Can one determine the density of an individual synthetic macromolecule?

Dendronized polymers (DPs) are large and compact main-chain linear polymers with a cylindrical shape and cross-sectional diameters of up to ∼15 nm. They are therefore considered molecular objects, and it was of interest whether given their experimentally accessible, well-defined dimensions, the density of individual DPs could be determined. We present measurements on individual, deposited DP chains, providing molecular dimensions from scanning and transmission electron microscopy and mass-per-length values from quantitative scanning transmission electron microscopy. These results are compared with density values obtained from small-angle X-ray scattering on annealed bulk specimen and with classical envelope density measurements, obtained using hydrostatic weighing or a density gradient column. The samples investigated comprise a series of DPs with side groups of dendritic generations g = 1-8. The key findings are a very large spread of the density values over all samples and methods, and a consistent increase of densities with g over all methods. While this work highlights the advantages and limitations of the applied methods, it does not provide a conclusive answer to the question of which method(s) to use for the determination of densities of individual molecular objects. We are nevertheless confident that these first attempts to answer this challenging question will stimulate more research into this important aspect of polymer and soft matter science.

Neutron Reflectometry Elucidates Protein Adsorption from Human Blood Serum onto PEG Brushes.

Poly(ethylene glycol) (PEG) brushes are reputed for their ability to prevent undesired protein adsorption to material surfaces exposed to biological fluids. Here, protein adsorption out of human blood serum onto PEG brushes anchored to solid-supported lipid monolayers was characterized by neutron reflectometry, yielding volume fraction profiles of lipid headgroups, PEG, and adsorbed proteins at subnanometer resolution. For both PEGylated and non-PEGylated lipid surfaces, serum proteins adsorb as a thin layer of approximately 10 Å, overlapping with the headgroup region. This layer corresponds to primary adsorption at the grafting surface and resists rinsing. A second diffuse protein layer overlaps with the periphery of the PEG brush and is attributed to ternary adsorption due to protein-PEG attraction. This second layer disappears upon rinsing, thus providing a first observation of the structural effect of rinsing on protein adsorption to PEG brushes.

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.

Poly(N-isopropylacrylamide) Phase Diagrams: Fifty Years of Research.

In 1968, Heskins and Guillet published the first systematic study of the phase diagram of poly(N-isopropylacrylamide) (PNIPAM), at the time a "young polymer" first synthesized in 1956. Since then, PNIPAM became the leading member of the growing families of thermoresponsive polymers and of stimuli-responsive, "smart" polymers in general. Its thermal response is unanimously attributed to its phase behavior. Yet, in spite of 50 years of research, a coherent quantitative picture remains elusive. In this Review we survey the reported phase diagrams, discuss the differences and comment on theoretical ideas regarding their possible origins. We aim to alert the PNIPAM community to open questions in this reputably mature domain.

General in vitro method to analyze the interactions of synthetic polymers with human antibody repertoires.

Recent reports on the hitherto underestimated antigenicity of poly(ethylene glycol) (PEG), which is widely used for pharmaceutical applications, highlight the need for efficient testing of polymer antigenicity and for a better understanding of its molecular origins. With this goal in mind, we have used the phage-display technique to screen large, recombinant antibody repertoires of human origin in vitro for antibodies that bind poly(vinylpyrrolidone) (PVP). PVP is a neutral synthetic polymer of industrial and clinical interest that is also a well-known model antigen in animal studies, thus allowing the comparison of in vitro and in vivo responses. We have identified 44 distinct antibodies that bind specifically to PVP. Competitive binding assays show that the PVP-antibody binding constant is proportional to the polymerization degree of PVP and that specific binding is detected down to the vinylpyrrolidone (VP) monomer level. Statistical analysis of anti-PVP antibody sequences identifies an amino-acid motif that is shared by many phage-display-selected anti-PVP antibodies that are similar to a previously described natural anti-PVP antibody. This suggests a role for this motif in specific antibody/PVP interactions. Interestingly, sequence analysis also suggests that only a single antibody chain containing this shared motif is responsible for antibody binding to PVP, as confirmed upon systematic deletion of either antibody chain for 90% of selected anti-PVP antibodies. Overall, a large number of antibodies in the human repertoires we have screened bind specifically to PVP through a small number of shared amino acid motifs, and preliminary comparison points to significant correlations between the sequences of phage-display-selected anti-PVP antibodies and their natural counterparts isolated from immunized mice in previous studies. This study pioneers the use of antibody phage-display to explore the antigenicity of biotechnologically relevant polymers. It also paves the way for a fast, cost-effective, and systematic in vitro analysis, thus reducing the need for animal immunization experiments. Moreover, identifying the encoding DNA sequence of polymer-binding antibodies via phage-display enables future applications of a molecular biology approach to protein-polymer conjugation, based on protein-antibody fusion.

