Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures.

Synthetic multichromophore systems are of great importance in artificial light harvesting devices, organic optoelectronics, tumor imaging and therapy. Here, we introduce a promising strategy for the construction of self-assembled peptide templated dye stacks based on coupling of a de novo designed pH sensitive peptide with a cyanine dye Cy5 at its N-terminus. Microscopic techniques, in particular cryogenic TEM (cryo-TEM) and cryo-electron tomography technique (cryo-ET), reveal two types of highly ordered three-dimensional assembly structures on the micrometer scale. Unbranched compact layered rods are observed at pH 7.4 and two-dimensional membrane-like assemblies at pH 3.4, both species displaying spectral features of H-aggregates. Molecular dynamics simulations reveal that the coupling of Cy5 moieties promotes the formation of both ultrastructures, whereas the protonation states of acidic and basic amino acid side chains dictates their ultimate three-dimensional organization.

The protofilament architecture of a de novo designed coiled coil-based amyloidogenic peptide.

Amyloid fibrils are polymers formed by proteins under specific conditions and in many cases they are related to pathogenesis, such as Parkinson's and Alzheimer's diseases. Their hallmark is the presence of a ß-sheet structure. High resolution structural data on these systems as well as information gathered from multiple complementary analytical techniques is needed, from both a fundamental and a pharmaceutical perspective. Here, a previously reported de novo designed, pH-switchable coiled coil-based peptide that undergoes structural transitions resulting in fibril formation under physiological conditions has been exhaustively characterized by transmission electron microscopy (TEM), cryo-TEM, atomic force microscopy (AFM), wide-angle X-ray scattering (WAXS) and solid-state NMR (ssNMR). Overall, a unique 2-dimensional carpet-like assembly composed of large coexisiting ribbon-like, tubular and funnel-like structures with a clearly resolved protofilament substructure is observed. Whereas electron microscopy and scattering data point somewhat more to a hairpin model of ß-fibrils, ssNMR data obtained from samples with selectively labelled peptides are in agreement with both, hairpin structures and linear arrangements.

Tubular J-aggregates of a new thiacarbocyanine Cy5 dye for the far-red spectral region - a spectroscopic and cryo-transmission electron microscopy study.

The aggregation behavior of a phenol-substituted thiacarbocyanine Cy5 dye (5-chloro-2-[5-[5-chloro-3-(4-sulfobutyl)-3H-benzothiazol-2-ylidene]-3-phenyl-penta-1,3-dienyl]-3-(4-sulfobutyl)-benzothiazol-3-ium hydroxide, inner salt, triethylammonium salt) in aqueous solution is investigated using steady-state absorption, linear dichroism, and fluorescence spectroscopies, as well as cryogenic transmission electron microscopy (cryo-TEM). By increasing the concentration, the dye self-assembles in pure water into dimers and H-aggregates, the latter being uniform particles of ∼2.6 nm size. In the presence of NaCl, two different types of J-aggregates are observed depending on salt concentration (varied from 10 to 100 mM). At low salt concentration (10 mM) a J-aggregate of extended mono-layered sheets prevails, which disappears after a few days, whereas a second type of J-aggregate emerges. Generally, the latter dominates in matured solutions in particular at high salt concentration and seems to be the thermodynamically stable species. This J-aggregate shows three perpendicularly polarized absorption bands and fluoresces in the far-red at around 800 nm. The most intensive and very narrow (fwhm of 238 cm-1) absorption band is centered at 796 nm. Cryo-TEM reveals uniform nanotubes of ∼7 nm diameter and micrometer length. They represent the first tubular cyanine dye J-aggregates that are active in the far-red. Moreover, the studied dye is a prime example of cyanine dyes showing two self-assembly pathways that lead to different species of J-aggregates with distinct optical and morphological properties.

Pinacyanol chloride forms mesoscopic H- and J-aggregates in aqueous solution--a spectroscopic and cryo-transmission electron microscopy study.

