Self-Sterilizing, Self-Cleaning Mixed Polymeric Multifunctional Antimicrobial Surfaces.

Mitigation of bacterial adhesion and subsequent biofilm formation is quickly becoming a strategy for the prevention of hospital-acquired infections. We demonstrate a basic strategy for surface modification that combines the ability to control attachment by microbes with the ability to inactivate microbes. The surface consists of two active materials: poly(p-phenylene ethynylene)-based polymers, which can inactivate a wide range of microbes and pathogens, and poly(N-isopropylacrylamide)-based polymers, which can switch between an hydrophobic "capture" state and a hydrophilic "release" state. The combination of these materials creates a surface that can both bind microbes in a switchable way and kill surface-bound microbes efficiently. Considerable earlier work with cationic poly(p-phenylene ethynylene) polyelectrolytes has demonstrated and characterized their antimicrobial properties, including the ability to efficiently destroy or deactivate Gram-negative and Gram-positive bacteria, fungi, and viruses. Similarly, much work has shown (1) that surface-polymerized films of poly(N-isopropylacrylamide) are able to switch their surface thermodynamic properties from a swollen, relatively hydrophilic state at low temperature to a condensed, relatively hydrophobic state at higher temperature, and (2) that this switch can control the binding and/or release of microbes to poly(N-isopropylacrylamide) surfaces. The active surfaces described herein were fabricated by first creating a film of biocidal poly(p-phenylene ethynylene) using layer-by-layer methods, and then conferring switchable adhesion by growing poly(N-isopropylacrylamide) through the poly(p-phenylene ethynylene) layer, using surface-attached polymerization initiators. The resulting multifunctional, complex films were then characterized both physically and functionally. We demonstrate that such films kill and subsequently induce widespread release of Gram-negative and Gram-positive bacteria.

AFM images of the dark biocidal action of cationic conjugated polyelectrolytes and oligomers on Escherichia coli.

Polymers and oligomers with conjugated phenylene ethynylene or thiophene ethynylene backbones have been shown to be potent antimicrobials. The mechanisms by which they act have been unclear, though AFM imaging of Escherichia coli cells before and after exposure to two such biocides, PPE-Th polymer and EO-OPE-1(C3), shows their effects on cell surface structure. Dried, unexposed E. coli cells could be imaged at resolution high enough to discern the physical structure of the cell surfaces, including individual porin proteins and their distribution on the cell. Exposure to 30 µg/mL PPE-Th polymer caused major cell surface disruption due to either emulsification of the outer membrane or the formation of polymer aggregates or both. In contrast, exposure to 30 µg/mL EO-OPE-1(C3) oligomer did not cause large-scale membrane disruption but did cause apparent reorganization of the surface proteins into linear arrays or protein-lipid-OPE complexes that dominate on a small scale. E. coli cells were also successfully imaged underwater, allowing a real-time AFM image series as cells were exposed to 30 µg/mL EO-OPE-1(C3). Solution exposure caused the cell surfaces to noticeably increase their roughness over time. These results agree with proposed mechanisms for cell killing by PPE-Th and EO-OPE-1(C3) put forth by Wang et al.1 in which PPE-Th kills by large-scale disruption of the outer membrane and EO-OPE-1(C3) kills by membrane reorganization with possible pore formation.

Conditions for liposome adsorption and bilayer formation on BSA passivated solid supports.

Planar solid supported lipid membranes that include an intervening bovine serum albumen (BSA) cushion can greatly reduce undesirable interactions between reconstituted membrane proteins and the underlying substrate. These hetero-self-assemblies reduce frictional coupling by shielding reconstituted membrane proteins from the strong surface charge of the underlying substrate, thereby preventing them from strongly sticking to the substrate themselves. The motivation for this work is to describe the conditions necessary for liposome adsorption and bilayer formation on these hetero-self-assemblies. Described here are experiments that show that the state of BSA is critically important to whether a lipid bilayer is formed or intact liposomes are adsorbed to the BSA passivated surface. It is shown that a smooth layer of native BSA will readily promote lipid bilayer formation while BSA that has been denatured either chemically or by heat will not. Atomic force microscopy (AFM) and fluorescence microscopy was used to characterize the surfaces of native, heat denatured, and chemically reduced BSA. The mobility of several zwitterionic and negatively charged lipid combinations has been measured using fluorescence recovery after photobleaching (FRAP). From these measurements diffusion constants and percent recoveries have been determined and tabulated. The effect of high concentrations of beta-mercaptoethanol (ß-ME) on liposome formation as well as bilayer formation was also explored.