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.

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.

3D Conformations of Thick Synthetic Polymer Chains Observed by Cryogenic Electron Microscopy.

The backbone conformations of individual, unperturbed synthetic macromolecules have so far not been observed directly in spite of their fundamental importance to polymer physics. Here we report the dilute solution conformations of two types of linear dendronized polymers, obtained by cryogenic transmission electron stereography and tomography. The three-dimensional trajectories show that the wormlike chain model fails to adequately describe the scaling of these thick macromolecules already beyond a few nanometers in chain length, in spite of large apparent persistence lengths and long before a signature of self-avoidance appears. This insight is essential for understanding the limitations of polymer physical models, and it motivated us to discuss the advantages and disadvantages of this approach in comparison to the commonly applied scattering techniques.

Neutron reflectometry from poly (ethylene-glycol) brushes binding anti-PEG antibodies: evidence of ternary adsorption.

Neutron reflectometry provides evidence of ternary protein adsorption within polyethylene glycol (PEG) brushes. Anti-PEG Immunoglobulin G antibodies (Abs) binding the methoxy terminated PEG chain segment specifically adsorb onto PEG brushes grafted to lipid monolayers on a solid support. The Abs adsorb at the outer edge of the brush. The thickness and density of the adsorbed Ab layer, as well as its distance from the grafting surface grow with increasing brush density. At high densities most of the protein is excluded from the brush. The results are consistent with an inverted "Y" configuration with the two FAB segments facing the brush. They suggest that increasing the grafting density favors narrowing of the angle between the FAB segments as well as overall orientation of the bound Abs perpendicular to the surface.

Dendronized Polymers: Molecular Objects between Conventional Linear Polymers and Colloidal Particles.

The term molecular object (MO) is introduced to describe single, shape persistent macromolecules that retain their form and mesoscopic dimensions irrespective of solvent quality and adsorption onto a surface. The concept is illustrated with results concerning homologous series of dendronized polymers (DP). In particular, we discuss imaging experiments quantifying deformation upon adsorption, defect characterization, and atomistic molecular dynamics simulations of DP structure. We argue that MOs such as high generation DP, with their large dimensions and high internal density, provide an opportunity to address fundamental questions regarding the onset of bulk-like behavior in single molecules. Illustrative examples of such questions concern the smallest MO exhibiting a glass transition, glassy behavior or a constant bulk density. The characteristics of DP MO are highlighted by comparison to polymer beads, polymeric micelles, globular proteins, and carbon nanotubes. We discuss future research directions and speculate on possibilities involving multiarmed and toroid DP and the effect of DP on friction and rheology, as well as their utilization for nanoconstruction.

Synthetic regimes due to packing constraints in dendritic molecules confirmed by labelling experiments.