The aggregation behaviour of the cationic pinacyanol chloride in aqueous solution is investigated using absorption and linear dichroism spectroscopies, optical microscopy and cryogenic transmission electron microscopy (cryo-TEM). The investigations are focused on solutions in a concentration range from 50 µM up to 1 mM. At a concentration of 0.7 mM H-aggregates are detected that are characterized by a broad absorption band centred at ∼511 nm. The aggregates possess a tubular architecture with a single-layer wall thickness of ∼2.5 nm and an outer diameter of ∼6.5 nm. Linear dichroism spectroscopy indicates that the molecules are packed with their long axis parallel to the tube axis. These H-aggregates are not stable, but transform into J-aggregates on the time scale of weeks. The kinetics of J-aggregation depends on the dye concentration and the route of sample preparation, but can also be enhanced by shear stress. J-aggregates possess a split absorption spectrum composed of two longitudinally polarized J-bands and one H-band that is polarized perpendicular to the aggregate axis. The J-aggregates are ∼9 nm wide and several micrometer long fibrils consisting of stacked pairs of ribbons with a dumbbell-shaped density cross-section. Upon aging these ribbons laterally stack face-to-face to form tape-like aggregates.

Formation of α-helical nanofibers by mixing ß-structured and α-helical coiled coil peptides.

The helical coiled coil is a well-studied folding motif that can be used for the design of nanometer-sized bioinspired fibrous structures with potential applications as functional materials. A two-component system of coiled coil based model peptides is investigated, which forms, under acidic conditions, uniform, hundreds of nanometers long, and ~2.6 nm thick trimeric α-helical fibers. In the absence of the other component and under the same solvent conditions, one model peptide forms ß-sheet-rich amyloid fibrils and the other forms stable trimeric α-helical coiled coils, respectively. These observations reveal that the complementary interactions driving helical folding are much stronger here than those promoting the intermolecular ß-sheet formation. The results of this study are important in the context of amyloid inhibition but also open up new avenues for the design of novel fibrous peptidic materials.

Photoinitiated growth of sub-7 nm silver nanowires within a chemically active organic nanotubular template.

Self-assembled supramolecular nanotubes of J-aggregated amphiphilic cyanine dye in aqueous solution are employed as chemically active templates for the photoinitiated formation of silver nanowires with a very small and homogeneous diameter of (6.4 +/- 0.5) nm. Key features of the template are (1) its small and well-defined diameter; (2) its photochemical activity, which allows photoinitiation of the structure formation; and (3) the processability in aqueous solution. The latter includes the potential to remove the template after the reaction, or to functionalize it further, e.g. with optoelectronically active polycations, providing access to quasi one-dimensional hybrid structures with well-defined metallic nanowires as a core.

Complex domain architecture of multicompartment micelles from a linear ABC triblock copolymer revealed by cryogenic electron tomography.

Cryo-electron tomography of raspberry-like multicompartment micelles formed by a linear ABC triblock copolymer in water revealed that the fluorocarbon domains may be dispersed all over the hydrocarbon core.

Structure Prediction of Self-Assembled Dye Aggregates from Cryogenic Transmission Electron Microscopy, Molecular Mechanics, and Theory of Optical Spectra.

Cryogenic transmission electron microscopy (cryo-TEM) studies suggest that TTBC molecules self-assemble in aqueous solution to form single-walled tubes with a diameter of about 35 Å. In order to reveal the arrangement and mutual orientations of the individual molecules in the tube, we combine information from crystal structure data of this dye with a calculation of linear absorbance and linear dichroism spectra and molecular dynamics simulations. We start with wrapping crystal planes in different directions to obtain tubes of suitable diameter. This set of tube models is evaluated by comparing the resulting optical spectra with experimental data. The tubes that can explain the spectra are investigated further by molecular dynamics simulations, including explicit solvent molecules. From the trajectories of the most stable tube models, the short-range ordering of the dye molecules is extracted and the optimization of the structure is iteratively completed. The final structural model is a tube of rings with 6-fold rotational symmetry, where neighboring rings are rotated by 30° and the transition dipole moments of the chromophores form an angle of 74° with respect to the symmetry axis of the tube. This model is in agreement with cryo-TEM images and can explain the optical spectra, consisting of a sharp red-shifted J-band that is polarized parallel to to the symmetry axis of the tube and a broad blue-shifted H-band polarized perpendicular to this axis. The general structure of the homogeneous spectrum of this hybrid HJ-aggregate is described by an analytical model that explains the difference in redistribution of oscillator strength inside the vibrational manifolds of the J- and H-bands and the relative intensities and excitation energies of those bands. In addition to the particular system investigated here, the present methodology can be expected to aid the structure prediction for a wide range of self-assembled dye aggregates.

Towards engineering of self-assembled nanostructures using non-ionic dendritic amphiphiles.

Engineering nanostructures of defined size and morphology is a great challenge in the field of self-assembly. Herein we report on the formation of supramolecular nanostructures of defined morphologies with subtle structural changes for a new series of dendritic amphiphiles. Subsequently, we studied their application as nanocarriers for guest molecules.