Switchable DNA-origami nanostructures that respond to their environment and their applications

Structural DNA nanotechnology, in which Watson-Crick base pairing drives the formation of self-assembling nanostructures, has rapidly expanded in complexity and functionality since its inception in 1981. DNA nanostructures can now be made in arbitrary three-dimensional shapes and used to scaffold many other functional molecules such as proteins, metallic nanoparticles, polymers, fluorescent dyes and small molecules. In parallel, the field of dynamic DNA nanotechnology has built DNA circuits, motors and switches. More recently, these two areas have begun to merge—to produce switchable DNA nanostructures, which change state in response to their environment. In this review, we summarise switchable DNA nanostructures into two major classes based on response type: molecular actuation triggered by local chemical changes such as pH or concentration and external actuation driven by light, electric or magnetic fields. While molecular actuation has been well explored, external actuation of DNA nanostructures is a relatively new area that allows for the remote control of nanoscale devices. We discuss recent applications for DNA nanostructures where switching is used to perform specific functions—such as opening a capsule to deliver a molecular payload to a target cell. We then discuss challenges and future directions towards achieving synthetic nanomachines with complexity on the level of the protein machinery in living cells.     

Structure and Conformation of Wild-Type Bacterial Lipopolysaccharide Layers at Air-Water Interfaces

The outer membrane of Gram-negative bacteria is of great scientific interest because it mediates the action of antimicrobial agents. The membrane surface is composed of lipopolysaccharide (LPS) molecules with negatively charged oligosaccharide headgroups. To a certain fraction, LPSs additionally display linear polysaccharides termed O-side chains (OSCs). Structural studies on bacterial outer surfaces models, based on LPS monolayers at air-water interfaces, have so far dealt only with rough mutant LPSs lacking these OSCs. Here, we characterize monolayers of wild-type LPS from Escherichia coli O55:B5 featuring strain-specific OSCs in the presence of defined concentrations of monovalent and divalent ions. Pressure-area isotherms yield insight into in-plane molecular interactions and monolayer elastic moduli. Structural investigations by x-ray and neutron reflectometry reveal the saccharide conformation and allow quantifying the area per molecule and the fraction of LPS molecules carrying OSCs. The OSC conformation is satisfactorily described by the self-consistent field theory for end-grafted polymer brushes. The monolayers exhibit a significant structural response to divalent cations, which goes beyond generic electrostatic screening.     

Interaction of basic polypeptides with phospholipid monolayers

Adsorption of the polylysine and of the copolypeptides: L-lysine/L-serine and L-lysine/L-phenylalanine on phospholipid monolayers has been investigated. The charge density of the monolayers was varied by using the negatively charged phosphatidyl serine and the neutral phosphatidyl choline at different ratios. The surface concentrations of the adsorbed polypeptides was determined by measuring the surface radiation of their radioactive label.The adsorbing capacity of the monolayer surfaces increases with their negative charge, however with respect to polypeptides the surface activity sequence is pL < pLS < pLφ. From the dependence of adsorption on the ionic strength it was concluded that it is controlled by three types of interaction: (1) electrostatic attraction to the negatively charged surface; (2) electrostatic repulsion between adsorbed polybases; (3) hydrophobic interactions involving specific structural arrangements. This is true even of the apparently neutral PC monolayer where the fixed phosphate groups form an electrical double layer with the more mobile choline groups which can be interpenetrated by the charged groups of the basic polypeptides.     

Formation of stable polypeptide monolayers at interfaces: controlling molecular conformation and orientation.

The molecular self-organization and structural properties of peptide assemblies at different interfaces, using either amphipathic or hydrophobic polypeptide helices, is described. The two peptides under investigation form stable monolayers on the water surface under the conservation of their molecular conformation, as studied by circular dichroism and polarization-modulation Fourier transform infrared (FTIR) spectroscopy. Using surface plasmon resonance and reflection-absorption FTIR, we show that such molecular layers can be transferred unaltered to solid substrates. Most importantly, the molecular orientation of the hydrophobic helices on solid supports such as gold can be controlled by choosing a particular procedure for the layer formation. The helices were oriented parallel to the interface in Langmuir-Blodgett monolayers, and perpendicular to the interface in self-assembled monolayers. Our reflection-absorption FTIR measurements have delivered for the first time direct experimental evidence for the molecular conformation and orientation of pure peptide monolayers. Suitable reference spectra of polypeptides with defined conformation and orientation are necessary to use this technique for the determination of the molecular orientation of peptides in monomolecular films. We have solved the problem for alpha-helical polypeptides by using bacteriorhodopsin as a reference in combination with synthetic alpha-helices of defined interfacial orientation. The present study shows the possibility of constructing immobilized peptide monolayers with predefined macroscopic properties and molecular structure by choosing the proper polypeptide amino acid sequence, the technique used for layer formation, and the supporting surface properties.     