Classical theory predicts that branching defects are unavoidable in large dendritic molecules when steric congestion is important. Here we report first experimental evidence of this effect via labelling measurements of an extended homologous series of generations g = 1...6 of dendronized polymers. This system exhibits a single type of defect interrogated specifically by the Sanger reagent thus permitting to identify the predicted upturn in the number of branching defects when g approaches g(max) and the polymer density approaches close packing. The average number of junctions and defects for each member of the series is recursively obtained from the measured molar concentrations of bound labels and the mass concentrations of the dendritic molecules. The number of defects increases at g=5 and becomes significant at g=6 for dendronized polymers where the g(max) was estimated to occur at 6.1 ≤ g(max) ≤ 7.1. The combination of labelling measurements with the novel theoretical analysis affords a method for characterizing high g dendritic systems.

Theoretical considerations on mechanisms of harvesting cells cultured on thermoresponsive polymer brushes.

Poly (N-isopropylacrylamide) (PNIPAM) brushes and hydrogels serve as temperature-responsive cell culture substrates. The cells adhere at 37 °C and are detached by cooling to below the lower critical solution temperature T(LCST) ≈ 32 °C, an effect hitherto attributed to change in PNIPAM hydration. The article proposes a mechanism coupling the change of hydration to integrin mediated environmental sensing for cell culture on brushes and hydrogels in serum containing medium. Hydration is associated with swelling and higher osmotic pressure leading to two effects: (i) The lower osmotic pressure in the collapsed brush/hydrogel favors the adsorption of serum borne extracellular matrix (ECM) proteins enabling cell adhesion; (ii) Brush/hydrogel swelling at T < T(LCST) gives rise to a disjoining force f(cell) due to confinement by the ventral membrane of a cell adhering via integrin-ECM bonds. f(cell) places the integrin-ECM bonds under tension thus accelerating their dissociation and promoting desorption of ECM proteins. Self consistent field theory of PNIPAM brushes quantifies the effect of the polymerization degree N, the area per chain Σ, and the temperature, T on ECM adsorption, f(cell) and the dissociation rate of integrin-ECM bonds. It suggests guidelines for tuning Σ and N to optimize adhesion at 37 °C and detachment at T < T(LCST). The mechanism rationalizes existing experimental results on the influence of the dry thickness and the RGD fraction on adhesion and detachment.

Stretching of homopolymeric RNA reveals single-stranded helices and base-stacking.

We have found strong supporting evidence for the helical structures of single-stranded nucleic acids by stretching individual molecules of polyadenylic acid [poly(A)] and polycytidylic acid [poly(C)]. Analyzing the force versus extension data using a two-state elastic model in which random-coil domains alternate with rigid helical domains allows one to extract the thermodynamic and structural properties. In addition, it also yields moderate to low cooperativity of the helix-coil transition for poly(A) and poly(C), respectively.

Hybridization isotherms of DNA microarrays and the quantification of mutation studies.

BACKGROUND: Diagnostic DNA arrays for detection of point mutations as markers for cancer usually function in the presence of a large excess of wild-type DNA. This excess can give rise to false positives as a result of competitive hybridization of the wild-type target at the mutation spot. Analysis of the DNA array data is typically qualitative, aimed at establishing the presence or absence of a particular point mutation. Our theoretical approach yields methods for quantifying the analysis to obtain the ratio of concentrations of mutated and wild-type DNA. METHOD: The theory is formulated in terms of the hybridization isotherms relating the hybridization fraction at the spot to the composition of the sample solutions at thermodynamic equilibrium. It focuses on samples containing an excess of single-stranded DNA and on DNA arrays with a low surface density of probes. The hybridization equilibrium constants can be obtained by the nearest-neighbor method. RESULTS: Two approaches allow acquisition of quantitative results from the DNA array data. In one, the signal of the mutation spot is compared with that of the wild-type spot. The implementation requires knowledge of the saturation intensity of the two spots. The second approach requires comparison of the intensity of the mutation spot at two different temperatures. In this case, knowledge of the saturation signal is not always necessary. CONCLUSIONS: DNA arrays can be used to obtain quantitative results on the concentration ratio of mutated DNA to wild-type DNA in studies of somatic point mutations.