Comparison of the A-T rich regions and the Bacillus subtilis RNA polymerase binding sites in phage ø29

By using a modification of the BAC spreading method for mounting the DNA for electron microscopy, partial denaturation maps of protein-free ø29 DNA and of ø29 DNA containing protein p3 were obtained. In ø29 P3-DNA1 the protein does not seem to influence the melting of the ends of the molecules. The comparison of the partial denaturation map and the B. subtilis RNA polymerase binding sites indicates that five of the seven early promoters (Al, A2, A3, B2 and C2) are located in A-T rich DNA regions whereas the other two early promoters (Bl and Cl) are located in less A-T rich sites.Peer reviewe

Transformation from Kinetically into Thermodynamically Controlled Self-Organization of Complex Helical Columns with 3D Periodicity Assembled from Dendronized Perylene Bisimides

The dendronized perylene 3,4:9,10-tetracarboxylic acid bisimide (PBI), (3,4,5)­12G1-1-PBI, was reported by our laboratory to self-assemble into complex helical columns containing dimers of dendronized PBI with one molecule in each stratum, with different intra- and interdimer rotation angles but identical intra- and interdimer distance of 3.5 Å, exhibiting a four-strata 2₁ helical repeat. A thermodynamically controlled 2D columnar hexagonal phase with short-range intracolumnar order represents the thermodynamic product at high temperature, while a kinetically controlled monoclinic columnar array with 3D periodicity is the thermodynamic product at low temperature. With heating and cooling rates higher than 10 °C/min to 1 °C/min, at low temperature the 2D columnar periodic array is the kinetic product for this dendronized PBI. Here the synthesis and structural analysis of a library of (3,4,5)<i>n</i>G1-<i>m</i>-PBI with <i>n</i> = 12 to 6 and <i>m</i> = 1 are reported. A combination of differential scanning calorimetry, X-ray diffraction on powder and orientated fibers, including pattern simulation and electron density map reconstruction, and solid-state NMR, all as a function of temperature and heating and cooling rate, was employed for their structural analysis. It was discovered that at low temperature the as-prepared <i>n</i> = 12 to 10 exhibit a 3D layered array that transforms irreversibly into columnar periodicities during heating and cooling. Also the kinetically controlled 3D columnar phase of <i>n</i> = 12 becomes thermodynamically controlled for <i>n</i> = 10, 9, 8, 7, and 6. This unprecedented transformation is expected to facilitate the design of functions from dendronized PBI and other self-assembling building blocks

Characterization of Fibrous Aggregated Morphologies and Other Complex Architectures Self-Assembled from Helical Alkyne and Triazole Polycarbodiimides (<i>R</i>)- and (<i>S</i>)‑Families in the Bulk and Thin Film

We report here the self-assembly studies of 22 polycarbodiimides (PCDs) in complex morphologies such as fibers, looped fibers, fibrous networks, ribbons, worm-like aggregates, toroidal structures, and craters that were examined by combination of TMAFM, TEM, SEM, and powder XRD methods as well as semiempirical modeling. Morphology characterization in the thin film (TMAFM, TEM) and in bulk (SEM, pXRD) revealed the formation of fiber-like aggregates assembled from the bundles of individual helices. In certain cases superhelical motifs of both right- and left-handed screw senses were identified. It seemed likely that the great variety of morphologies observed is a result of extensive hydrophobic side chain/side chain interactions of the singular polycarbodiimide strands

Complex Columnar Hexagonal Polymorphism in Supramolecular Assemblies of a Semifluorinated Electron-Accepting Naphthalene Bisimide

