinct in vivo behavior. When intravenously injected in mice, AuNC-SNAs display prolonged blood circulation, lower liver accumulation, and higher tumor accumulation than AuNP-SNAs. Thus, SNA-like properties persist at the sub-10-nm length scale and oligonucleotide arrangement and surface density are responsible for the biological properties of SNAs. This work has implications for the design of new nanocarriers for therapeutic applications.     

Development of a coordination chemistry-based approach for functional supramolecular structures

The weak-link approach (WLA) to supramolecular assemblies allows for the design of multimetallic two- and three-dimensional arrays, host-guest architectures, sensors, catalysts, switches, and signal amplification devices. This Account describes the course of our investigations in this area beginning with the development of a chemical tool kit of building blocks consisting of multiple metals and ligands. These building blocks can be rationally mixed and matched to provide structures with a wide range of properties that have been used to develop functional supramolecular architectures, including chemical sensors and allosteric catalysts.     

A fluorescence-based method for determining the surface coverage and hybridization efficiency of thiol-capped oligonucleotides bound to gold thin films and nanoparticles

Using a fluorescence-based method, we have determined the number of thiol-derivatized single-stranded oligonucleotides bound to gold nanoparticles and their extent of hybridization with complementary oligonucleotides in solution. Oligonucleotide surface coverages of hexanethiol 12-mer oligonucleotides on gold nanoparticles (34 +/- 1 pmol/cm2) were significantly higher than on planar gold thin films (18 +/- 3 pmol/cm2), while the percentage of hybridizable strands on the gold nanoparticles (1.3 +/- 0.3 pmol/cm2, 4%) was lower than for gold thin films (6 +/- 2 pmol/cm2, 33%). A gradual increase in electrolyte concentration over the course of oligonucleotide deposition significantly increases surface coverage and consequently particle stability. In addition, oligonucleotide spacer sequences improve the hybridization efficiency of oligonucleotide-modified nanoparticles from approximately 4 to 44%. The surface coverage of recognition strands can be tailored using coadsorbed diluent oligonucleotides. This provides a means of indirectly controlling the average number of hybridized strands per nanoparticle. The work presented here has important implications with regard to understanding interactions between modified oligonucleotides and metal nanoparticles, as well as optimizing the sensitivity of gold nanoparticle-based oligonucleotide detection methods.     

Voltammetric and Scanning Electrochemical Microscopic Studies of the Adsorption Kinetics and Self-Assembly of n-Alkanethiol Monolayers on Gold

The adsorption kinetics and self-assembly of hexadecyl mercaptan on gold have been investigated by scanning electrochemical microscopy (SECM), chronoamperometry, and cyclic voltammetry. The developed methodology allows one to evaluate the surface coverage and the average size of the defects in the monolayer film from the effective rate constant of electron transfer. Two kinetic regimes of self-assembly were identified: a rapid initial adsorption of hexadecyl mercaptan onto a clean gold surface from 5 mM solution (more than 90% coverage obtained in 1 to 5 min), and a slower subsequent annealing of a thiol monolayer resulting in a more compact film. Typically, a long-chain-length thiol-treated gold surface acts as an electronically insulating surface after about 1 h. The SECM images of partially covered gold surfaces were always featureless, suggesting that the defects in the film were smaller than 0.5 μm for any exposure time ≥ 1 min.     

Additive spectral method for fuzzy cluster analysis of similarity data including community structure and affinity matrices

An additive spectral method for fuzzy clustering is proposed. The method operates on a clustering model which is an extension of the spectral decomposition of a square matrix. The computation proceeds by extracting clusters one by one, which makes the spectral approach quite natural. The iterative extraction of clusters, also, allows us to draw several stopping rules to the procedure. This applies to several relational data types differently normalized: network structure data (the first eigenvector subtracted), affinity between multidimensional vectors (the pseudo-inverse Laplacian transformation), and conventional relational data including in-house data of similarity between research topics according to working of a research center. The method is experimentally compared with several classic and recent techniques and shown to be competitive.