Shell-by-shell synthesis of tin oxide hollow colloids with nanoarchitectured walls: cavity size tuning and functionalization.
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Colloids↗
Biomedical subjects
Lynden A Archer
Publications and source records attributed to Lynden A Archer.
Spontaneous sharp bending of DNA: role of melting bubbles.
The role of centrally located and distributed base pair mismatches ('melting bubbles') on localized bending and stiffness of short dsDNA fragments is evaluated using time-dependent fluorescence lifetime measurements. Distributed melting bubbles are found to induce larger bending angles and decreased levels of stiffness in DNA than centrally located ones of comparable overall size. Our results indicate that spontaneous local opening-up of the DNA duplex could facilitate sharp bending of short DNA strands even in the absence of DNA binding proteins. We also find that the occurrence of two closely spaced melting bubbles will generally be favored when a large energetic barrier must be overcome in forming the desired bent DNA structure.
Base Pair Mismatch↗
Comprehensive interpretation of gel electrophoresis data.
From temperature analysis of polyacrylamide gel electrophoresis data for rigid-rod DNA analytes, it is proposed that an entropic force term is responsible for the discrepancy between Ogston-Morris-Rodbard-Chrambach model predictions and experimental results. This entropic force originates from reduction of the orientational freedom of anisotropic analytes in small pores of polyacrylamide gels. Time-dependent fluorescence anisotropy decay measurements confirm that, even in the absence of an external field, orientation of anisotropic analytes is restricted in polyacrylamide gels. A new comprehensive model is proposed that takes this effect into consideration. Predictions based on this model are found to compare favorably with experimental data for linear and three-arm asymmetrically branched rigid-rod DNA analytes covering a broad range of molecular aspect ratios and sizes. A new length scale is also proposed for describing the effect of analyte topology on electrophoretic mobility. This length scale reduces to the analyte radius of gyration in the limiting cases of spherically symmetric and linear rigid-rod species. Based on these results, a general approach is proposed for interpreting gel electrophoresis data of charged analytes possessing simple and complex topologies.
Acrylic Resins↗
Platinum-functionalized octahedral silica nanocages: synthesis and characterization.
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Journal Article↗
Molecular relaxation dynamics of self-assembled monolayers.
Dielectric relaxation spectroscopy is used to quantify molecular motion in alkylsilane SAMs coated on porous glass over a broad temperature range, -30 to -150 degrees C. Systematic measurements using SAMs with variable coating densities allow us to determine the effect of monolayer disorder on molecular mobility in thin molecular films. A relaxation process with an activation energy of approximately 25 kJ/mol is found to dominate dynamics of SAM-chain segments near the substrate. By introducing polar CN groups at the ends of the chain, we show that the relaxation process in the monolayer canopy can be isolated and studied. This approach can be generalized to other substituent polar groups to probe localized relaxation dynamics in surface-grafted monolayer films.
Journal Article↗
Step-growth synthesis and interfacial friction properties of surface dendron coatings.
We report a new procedure for synthesizing self-assembled two-tiered coatings comprised of a tethered carbosilane dendron canopy layer over an alkylsilane sublayer. The sublayer is anchored to a silicon substrate, and the areal density of the canopy can be controlled by changing the concentration of reactive vinyl groups on the sublayer surface. The structure of the dendron layer is characterized by angle-resolved X-ray photoelectron spectroscopy (ARXPS), water contact angle, and ellipsometry. Steric hindrance due to close packing of functional groups has a strong effect on the reaction efficiency, and dendron structure can be obtained only in canopies with low areal densities. Lateral force microscopy (LFM) is used to study interfacial friction and adhesion properties of the coatings. Structural variations in the canopy layer are found to play a crucial role in interfacial friction properties of these coatings.
Adsorption↗
Electrophoretic mobility of linear and star-branched DNA in semidilute polymer solutions.
Electrophoresis of large linear T2 (162 kbp) and 3-arm star-branched (N(Arm) = 48.5 kbp) DNA in linear polyacrylamide (LPA) solutions above the overlap concentration c* has been investigated using a fluorescence visualization technique that allows both the conformation and mobility mu of the DNA to be determined. LPA solutions of moderate polydispersity index (PI approximately 1.7-2.1) and variable polymer molecular weight Mw (0.59-2.05 MDa) are used as the sieving media. In unentangled semidilute solutions (c* < c < c(e)), we find that the conformational dynamics of linear and star-branched DNA in electric fields are strikingly different; the former migrating in predominantly U- or I-shaped conformations, depending on electric field strength E, and the latter migrating in a squid-like profile with the star-arms outstretched in the direction opposite to E and dragging the branch point through the sieving medium. Despite these visual differences, mu for linear and star-branched DNA of comparable size are found to be nearly identical in semidilute, unentangled LPA solutions. For LPA concentrations above the entanglement threshold (c > c(e)), the conformation of migrating linear and star-shaped DNA manifest only subtle changes from their unentangled solution features, but mu for the stars decreases strongly with increasing LPA concentration and molecular weight, while mu for linear DNA becomes nearly independent of c and Mw. These findings are discussed in the context of current theories for electrophoresis of large polyelectrolytes.
