Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch.

Turnip crinkle virus contains a T-shaped, ribosome-binding, translation enhancer (TSS) in its 3'UTR that serves as a hub for interactions throughout the region. The viral RNA-dependent RNA polymerase (RdRp) causes the TSS/surrounding region to undergo a conformational shift postulated to inhibit translation. Using optical tweezers (OT) and steered molecular dynamic simulations (SMD), we found that the unusual stability of pseudoknotted element H4a/Ψ3 required five upstream adenylates, and H4a/Ψ3 was necessary for cooperative association of two other hairpins (H5/H4b) in Mg2+. SMD recapitulated the TSS unfolding order in the absence of Mg2+, showed dependence of the resistance to pulling on the 3D orientation and gave structural insights into the measured contour lengths of the TSS structure elements. Adenylate mutations eliminated one-site RdRp binding to the 3'UTR, suggesting that RdRp binding to the adenylates disrupts H4a/Ψ3, leading to loss of H5/H4b interaction and promoting a conformational switch interrupting translation and promoting replication.

FDA Regulation of Neurological and Physical Medicine Devices: Access to Safe and Effective Neurotechnologies for All Americans.

The United States Food and Drug Administration (FDA) ensures that patients in the U.S. have access to safe and effective medical devices. The Division of Neurological and Physical Medicine Devices reviews medical technologies that interface with the nervous system. This article addresses how to navigate the FDA's regulatory landscape to successfully bring medical devices to patients.

Polystyrene as a model system to probe the impact of ambient gas chemistry on polymer surface modifications using remote atmospheric pressure plasma under well-controlled conditions.

An atmospheric pressure plasma jet (APPJ) was used to treat polystyrene (PS) films under remote conditions where neither the plume nor visible afterglow interacts with the film surface. Carefully controlled conditions were achieved by mounting the APPJ inside a vacuum chamber interfaced to a UHV surface analysis system. PS was chosen as a model system as it contains neither oxygen nor nitrogen, has been extensively studied, and provides insight into how the aromatic structures widespread in biological systems are modified by atmospheric plasma. These remote treatments cause negligible etching and surface roughening, which is promising for treatment of sensitive materials. The surface chemistry was measured by X-ray photoelectron spectroscopy to evaluate how ambient chemistry, feed gas chemistry, and plasma-ambient interaction impact the formation of specific moieties. A variety of oxidized carbon species and low concentrations of NOx species were measured after APPJ treatment. In the remote conditions used in this work, modifications are not attributed to short-lived species, e.g., O atoms. It was found that O3 does not correlate with modifications, suggesting that other long-lived species such as singlet delta oxygen or NOx are important. Indeed, surface-bound NO3 was observed after treatment, which must originate from gas phase NOx as neither N nor O are found in the pristine film. By varying the ambient and feed gas chemistry to produce O-rich and O-poor conditions, a possible correlation between the oxygen and nitrogen composition was established. When oxygen is present in the feed gas or ambient, high levels of oxidation with low concentrations of NO3 on the surface were observed. For O-poor conditions, NO and NO2 were measured, suggesting that these species contribute to the oxidation process, but are easily oxidized when oxygen is present. That is, surface oxidation limits and competes with surface nitridation. Overall, surface oxidation takes place easily, but nitridation only occurs under specific conditions with the overall nitrogen content never exceeding 3%. Possible mechanisms for these processes are discussed. This work demonstrates the need to control plasma-ambient interactions and indicates a potential to take advantage of plasma-ambient interactions to fine-tune the reactive species output of APP sources, which is required for specialized applications, including polymer surface modifications and plasma medicine.

Direct observation of dynamic mechanical regulation of DNA condensation by environmental stimuli.

Gene delivery is a promising way to treat hereditary diseases and cancer; however, there is little understanding of DNA:carrier complex mechanical properties, which may be critical for the protection and release of nucleic acids. We applied optical tweezers to directly measure single-molecule mechanical properties of DNA condensed using 19-mer poly-L-lysine (PLL) or branched histidine-lysine (HK) peptides. Force-extension profiles indicate that both carriers condense DNA actively, showing force plateaus during stretching and relaxation cycles. As the environment such as carrier concentration, pH, and the presence of zinc ions changes, DNA:HK complexes showed dynamically regulated mechanical properties at multiple force levels. The fundamental knowledge from this study can be applied to design a mechanically tailored complex which may enhance transfection efficiency by controlling the stability of the complex temporally and spatially.