Coarse-grained model DNA: structure, sequences, stems, circles, hairpins.

A coarse-grained model for DNA that is intended to function realistically at the level of individual bases is reported. The model is composed of residues with up to eight coarse-grained beads each, which is sufficient for DNA-like base stacking and base-base recognition by hydrogen bonding. The beads interact by means of short-ranged pair potentials and a simple implicit solvent model. Movement is simulated by Brownian dynamics without hydrodynamic coupling. The main stabilizing forces are base stacking and hydrogen bonding, as modified by the effects of solvation. Complementary double-stranded chains of such residues form stable double helices over long runs (~10 µs) at or near room temperature, with structural parameters close to those of B-form DNA. Most mismatched chains or mismatched regions within a complementary molecule melt and become disordered. Long-range fluctuations and elastic properties, as measured by bending and twisting persistence lengths, are close to experimental values. Single-stranded chains are flexible, with transient stretches of free bases in equilibrium with globules stabilized by intrastrand stacking and hydrogen bonding. Model DNAs in covalently closed loops form right- or left-handed supercoils, depending on the sign of overtwist or undertwist. Short stem-loop structures melt at elevated temperatures and reanneal when the temperature is carefully lowered. Overall, most qualitative properties of real DNA arise naturally in the model from local interactions at the base-pair level.

Single particle tracking reveals corralling of a transmembrane protein in a double-cushioned lipid bilayer assembly.

A predominate question associated with supported bilayer assemblies containing proteins is whether or not the proteins remain active after incorporation. The major cause for concern is that strong interactions with solid supports can render the protein inactive. To address this question, a large transmembrane protein, the serotonin receptor, 5HT(3A), has been incorporated into several supported membrane bilayer assemblies of increasing complexity. The 5HT(3A) receptor has large extracellular domains on both sides of the membrane, which could cause strong interactions. The bilayer assemblies include a simple POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) supported planar bilayer, a "single-cushion" POPC bilayer with a PEG (poly(ethylene glycol)) layer between membrane and support, and a "double-cushion" POPC bilayer with both a PEG layer and a layer of BSA (bovine serum albumin). Single-cushion systems are designed to lift the bilayer from the surface, and double-cushion systems are designed to both lift the membrane and passivate the solid support. As in previously reported work, protein mobilities measured by ensemble fluorescence recovery after photobleaching (FRAP) are quite low, especially in the double-cushion system. But single-particle tracking of fluorescent 5HT(3A) molecules shows that individual proteins in the double-cushion system have quite high local mobilities but are spatially confined within small corralling domains ( 450 nm). Comparisons with the simple POPC membrane and the single-cushion POPC−PEG membrane reveal that BSA both serves to minimize interactions with the solid support and creates the corrals that reduce the long-range (ensemble averaged) mobility of large transmembrane proteins. These results suggest that in double-cushion assemblies proteins with large extra-membrane domains may remain active and unperturbed despite low bulk diffusion constants.

Understanding the force-vs-distance profiles of terminally attached poly(N-isopropyl acrylamide) thin films.

In this work, we examine the interaction between thin films composed of terminally anchored poly(N-isopropyl acrylamide) (PNIPAAm) immersed in water and test surfaces. Understanding this force of interaction can be important when using PNIPAAm surfaces in biotechnological applications such as biological cell cultures. The two novel contributions that are presented here are (1) the use of a recently developed self-consistent field (SCF) theory to predict the force-vs-distance profiles, and (2) the use of a modified polymer scaling theory to estimate the wet film thickness from experimental force-vs-distance profiles. SCF theory was employed to model the equilibrium structure of the uncompressed PNIPAAm chains, and the force between a compressed polymer film and a test surface as a function of wall separation distance. The parameters that were varied include temperature, polymer molecular weight, and surface coverage. The force-vs-distance profiles obtained at low and high temperatures with the SCF theory were in qualitative agreement with the experimentally measured profiles reported in the literature. We also compared the results of our SCF theory to the Alexander de Gennes scaling theory and found agreement at large separation distance. We also propose a method to estimate the wet polymer film thickness from a force-vs-distance profile obtained from an atomic force microscope measurement. The main novelties of this approach are that we employed a density functional theory corrected version of scaling theory proposed by McCoy et al. [McCoy, J. D.; Curro, J. G. J. Chem. Phys. 2005, 122, 164905], and we provide equations to account for various geometries of AFM tips.