Simple synthetic methods for a strongly electron-accepting naphthalene bisimide (NBI) derivative functionalized with a new environmentally friendly chiral racemic semifluorinated alkyl group and with AB₃ minidendrons containing the same semifluorinated group are reported. The semifluorinated dendron was attached to the imide groups of the NBI via one, two, and three (<i>m</i> = 1, 2, 3) methylenic units. The NBI-containing semifluorinated groups and the dendronized NBI with <i>m</i> = 1 and 2 self-organize into lamellar crystals. The dendronized NBI with <i>m</i> = 3 self-assembles into an unprecedentedly complex and ordered column that self-organizes in a columnar hexagonal periodic array. This array undergoes a continuous transition to a columnar hexagonal superlattice that does not display a first-order phase transition during analysis by differential scanning calorimetry at heating and cooling rates of 10 and 1 °C/min. These complex columnar hexagonal periodic arrays with intramolecular order could be elucidated only by a combination of powder and fiber X-ray diffraction studies and solid-state NMR experiments. The lamellar crystals self-organized from <i>m</i> = 1 and the two highly ordered columnar hexagonal periodic arrays of <i>m</i> = 3 are assembled via thermodynamically controlled processes. Since strongly electron-accepting derivatives are of great interest to replace fullerene acceptors in organic photovoltaics and for other supramolecular electronic materials, the multitechnique structural analysis methodology elaborated here must be taken into consideration in all related studies

Screening Libraries of Semifluorinated Arylene Bisimides to Discover and Predict Thermodynamically Controlled Helical Crystallization

Synthesis, structural, and retrostructural analysis of a library containing 16 self-assembling perylene (PBI), 1,6,7,12-tetrachloroperylene (Cl₄PBI), naphthalene (NBI), and pyromellitic (PMBI) bisimides functionalized with environmentally friendly AB₃ chiral racemic semifluorinated minidendrons at their imide groups via <i>m</i> = 0, 1, 2, and 3 methylene units is reported. These semifluorinated compounds melt at lower temperatures than homologous hydrogenated compounds, permitting screening of all their thermotropic phases via structural analysis to discover thermodynamically controlled helical crystallization from propeller-like, cogwheel, and tilted molecules as well as lamellar-like structures. Thermodynamically controlled helical crystallization was discovered for propeller-like PBI, Cl₄PBI and NBI with <i>m</i> = 0. Unexpectedly, assemblies of twisted Cl₄PBIs exhibit higher order than those of planar PBIs. PBI with <i>m</i> = 1, 2, and 3 form a thermodynamically controlled columnar hexagonal 2D lattice of tilted helical columns with intracolumnar order. PBI and Cl₄PBI with <i>m</i> = 1 crystallize via a recently discovered helical cogwheel mechanism, while NBI and PMBI with <i>m</i> = 1 form tilted helical columns. PBI, NBI and PMBI with <i>m</i> = 2 generate lamellar-like structures. 3D and 2D assemblies of PBI with <i>m</i> = 1, 2, and 3, NBI with <i>m</i> = 1 and PMBI with <i>m</i> = 2 exhibit 3.4 Å π–π stacking. The library approach applied here and in previous work enabled the discovery of six assemblies which self-organize via thermodynamic control into 3D and 2D periodic arrays, and provides molecular principles to predict the supramolecular structure of electronically active components

“Single–Single” Amphiphilic Janus Dendrimers Self-Assemble into Uniform Dendrimersomes with Predictable Size

An accelerated modular synthesis of six libraries containing 29 amphiphilic Janus dendrimers, employed to discover and predict functions <i>via</i> primary structures, is reported. These dendrimers were constructed from a single hydrophobic and a single hydrophilic dendron, interconnected with l-Ala to form two constitutional isomeric libraries, with Gly to produce one library, and with l-propanediol ester to generate two additional constitutional isomeric libraries. They are denoted “single–single” amphiphilic Janus dendrimers. Assemblies obtained by injection of their ethanol solution into water were analyzed by dynamic light scattering and cryogenic transmission electron microscopy. A diversity of complex structures including soft and hard dendrimersomes, cubosomes, solid lamellae, and rod-like micelles were obtained in water. It was discovered that the “single–single” amphiphilic Janus dendrimers containing three triethylene glycol groups in the hydrophilic dendron favored the formation of dendrimersomes. Assemblies in bulk analyzed by differential scanning calorimetry and powder X-ray diffraction revealed that the amphiphilic Janus dendrimers with melting point or glass transition below room temperature self-assemble into soft dendrimersomes in water, while those with higher temperature transitions produce hard assemblies. In the range of concentrations where their size distribution is narrow, the diameter of the dendrimersomes is predictable by the <i>d</i>-spacing of their assemblies in bulk. These results suggested the synthesis of Library 6 containing two simpler constitutional isomeric benzyl ester based amphiphilic Janus dendrimers that self-assemble in water into soft dendrimersomes and multidendrimersome dendrimersomes with predictable dimensions