Interaction of electrically charged lipid monolayers with malate dehydrogenase.

Malate dehydrogenase was adsorbed onto monomolecular lipid films, using a multicompartment trough. The quantity of adsorbed protein and its enzymatic activity were studied with monolayers of various electrical charge densities and subphases of various electrolyte compositions. A closely packed layer of enzyme molecules was adsorbed onto negatively charged films, whereas considerably less protein was adsorbed onto neutral and positively charged monolayers. Electrolytes reduce the quantity of adsorbed protein. The adsorption was found to be irreversible even at high ionic strength. When adsorbed to uncharged lipid films the enzyme is nearly inactive, whereas negatively charged lipid headgroups enhance the specific activity of the enzyme.     

Interaction of electrically charged lipid monolayers with malate dehydrogenase

Malate dehydrogenase was adsorbed onto monomolecular lipid films, using a multicompartment trough. The quantity of adsorbed protein and its enzymatic activity were studied with monolayers of various electrical charge densities and subphases of various electrolyte compositions. A closely packed layer of enzyme molecules was adsorbed onto negatively charged films, whereas considerably less protein was adsorbed onto neutral and positively charged monolayers. Electrolytes reduce the quantity of adsorbed protein. The adsorption was found to be irreversible even at high ionic strength. When adsorbed to uncharged lipid films the enzyme is nearly inactive, whereas negatively charged lipid headgroups enhance the specific activity of the enzyme.     

Adhesive and conformational behaviour of mycolic acid monolayers

We have studied the pH-dependent interaction between mycolic acid (MA) monolayers and hydrophobic and hydrophilic surfaces using molecular (colloidal probe) force spectroscopy. In both cases, hydrophobic and hydrophilic monolayers (prepared by Langmuir-Blodgett and Langmuir-Schaefer deposition on silicon or hydrophobized silicon substrates, respectively) were studied. The force spectroscopy data, fitted with classical DLVO (Derjaguin, Landau, Verwey, and Overbeek) theory to examine the contribution of electrostatic and van der Waals forces, revealed that electrostatic forces are the dominant contribution to the repulsive force between the approaching colloidal probe and MA monolayers. The good agreement between data and the DLVO model suggest that beyond a few nm away from the surface, hydrophobic, hydration, and specific chemical bonding are unlikely to contribute to any significant extent to the interaction energy between the probe and the surface. The pH-dependent conformation of MA molecules in the monolayer at the solid-liquid interface was studied by ellipsometry, neutron reflectometry, and with a quartz crystal microbalance. Monolayers prepared by the Langmuir-Blodgett method demonstrated a distinct pH-responsive behaviour, while monolayers prepared by the Langmuir-Schaefer method were less sensitive to pH variation. It was found that the attachment of water molecules plays a vital role in determining the conformation of the MA monolayers.     

microAg particle-based molecular sensing/recognition via surface-enhanced Raman spectroscopy

In this study, we demonstrate that powders of commercially available 2-microm-sized Ag (microAg) can be used as a core material for constructing molecular sensing/recognition units operating via surface-enhanced Raman scattering (SERS). This is possible because microAg powders are very efficient substrates for both the infrared and Raman-spectroscopic characterization of molecular adsorbates prepared in a similar manner on silver surfaces. The Raman spectrum of organic monolayers on powdered silver is a SERS spectrum. The agglomeration of microAg particles in a highly concentrated buffer solution could be prevented by the deposition of polar molecules like 1,4-phenylenediisocyanide (1,4-PDI), and mixed self-assembled monolayers of 1,4-PDI and N-(+)-biotinyl-6-aminocaproic acid on microAg particles were then confirmed via the SERS of 1,4-PDI to selectively recognize the avidin arrays formed on a separate biotinylated substrate. According to a dose response curve, avidin at >10(-6)g/mL could be easily identified by the present method. In addition, the non-specific adsorption of microAg particles was found to be negligibly small, probably because the Ag particles were too heavy to be retained on organic substrates solely by non-specific interaction.     