Enhanced silencing and stabilization of siRNA polyplexes by histidine-mediated hydrogen bonds.

Branched peptides containing histidines and lysines (HK) have been shown to be effective carriers for DNA and siRNA. We anticipate that elucidation of the binding mechanism of HK with siRNA will provide greater insight into the self-assembly and delivery of the HK:siRNA polyplex. Non-covalent bonds between histidine residues and nucleic acids may enhance the stability of siRNA polyplexes. We first compared the polyplex biophysical properties of a branched HK with those of branched asparagine-lysine peptide (NK). Consistent with siRNA silencing experiments, gel electrophoresis demonstrated that the HK siRNA polyplex maintained its integrity with prolonged incubation in serum, whereas siRNA in complex with NK was degraded in a time-dependent manner. Isothermal titration calorimetry of various peptides binding to siRNA at pH 7.3 showed that branched polylysine, interacted with siRNA was initially endothermic, whereas branched HK exhibited an exothermic reaction at initial binding. The exothermic interaction indicates formation of non-ionic bonds between histidines and siRNA; purely electrostatic interaction is entropy-driven and endothermic. To investigate the type of non-ionic bond, we studied the protonation state of imidazole rings of a selectively (15)N labeled branched HK by heteronuclear single quantum coherence NMR. The peak of Nδ1-H tautomers of imidazole shifted downfield (in the direction of deprotonation) by 0.5-1.0 ppm with addition of siRNA, providing direct evidence that histidines formed hydrogen bonds with siRNA at physiological pH. These results establish that histidine-rich peptides form hydrogen bonds with siRNA, thereby enhancing the stability and biological activity of the polyplex in vitro and in vivo.

Direct observation of amyloid nucleation under nanomechanical stretching.

Self-assembly of amyloid nanofiber is associated with both functional biological and pathological processes such as those in neurodegenerative diseases. Despite intensive studies, the stochastic nature of the process has made it difficult to elucidate a molecular mechanism for the key amyloid nucleation event. Here we investigated nucleation of the silk-elastin-like peptide (SELP) amyloid using time-lapse lateral force microscopy (LFM). By repeated scanning of a single line on a SELP-coated mica surface, we observed a sudden stepwise height increase. This corresponds to nucleation of an amyloid fiber, which subsequently grew perpendicular to the scanning direction. The lateral force profiles followed either a worm-like chain model or an exponential function, suggesting that the atomic force microscopy (AFM) tip stretches a single or multiple SELP molecules along the scanning direction. The probability of nucleation correlated with the maximum stretching force and extension, implying that stretching of SELP molecules is a key molecular event for amyloid nucleation. The mechanically induced nucleation allows for positional and directional control of amyloid assembly in vitro, which we demonstrate by generating single nanofibers at predetermined nucleation sites.

Direct force measurement of single DNA-peptide interactions using atomic force microscopy.

The selective interactions between DNA and miniature (39 residues) engineered peptide were directly measured at the single-molecule level by using atomic force microscopy. This peptide (p007) contains an α-helical recognition site similar to leucine zipper GCN4 and specifically recognizes the ATGAC sequence in the DNA with nanomolar affinity. The average rupture force was 42.1 pN, which is similar to the unbinding forces of the digoxigenin-antidigoxigenin complex, one of the strongest interactions in biological systems. The single linear fit of the rupture forces versus the logarithm of pulling rates showed a single energy barrier with a transition state located at 0.74 nm from the bound state. The smaller koff compared with that of other similar systems was presumably due to the increased stability of the helical structure by putative folding residues in p007. This strong sequence-specific DNA-peptide interaction has a potential to be utilized to prepare well-defined mechanically stable DNA-protein hybrid nanostructures.

Directed patterning of the self-assembled silk-elastin-like nanofibers using a nanomechanical stimulus.

We investigate the effects of the frequency and density of a nanomechanical stimulus on nucleation and growth of silk-elastin-like protein polymer (SELP) nanofibers. Repetitive tappings are crucial to create nucleation areas and a potential molecular level mechanism was proposed. Using this technique mechanically guided nanofiber patterns were successfully created.

Electrochemical synthesis and one step modification of PMProDot nanotubes and their enhanced electrochemical properties.

