Avraham Halperin

Grafted poly(ethylene oxide) brushes as nonfouling surface coatings

The identification of design criteria for the prevention of surface fouling by protein adsorption has been an elusive research goal. The current ideas in this domain assume two different directions. One focuses on correlating protein adsorption with macroscopic surface properties such as the water wettability. The second approach involves tailoring the molecular interactions between the adsorbing proteins and the surface. In this paper, we focus on the experimental results and theoretical ideas concerned with tuning the interfacial forces by means of terminally grafted PEO chains.

Tuning Polymer Thickness: Synthesis and Scaling Theory of Homologous Series of Dendronized Polymers

The thickness of dendronized polymers can be tuned by varying their generation g and the dendron functionality X. Systematic studies of this effect require (i) synthetic ability to produce large samples of high quality polymers with systematic variation of g, X and of the backbone polymerization degree N, (ii) a theoretical model relating the solvent swollen polymer diameter, r, and persistence length, lambda, to g and X. This article presents an optimized synthetic method and a simple theoretical model. Our theory approach, based on the Boris-Rubinstein model of dendrimers predicts r approximately n(1/4)g(1/2) and lambda approximately n(2) where n = [(X - 1)(g) - 1]/(X - 2) is the number of monomers in a dendron. The average monomer concentration in the branched side chains of a dendronized polymer increases with g in qualitative contrast to bottle brushes whose side chains are linear. The stepwise, attach-to, synthesis of X = 3 dendronized polymers yielded gram amounts of g = 1-4 polymers with N approximately = 1000 and N approximately = 7000 as compared to earlier maxima of 0.1 g amounts and of N approximately = 1000. The method can be modified to dendrons of different X. The conversion fraction at each attach-to step, as quantified by converting unreacted groups with UV labels, was 99.3% to 99.8%. Atomic force microscopy on mixed polymer samples allows to distinguish between chains of different g and suggests an apparent height difference of 0.85 nm per generation as well as an increase of persistence length with g. We suggest synthetic directions to allow confrontation with theory.

Sensitivity, Specificity, and the Hybridization Isotherms of DNA Chips

Competitive hybridization, at the surface and in the bulk, lowers the sensitivity of DNA chips. Competitive surface hybridization occurs when different targets can hybridize with the same probe. Competitive bulk hybridization takes place when the targets can hybridize with free complementary chains in the solution. The effects of competitive hybridization on the thermodynamically attainable performance of DNA chips are quantified in terms of the hybridization isotherms of the spots. These relate the equilibrium degree of the hybridization to the bulk composition. The hybridization isotherm emerges as a Langmuir isotherm modified for electrostatic interactions within the probe layer. The sensitivity of the assay in equilibrium is directly related to the slope of the isotherm. A simpler description is possible, in terms of c(50) values specifying the bulk composition corresponding to 50% hybridization at the surface. The effects of competitive hybridization are important for the quantitative analysis of DNA chip results, especially when used to study point mutations.

On the hybridization isotherms of DNA microarrays: the Langmuir model and its extensions

The design of DNA chip experiments utilizes hybridization isotherms relating the equilibrium hybridization at the surface to the composition of the solution. Within this family, the Langmuir isotherm is the simplest and the most frequently used. This tutorial review summarizes the domain of validity of the Langmuir isotherm and discusses the modifications necessary to allow for competitive hybridization in the bulk and at the surface, probe polydispersity and interactions between the probe sites. The equilibrium constant of hybridization at an impenetrable surface is described, as well as the relative merits of the melting temperature and c50 as design parameters. The relevance to various experimental situations, including two-colour experiments, study of point mutations for cancer diagnostics, genotyping of pooled samples and aspects of Latin square experiments, is discussed.

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized.

Effects of stacking on the configurations and elasticity of single-stranded nucleic acids

Stacking interactions in single-stranded nucleic acids give rise to configurations of an annealed rod-coil multiblock copolymer. Theoretical analysis identifies the following resulting signatures for long homopolynucleotides: a nonmonotonic dependence of size on temperature, the corresponding effects on cyclization and a plateau in the extension force law. Explicit numerical results for polydeoxyadenylate [poly(dA)] and polyriboadenylate [poly(rU)] are presented.