Acrylic Resins↗
Surface migration of branched molecules: analysis of energetic and entropic factors.
We have introduced energetic factors into the response theory developed by Wu and Fredrickson [Macromolecules 29, 7919 (1996)] to predict the enrichment of branched molecules due to architectural effects at surfaces. This development simultaneously increases the utility of the theory for guiding experimental investigations, and makes possible a rigorous assessment of theoretical predictions in careful studies of isotopically labeled linear/branched species binary blends at surfaces. For example, the introduction of energetic factors allows us to predict the existence of a crossover molecular weight, below which an energetically unfavorable species at a surface can be enriched entirely due to architecture. For binary blends of linear chains, the degree of polymerization (Kuhn) of the energetically unfavorable species at the crossover point is r(c) approximately =2U(e)/DeltaU(s). Here, U(e) is the attraction of chain ends towards the surface and DeltaU(s) is the difference in the interaction potential of main chain segments to the surface due to chemical differences and/or isotopic labeling. We also show that surface segregation of an additive in a host polymer due to architectural effects alone is significantly enhanced as the spinodal temperature of a branched/linear blend is approached. Detailed comparisons of the modified response theory with lattice simulations are used to evaluate the theory and to determine the limits of its applicability.
Journal Article↗
Mismatch-induced DNA unbending upon duplex opening.
A DNA duplex can be torn open at a specific position by introducing a branch or bulge to create an asymmetric three-way junction (TWJ). The opened duplex manifests a bent conformation (bending angle approximately 60 degrees , relative to the unopened form), which leads to a dramatic decrease in gel electrophoretic mobility. In the presence of a basepair mismatch at the opening position, the DNA backbone becomes less bent and assumes a distorted T-shaped structure, resulting in an increase in polyacrylamide gel electrophoretic mobility. Both conformational changes are confirmed using fluorescence resonance energy transfer experiments and found to be similar to the signature conformational changes of DNA duplex upon MutS protein binding. Our results imply that some structural rearrangements essential for mismatch recognition are achievable without protein interference. The gel electrophoretic mobility data for DNA TWJs with and without base mismatches correlates well with rotational diffusivity, computed by taking into account the conformational change of TWJ induced by base mismatch.
Base Pair Mismatch↗
Interfacial friction of surfaces grafted with one- and two-component self-assembled monolayers.
We present a quantitative study of the nanoscale frictional properties of one-component (pure) and two-component (mixed) alkylsilane self-assembled monolayers (SAMs). The load and velocity dependence of the friction force was measured in air and ethanol using lateral force microscopy (LFM). It was observed that for SAMs with well-ordered structure (pure SAMs and mixed SAMs composed of two long chain molecules) friction depends nonlinearly on load, at low loads, both in air and in ethanol. These observations are consistent with the low-load contact area predictions of the Johnson-Kendall-Roberts (JKR) theory, indicating that for well-ordered SAMs friction force is proportional to contact area and that the true contact area is determined by elastic deformation of the SAM by the LFM probe. In ambient air, the magnitude of the friction force measured using mixed SAMs is found to be similar to that obtained using pure SAMs at the same external load. Changing the medium to ethanol, however, leads to dramatically lower friction in the mixed SAMs. An analysis of the friction data using a thermally activated Eyring model that takes into account the monolayer viscoelasticity suggests that the better friction properties of the mixed SAMs are a consequence of greater disorder and higher molecular mobility in the outer layer/canopy. These findings indicate that multi-tiered SAM coatings comprising a highly ordered underlayer and a disordered, mobile canopy can provide the basis for low-friction coatings for small mechanical systems.
Friction↗
Surface enrichment of branched polymers in linear hosts: effect of asymmetry in intersegmental interactions and density gradients.