Poly (3,4-(2-methylene)propylenedioxythiophene) (PMProDot) nanotubes were synthesized within the pores of polycarbonate and were further modified with styrene and vinylcarbazole by a one step electrochemical method through the methylene functional group. The enhanced electrochemical and electrochromic properties of composite nanotubes were investigated using FTIR, UV/Vis absorbance spectroscopy, and AFM.

Single-molecule methods to study cell adhesion molecules.

Single molecule techniques are used to characterize the biophysical properties of individual molecules in a mechanically well-controlled environment. The information obtained from direct force measurements can provide the dynamic adhesion forces of cell adhesion molecules, which may shed insights on molecular mechanisms of cellular adhesion. In addition, single-molecule techniques enable us to observe the detailed distributions of individual molecular behaviors that cannot be readily obtained from ensemble measurements. In this chapter, the protocols of using atomic force microscopy and optical tweezers to study cell adhesion molecules are presented.

Nanomechanical stimulus accelerates and directs the self-assembly of silk-elastin-like nanofibers.

One-dimensional nanostructures are ideal building blocks for functional nanoscale assembly. Peptide-based nanofibers have great potential in building smart hierarchical structures due to their tunable structures at the single residue level and their ability to reconfigure themselves in response to environmental stimuli. We observed that pre-adsorbed silk-elastin-based protein polymers self-assemble into nanofibers through conformational changes on a mica substrate. Furthermore, we demonstrate that the rate of self-assembly was significantly enhanced by applying a nanomechanical stimulus using atomic force microscopy. The orientation of the newly grown nanofibers was mostly perpendicular to the scanning direction, implying that the new fiber assembly was locally activated with directional control. Our method provides a novel way to prepare nanofiber patterned substrates using a bottom-up approach.

Surface Induced nanofiber growth by self-assembly of a silk-elastin-like protein polymer.

Many synthetic and natural peptides are known to self-assemble to form various nanostructures. During the self-assembling process, environmental conditions such as salt concentration, pH, temperature, and surface characteristics play a critical role by influencing intermolecular interactions, and hence the process of self-assembly. Here we studied the self-assembly of a genetically engineered protein polymer composed of silk-like and elastin-like repeats on a mica surface. Silk-elastin-like protein polymers (SELPs) consist of tandem repeats of Gly-Ala-Gly-Ala-Gly-Ser from Bombyx mori (silkworm) and Gly-Val-Gly-Val-Pro from mammalian elastin. At a very low polymer concentration of 1 mug/mL, SELPs self-assembled into nanofibrous structures on a mica surface. Examination using atomic force microscopy (AFM) and dynamic light scattering techniques showed that SELPs self-assembled into nanofibers in the presence of the mica surface but not in the bulk state. Ionic strength had a significant influence on nanofiber growth, indicating the importance of electrostatic interactions between the polymer and the mica surface. At low ionic strength, the kinetics of nanofiber growth showed that the mica surface effectively removed a lag phase by providing nucleating sites, facilitating nanofiber self-assembly of SELPs. Furthermore, self-assembly on additional substrates such as silicon and a hydrophobic pyrolytic carbon surface revealed that the charged hydrophilic surface provides the optimal surface to facilitate self-assembly of SELPs.

Nanomechanics of opposing glycosaminoglycan macromolecules.

In this study, the net intermolecular interaction force between a chondroitin sulfate glycosaminoglycan (GAG)-functionalized probe tip and an opposing GAG-functionalized planar substrate was measured as a function of probe tip-substrate separation distance in aqueous electrolyte solutions using the technique of high resolution force spectroscopy. A range of GAG grafting densities as near as possible to native cartilage was used. A long-range repulsive force between GAGs on the probe tip and substrate was observed, which increased nonlinearly with decreasing separation distance between probe tip and substrate. Data obtained in 0.1 M NaCl was well predicted by a recently developed Poisson-Boltzmann-based theoretical model that describes normal electrostatic double layer interaction forces between two opposing surfaces of end-grafted, cylindrical rods of constant volume charge density and finite length, which interdigitate upon compression. Based on these results, the nanomechanical data and interdigitated rod model were used together to estimate the electrostatic component of the equilibrium modulus of cartilage tissue, which was then compared to that of normal adult human ankle cartilage measured in uniaxial confined compression.