Neutron Reflectometry Elucidates Density Profiles of Deuterated Proteins Adsorbed onto Surfaces Displaying Poly(ethylene glycol) Brushes: Evidence for Primary Adsorption

The concentration profile of deuterated myoglobin (Mb) adsorbed onto polystyrene substrates displaying poly(ethylene glycol) (PEG) brushes is characterized by neutron reflectometry (NR). The method allows to directly distinguish among primary adsorption at the grafting surface, ternary adsorption within the brush, and secondary adsorption at the brush outer edge. It complements depth-insensitive standard techniques, such as ellipsometry, radioactive labeling, and quartz crystal microbalance. The study explores the effect of the PEG polymerization degree, N, and the grafting density, σ, on Mb adsorption. In the studied systems there is no indication of secondary or ternary adsorption, but there is evidence of primary adsorption involving a dense inner layer at the polystyrene surface. For sparsely grafted brushes the primary adsorption involves an additional dilute outer protein layer on top of the inner layer. The amount of protein adsorbed in the inner layer is independent of N but varies with σ, while for the outer layer it is correlated to the amount of grafted PEG and is thus sensitive to both N and σ. The use of deuterated proteins enhances the sensitivity of NR and enables monitoring exchange between deuterated and hydrogenated species.

Thermoresponsive cell culture substrates based on PNIPAM brushes functionalized with adhesion peptides: theoretical considerations of mechanism and design.

Thermoresponsive tissue culture substrates based on PNIPAM brushes are used to harvest confluent cell sheets for tissue engineering. The prospect of clinical use imposes the utilization of culture medium free of bovine serum, thus suggesting conjugation with adhesion peptides containing the RGD minimal recognition sequence. The optimum position of the RGD along the chain should ensure both cell adhesion at 37 °C and cell detachment at T(L) below the lower critical solution temperature of PNIPAM. Design guidelines are formulated from considerations of brush confinement by the cells: (i) Cell adhesion at 37 °C is controlled by the RGDs accessible without brush compression. (ii) Cell detachment at T(L) is driven by a disjoining force due to confinement of the swollen brush by cells retaining integrin-RGD bonds formed at 37 °C. These suggest placing the RGDs at the grafting surface or its vicinity. Randomly placed RGDs do not enable efficient detachment because a large fraction of the integrin-RGD bonds are not sufficiently tensioned at T(L), in line with experimental observations (Ebara, M.; Yamato, M.; Aoyagi, T.; Kikuchi, A.; Sakai, K.; Okano, T. Immobilization of celladhesive peptides to temperature-responsive surfaces facilitates both serum-free cell adhesion and noninvasive cell harvest. Tissue Eng. 2004, 10, 1125-1135). The theory framework enables analysis of culture media based on polymer brushes conjugated with adhesion peptides in general.

Computer simulation of dendronized polymers : organization and characterization at the atomistic level

Atomistic molecular dynamics simulations in chloroform and solvent-free environments are used to build and study a homologous series of neutral dendronized linear polymers (DPs), whose repeat units are regularly branched dendrons of generations g = 1–7, excluding g = 5. We find that a DP with g ≤ 4 displays an elongated conformation, while a DP with g = 6 exhibits a helical backbone. The conformations essentially differ in their alternating (elongated) or regular (helical) twist with respect to the macromolecular axis, at similar average distance between repeat units (2.1–2.3 A). With increasing g the dendrons tend to induce an increasing strain, stiffness and overall cylindrical shape onto the DP; the existence of DPs with g ≥ 7 is excluded. The fractal dimensionality of the backbone appears similar for DPs with g ≤ 4, while a discontinuous fractal behavior found for g = 6 is consistent with its helical backbone. Profiles describing the variation of the density as a function of the distance to the molecular backbone are extracted to analyze conformational effects of both backbone and sidegroups. For the solvent-free case the average density grows from 0.97 to 1.11 g cm−3 upon increasing g, while the radial density profile is basically constant at 1.1–1.2 g cm−3 and insensitive to g at intermediate distances, where dendrons are able to interpenetrate. The variation of obtained DP thicknesses is successfully compared with experimental estimates deduced from transmission electron microscopy measurements of polymers deposited onto attractive mica surfaces. Finally, we examine and discuss the distribution of solvent molecules inside elongated structures.

Polymeric vs. Monomeric Amphiphiles: Design Parameters

The distinctive features of polymeric surfactants as compared to monomeric, low molecular amphiphiles are reviewed from a theoretical point of view. The relative importance of the configurational entropy is discussed and illustrated for polymeric micelles formed from three different types of diblock copolymers. When the number of amphiphilic motifs within the polymer increases, distinctively polymeric features appear. Bridging and exchange interactions play an important role when the number of blocks is three and above. This gives rise to the formation of physical gels. Intrachain self‐assembly occurs in multiblock copolymers and polysoaps and affects the configurations, dimensions and elasticity of the single chain.