Variable density lattice treatment of surface enrichment of f-arm star-branched chains in star/linear polymer blends is compared with results of an analytical response theory proposed by Wu and Fredrickson [Macromolecules 29, 7919 (1996)]. We find that differences in treating the intersegmental interactions in the small interfacial region near a free surface lead to significant differences in the potentials by which polymer chain ends are attracted towards the surface. Consideration of an asymmetric relationship between segment potentials and density changes in polystyrene at 450 K and 0.1 MPa, for example, gives typically a threefold to fourfold enhancement in composition of star molecules at a vacuum interface. When contributions from gradients in density are included in the analysis even greater levels of surface enhancement (fivefold to sixfold increases) are observed. By appropriately estimating the attraction of chain ends and repulsion of branch points at a free surface, we show that concentration profiles of branched polymers predicted in the lattice model are consistent with results obtained in the analytical response theory.
Journal Article↗
Effect of topological asymmetry on the electrophoretic mobility of branched DNA structures with and without single-base mismatches.
The electrophoretic mobility of three-arm star DNA structures with varying degrees of branch length asymmetry has been investigated in polyacrylamide (PAA) hydrogels. We report the effect of single-base mismatches, adjacent to the branch point, on the mobility of branched DNA with three different arm lengths. Branched DNA structures were formed using wild-type and mutated fragments of the p53 tumor suppressor gene, which is believed to play an important role in cancer development. Branching was directed at the site of several previously characterized mutations in exon 7 of p53. At a given gel concentration, the mobility of branched DNA with fully complementary base pairing is found to increase as the degree of branch length asymmetry is increased. Ferguson analysis of the gel electrophoresis data leads to a retardation coefficient that is strongly dependent on topology. This finding can be explained in terms of a minimum molecular cross-section for each molecule. Specifically, we show that structures with the smallest molecular cross-section can access more pores in the gel, which leads to higher mobility. Our results can also be understood by considering the rotational diffusivity of branched DNA. Asymmetric DNA stars with higher calculated rotational diffusivities also have higher mobilities. When a mutated base is present in junctions with low degrees of branch length asymmetry, adjacent to the branch point, the mobility increases in comparison to the fully complementary molecules. The reason for this increased mobility is unclear, here, we propose that the mismatched base introduces additional flexibility to the arm containing the mutation leading to higher conformational freedom and enhanced mobility in gels. When a mismatched base is present in junctions with high degrees of branch length asymmetry, the opposite result is obtained. Here, the mutated species has a lower mobility. This result is argued to arise from incomplete hybridization and/or frayed ends. Finally, we have shown that by using two of the branch point oligonucleotides as probe molecules, mutations known to occur at specific sites can be detected through the mobility shift. If the sequences of the probe chains are changed in a controlled manner, the location and base of the mutant can also be determined.
Base Pair Mismatch↗
Layered organosilicate nanoparticles with liquidlike behavior.
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Hydrolysis↗
A liquid derivative of 12-tungstophosphoric acid with unusually high conductivity.
Surface functionalization of the solid heteropolyacid H3PW12O40 with a bulky PEG-containing quaternary ammonium cation through partial proton exchange leads to a polyoxometalate-based liquid salt with high-temperature proton conductivity ( approximately 10-3 S cm-1 at 140 degrees C) under dry conditions. The proton conductivity of the liquid salt is 4 orders of magnitude higher than that of the solid analogue under identical conditions and shows super ionic behavior as defined by Walden plot.
Journal Article↗
Monte Carlo simulation of structure and nanoscale interactions in polymer nanocomposites.
Off-lattice Monte Carlo simulations in the canonical ensemble are used to study polymer-particle interactions in nanocomposite materials. Specifically, nanoscale interactions between long polymer chains (N=550) and strongly adsorbing colloidal particles of comparable size to the polymer coils are quantified and their influence on nanocomposite structure and dynamics investigated. In this work, polymer-particle interactions are computed from the integrated force-distance curve on a pair of particles approaching each other in an isotropic polymer medium. Two distinct contributions to the polymer-particle interaction potential are identified: a damped oscillatory component that is due to chain density fluctuations and a steric repulsive component that arises from polymer confinement between the surfaces of approaching particles. Significantly, in systems where particles are in a dense polymer melt, the latter effect is found to be much stronger than the attractive polymer bridging effect. The polymer-particle interaction potential and the van der Waals potential between particles determine the equilibrium particle structure. Under thermodynamic equilibrium, particle aggregation is observed and there exists a fully developed polymer-particle network at a particle volume fraction of 11.3%. Near-surface polymer chain configurations deduced from our simulations are in good agreement with results from previous simulation studies.