Conformation of Single and Interacting Lipopolysaccharide Surfaces Bearing O-Side Chains

The outer surfaces of Gram-negative bacteria are composed of lipopolysaccharide (LPS) molecules exposing oligo- and polysaccharides to the aqueous environment. This unique, structurally complex biological interface is of great scientific interest as it mediates the interaction of bacteria with antimicrobial agents as well as with neighboring bacteria in colonies and biofilms. Structural studies on LPS surfaces, however, have so far dealt almost exclusively with rough mutant LPS of reduced molecular complexity and limited biological relevance. Here, by using neutron reflectometry, we structurally characterize planar monolayers of wild-type LPS from Escherichia coli O55:B5 featuring strain-specific O-side chains in the presence and absence of divalent cations and under controlled interaction conditions. The model used for the reflectivity analysis is self-consistent and based on the volume fraction profiles of all chemical components. The saccharide profiles are found to be bimodal, with dense inner oligosaccharides and more dilute, extended O-side chains. For interacting LPS monolayers, we establish the pressure-distance curve and determine the distance-dependent saccharide conformation.     

Role of diffusion potential on the flow of angiotensin II,bradykinin and related molecules through cellophane membranes

The diffusion of electrically charged peptides (angiotensin II, bradykinin and [Suc¹]angiotensin II) across tight cellophane membranes, obtained by different degrees of acetylation, shows a kinetic behaviour which was interpreted in the literature as indicative of the existence of different molecular conformations presenting slow interconversion velocities and different permeabilities across the membrane. A diffusion potential (Δψ) was found to be present across the membrane along diffusion experiments performed in low ionic strength. Upon annihilation of δψ by chemical voltage clamping (by equally increasing the ionic strength on both bathing solutions) the diffusion rate was decreased and the flow followed first order kinetics, indicating a major role of Δψ in the process. As the ionic strength increase could also affect molecular conformation, the role of Δψ on the diffusion of those molecules was tested by fitting flux and Δψ experimental results by an integrated form of Nernst-Planck flux equation. It is concluded that the deviation from first order diffusion kinetics, observed in low ionic strength, is solely due to the diffusion potential, and not to the existence of more than one molecular conformation in aqueous solution. This study was extended to amino acids and other related charged molecules.     

How organic molecules can control electronic devices.

This article examines a somewhat counter-intuitive approach to molecular-based electronic devices. Control over the electronic energy levels at the surfaces of conventional semiconductors and metals is achieved by assembling on the solid surfaces, poorly organized, partial monolayers (MLs) of molecules instead of the more commonly used ideal ones. Once those surfaces become interfaces, these layers exert electrostatic rather than electrodynamic control over the resulting devices, based on both electrical monopole and dipole effects of the molecules. Thus electronic transport devices, incorporating molecules, can be constructed without current flow through the molecules. This is illustrated for a gallium arsenide (GaAs) sensor as well as for gold-silicon (Au-Si) and Au-GaAs diodes. Incorporating molecules into solid interfaces becomes possible, using a 'soft' electrical contacting procedure, so as not to damage the molecules. Because there are only a few molecular restrictions, this approach opens up possibilities for the use of more complex (including biologically active) molecules as it circumvents requirements for ideal MLs and for molecules that can tolerate actual electron transport through them.     