Framework model for DNA polymerases.

DNA polymerases are complex machines with both chemical and mechanical functions. Recent crystal structures, ensemble kinetics, and single-molecule investigations have helped to elucidate the main properties of several DNA polymerases, all of which share common structural elements and a common basic mechanism, despite wide variations in amino acid sequence. The framework model is intended to aid in the understanding of these common features (and differences). It defines a class of models that automatically incorporates most of what is known about DNA polymerases within a single theoretical structure so that it is easier to make comparisons between them and to generate detailed models for specific polymerases. The framework model has three main elements: (1) a set of four key variables that describe the important motions within the protein-DNA-nucleotide complex, (2) a complete set of conformational states for the protein-DNA-nucleotide system, and (3) an approximate potential energy surface that controls the motions and transition rates between states. As an example application, we use the general framework ideas to build a detailed model for the HIV reverse transcriptase that is consistent with existing data, and predicts force-velocity curves and stepping-statistics histograms that can be directly compared to experiment.

Stepping statistics of single HIV-1 reverse transcriptase molecules during DNA polymerization.

DNA polymerases are protein machines that processively incorporate complimentary nucleotides into a growing double-stranded DNA (ds-DNA). Single-base nucleotide incorporation rates have been determined by stalling and restarting various polymerases, but intrinsic processive rates have been difficult to obtain, particularly for polymerases with low processivity, such as the human immunodeficiency virus type 1 reverse transcriptase (HIV RT) polymerase. Here we find, using a new fluorescence-based single-molecule polymerization assay, that the intrinsic processive DNA-dependent polymerization of HIV RT is approximately Poissionian (i.e. each nucleotide is added sequentially) with a rate of about 100 bases per second at 21 degrees C. From the same experiments, based on the stepping statistics of polymerization, we also estimate the rates for HIV RT early termination and final release of completely replicated primer-template DNA. In addition, by measuring the rate of polymerization as a function of temperature, we have estimated the activation energy for processive nucleotide incorporation.

Closing of the fingers domain generates motor forces in the HIV reverse transcriptase.

Using the force sensor of an atomic force microscope, motor forces of the human immunodeficiency virus-1 reverse transcriptase were measured during active replication of a short DNA transcript. At low load forces the polymerase is mechanically slowed, whereas at high force (approximately 15 piconewton) it stalls. From recordings of estimated polymerase turnover velocity versus load force, an approximate force-velocity curve has been constructed. The shape of the curve suggests that load force strongly inhibits the rate-limiting step of the polymerase turnover cycle and that the combined effect of load on all steps involves an effective motion of about 1.6 nm. Earlier results from pre-steady-state kinetics experiments have identified the rate-limiting step as the closing of the fingers domain to form a tight catalytic complex. Together these findings indicate that the closing of the fingers domain is a major force-generating step for human immunodeficiency virus reverse transcriptase and, by extension, for all DNA polymerase machines.

Reversible control of free energy and topography of nanostructured surfaces.

We describe a facile method for the formation of dynamic nanostructured surfaces based on the modification of porous anodic aluminum oxide with poly(N-isopropyl acrylamide) (PNIPAAm) via surface-initiated atom transfer radical polymerization. The dynamic structure of these surfaces was investigated by atomic force microscopy (AFM), which showed dramatic changes in the surface nanostructure above and below the aqueous lower critical solution temperature of PNIPAAm. These changes in surface structure are correlated with changes in the macroscopic wettability of the surfaces, which was probed by water contact angle measurements. Principal component analysis was used to develop a quantitative correlation between AFM image intensity histograms and macroscopic wettability. Such correlations and dynamic nanostructured surfaces may have a variety of uses.