Journal Article↗
Effect of matrix chain length on the electrophoretic mobility of large linear and branched DNA in polymer solutions.
We study the effect of matrix chain molecular weight Mw and concentration c on the electrophoretic mobility micro of large linear and star-like, branched DNA in polymer solutions. Polyethylene oxide (PEO) with narrow molecular weight distributions form the main focus of this study. For PEO concentrations ranging from one half the overlap concentration, c*, to 3c*, the effective drag coefficient, zeta is identical with (mu0/mu) - 1, satisfies the following approximate scaling relationship, zeta approximately cMw(0.7). Here, mu0 is the electrophoretic mobility in free solution. While the concentration dependence is consistent with predictions from the transient entanglement coupling (TEC) model, the molecular weight dependence is significantly weaker. Although a similar dependence of mobility on Mw can be predicted when nonentangling collisions are the dominant source of drag, a model based on these collisions alone cannot reproduce the experimental observations. We also find that the architecture of large DNA does not affect either the concentration dependence or molecular weight dependence of the electrophoretic mobility.
DNA↗
Influence of branch length asymmetry on the electrophoretic mobility of rigid rod-like DNA.
The electrophoretic mobility of three-arm asymmetric star DNA molecules, produced by incorporating a short DNA branch at the midpoint of rigid-rod linear DNA fragments, is investigated in polyacrylamide gels. We determine how long the added branch must be to separate asymmetric star DNA from linear DNA with the same total molecular weight. This work focuses on two different geometric progressions of small DNA molecules. First, branches of increasing length were introduced at the center of a linear DNA fragment of constant length. At a given gel concentration, we find that relatively small branch lengths are enough to cause a detectable reduction in electrophoretic mobility. The second geometric progression starts with a small branch on a linear DNA fragment. As the length of this branch is increased, the DNA backbone length is decreased such that the total molar mass of the molecule remains constant. The branch length was then increased until the asymmetric branched molecule becomes a symmetric three-arm star polymer, allowing the effect of molecular topology on mobility to be studied independent of size effects. DNA molecules with very short branches have a mobility smaller than linear DNA of identical molar mass. The reason for this change in mobility when branching is introduced is not known, however, we explore two possible explanations in this article. (i) The branched DNA could have a greater interaction with the gel than linear DNA, causing it to move slower; (ii) the linear DNA could have modes of motion or access to pores that are unavailable to the branched DNA.
Acrylic Resins↗
Topological effects on the electrophoretic mobility of rigid rodlike DNA in polyacrylamide gels.
The electrophoretic migration of rigid rodlike DNA structures with well defined topologies has been investigated in polyacrylamide (PA) hydrogels prepared by copolymerization of acrylamide and N, N'-methylenebisacrylamide. Previous studies have reported structural and dynamic characteristics of linear and branched DNA during electrophoresis in PA gels using a variety of experimental parameters. However, a thorough investigation aimed at establishing specific relationships between topological features of rigid rodlike DNA structures and their electrophoretic behavior is still needed. In order to study these topological effects on mobility, an intensive examination of the electrophoretic mobility of small linear and starlike DNA was performed. A series of model DNA structures with well-defined branched topologies were synthesized with varying molecular parameters, such as number of arms surrounding the branch point and arm length. The electrophoretic mobility of these structures was then contrasted with a series of data obtained using linear DNA of comparable molecular size. When large DNA stars (M >/= 60 bp) were compared with linear DNA of identical molecular weight, the Ferguson plots were quite different. However, small DNA stars (24-32 bp) and linear analogues had identical Ferguson plots. This indicates that a different motional mode or greater interaction with the gel exists for the larger DNA stars. When the total molecular weight of the DNA stars was held constant and the number of arms varied, the Ferguson plots for all the stars were identical. Additionally, a critical pore size was reached when the ratio of linear DNA mobility to star DNA mobility increased dramatically. Thus, while the incorporation of a single branch point can produce a large reduction in mobility, above a critical molecular size, the incorporation of additional branch points does not appear to provide further reduction in mobility. This finding is consistent with the transport properties of large synthetic star polymers, where a large reduction in their diffusion coefficient is observed when a single branch is added. When additional arms are incorporated, large synthetic stars do not display an appreciable further reduction in diffusion coefficient. The effect of arm length on mobility for rigid rod DNA stars was also studied. For four-arm DNA stars, the mobility was found to scale as an exponential function of the arm length. Finally, a recently proposed phenomenological model was used to successfully fit the mobility data for linear rigid rod DNA at various concentrations of PA.
DNA↗