Interactions of thrombin with fibrinogen adsorbed on methyl-, hydroxyl-, amine-, and carboxyl-terminated self-assembled monolayers

We have examined the initial phase of fibrin formation, thrombin-catalyzed fibrinopeptide cleavage, from adsorbed fibrinogen using surface plasmon resonance and liquid chromatography-mass spectrometry. Fibrinogen adsorption impaired thrombin-fibrinogen interactions compared to the interactions of thrombin with fibrinogen in solution. The properties of the underlying substrate significantly affected the extent and kinetics of fibrinopeptide cleavage, and the conversion of adsorbed fibrinogen to fibrin. Fibrinogen adsorbed on negatively charged surfaces (carboxyl-terminated self-assembled monolayers) released a smaller amount of fibrinopeptides, at a reduced rate relative to those of hydrophobic, hydrophilic, and positively charged surfaces (methyl-, hydroxyl-, and amine-terminated self-assembled monolayers, respectively). Additionally, the conversion of adsorbed fibrinogen to fibrin was comparatively inefficient at the negatively charged surface. These data correlated well with trends previously reported for fibrin proliferation as a function of surface properties. We conclude that thrombin interactions with adsorbed fibrinogen determine the extent of subsequent fibrin proliferation on surfaces.     

Characterization of spore surfaces from a Geobacillus sp. isolate by pH dependence of surface charge and infrared spectra

Aims: The surfaces of spores from a Geobacillus sp. isolated from a milk powder production line were examined to obtain fundamental information relevant to bacterial spore adhesion to materials. Materials and Results: The surfaces of spores were characterized using transmission electron microscopy and infrared spectroscopy. Thin sections of spores stained with ruthenium red revealed an exosporium with a hair‐like nap around the spores. Attenuated total reflection infrared spectra of the spores exposed to different pH solutions on a ZnSe prism revealed that pH‐sensitive carboxyl and phosphodiester groups associated with proteins and polysaccharides contributed to the spore’s negative charge which was revealed by our previous zeta potential measurements on the spores. Lowering the pH to the isoelectric point of spores resulted in an increase in intensity of all spectral bands, indicating that the spores moved closer to the zinc selenide (ZnSe) surface as the charged surface groups were neutralized and the spore surface polymers compressed. The attachment of spores to stainless steel was threefold higher at pH 3 compared with pH 7. Conclusions: This research showed that spore attachment to surfaces is influenced by electrostatic interactions, surface polymer conformation and associated steric interactions. Significance and Impact of the Study: The adhesion of thermophilic spores is largely controlled by functional groups of surface polymers and polymer conformation.     

Formation of supported phospholipid bilayers on molecular surfaces: role of surface charge density and electrostatic interaction

Electrostatic interaction is known to play important roles in the adsorption of charged lipids on oppositely charged surfaces. Here we show that, even for charge neutral (zwitterionic) lipids, electrostatic interaction is critical in controlling the adsorption and fusion of lipid vesicles to form supported phospholipid bilayers (SPBs) on surfaces. We use terminally functionalized alkanethiol self-assembled monolayers (SAMs) to systematically control the surface charge density. Charge neutral egg phophatidylcholine (eggPC) vesicles readily fuse into SPBs on either a positively charged 11-aminino-1-undecanethiol SAM or a negatively charged 10-carboxy-1-decanethiol SAM when the density of surface charge groups is > or = 80%. These processes depend critically on the buffer environment: fusion of adsorbed vesicles to form SPBs on each charged molecular surface does not occur when the molecular ion of the buffer used is of the opposite charge type. We attribute this to the high entropic repulsion (electric double layer repulsion) due to the large size of molecular counterions. On the other hand, such a critical dependence on buffer type is not observed when charged lipids are used. This study suggests the general importance of controlling electrostatic interaction in the formation of stable SPBs.     

The Role of histidine residues in low-pH-mediated viral membrane fusion

A central event in the invasion of a host cell by an enveloped virus is the fusion of viral and cell membranes. For many viruses, membrane fusion is driven by specific viral surface proteins that undergo large-scale conformational rearrangements, triggered by exposure to low pH in the endosome upon internalization. Here, we present evidence suggesting that in both class I (helical hairpin proteins) and class II (beta-structure-rich proteins) pH-dependent fusion proteins the protonation of specific histidine residues triggers fusion via an analogous molecular mechanism. These histidines are located in the vicinity of positively charged residues in the prefusion conformation, and they subsequently form salt bridges with negatively charged residues in the postfusion conformation. The molecular surfaces involved in the corresponding structural rearrangements leading to fusion are highly conserved and thus might provide a suitable common target for the design of antivirals, which could be active against a diverse range of pathogenic viruses.     

Deconstructing the DGAT1 Enzyme: Membrane Interactions at Substrate Binding Sites

Diacylglycerol acyltransferase 1 (DGAT1) is a key enzyme in the triacylglyceride synthesis pathway. Bovine DGAT1 is an endoplasmic reticulum membrane-bound protein associated with the regulation of fat content in milk and meat. The aim of this study was to evaluate the interaction of DGAT1 peptides corresponding to putative substrate binding sites with different types of model membranes. Whilst these peptides are predicted to be located in an extramembranous loop of the membrane-bound protein, their hydrophobic substrates are membrane-bound molecules. In this study, peptides corresponding to the binding sites of the two substrates involved in the reaction were examined in the presence of model membranes in order to probe potential interactions between them that might influence the subsequent binding of the substrates. Whilst the conformation of one of the peptides changed upon binding several types of micelles regardless of their surface charge, suggesting binding to hydrophobic domains, the other peptide bound strongly to negatively-charged model membranes. This binding was accompanied by a change in conformation, and produced leakage of the liposome-entrapped dye calcein. The different hydrophobic and electrostatic interactions observed suggest the peptides may be involved in the interactions of the enzyme with membrane surfaces, facilitating access of the catalytic histidine to the triacylglycerol substrates.     

Self-programmable,Self-assembling Two-dimensional Genetic Matter

Putative two-dimensional coding systems can beconstructed from aqueous solutions of purine andpyrimidine nucleic acid bases evaporated at moderatetemperatures on the surfaces of inorganic solids. Theresultant structures are monolayers which are formedspontaneously by molecular self-assembly and they havebeen observed with molecular resolution by scanningtunnelling microscopy (STM). When formed fromsolutions of a single base, the monolayers of adenineand uracil have crystalline characteristics and theSTM images can be interpreted in terms of thegeometrical placement of planar arranged moleculesthat interact laterally by intermolecular hydrogenbonding. When formed from solutions containing amixture of adenine and uracil, the monolayers haveaperiodic structures. Small crystalline domainswithin these monolayers can be interpreted in terms ofthe single phase configurations of the molecules andthe remaining aperiodic structures can presumably beinterpreted, geometrically, in terms of the 21theoretically possible adenine-adenine, uracil-uraciland adenine-uracil hydrogen bonding interactions. Wepropose that combinatorial arrangements of planararranged purine and pyrimidine bases could provide thenecessary complexity to act as a primitive geneticmechanism and may have relevance to the origin of life.     

Electrical discontinuity of tissue substitute models at 27.12 MHz

Tissue-substitute models consisting of layers of synthetic, electrically equivalent subcutaneous fat, muscle, and bone shaped in conformation with the normal anatomy are used for rapid determination of distribution of temperature and specific absorption rate throughout the tissues when exposed to electromagnetic radiation. The surfaces of the bisected models are approximated during a short exposure period, then separated and scanned with a thermograph. A method was developed to eliminate the electrical discontinuity at the bisected surfaces while allowing separation and subsequent thermographic scanning. A thin layer of silk screen wetted with propylene glycol saturated with sodium chloride was used at the fat interface and a 0.9% sodium chloride solution was used to wet the screen at the muscle interface to eliminate electrical discontinuity during exposure to 27.12-MHz diathermy. Tests showed that in the presence of an electrical discontinuity the heating pattern was grossly distorted. With the method used, the electrical discontinuity is minimized and the subsequent thermographic scanning reveals that the heating pattern is equivalent to that of an intact model.     

Sum-frequency generation spectroscopy of DNA monolayers

The anchoring of thiolated single-stranded DNA (HS-ssDNA) monolayers onto platinum substrates was investigated by sum-frequency generation spectroscopy. Different buffer solutions were used for the preparation of the adlayers. Vibrational fingerprints in the 2700-3100 cm(-1) spectral range showed the intercalation of Tris/EDTA (TE) buffer molecules within the HS-ssDNA self-assembled monolayer. Buffer contribution to SFG can be quenched either by using SFG inactive molecules like KH(2)PO(4)/K(2)HPO(4)/NaCl (PBS) or by repeated rinsing of the DNA layer with pure water. Comparing the SFG spectra of HS-ssDNA and mercaptohexanol (MCH), which had been self-assembled onto the same substrate, enabled us to infer ordering of the anchor arms and strong disordering of the DNA strands of HS-ssDNA monolayers self-assembled on platinum.