6 research outputs found
Comparison of the A-T rich regions and the Bacillus subtilis RNA polymerase binding sites in phage Ćø29
By using a modification of the BAC spreading method for mounting the DNA for electron microscopy, partial denaturation maps of protein-free Ćø29 DNA and of Ćø29 DNA containing protein p3 were obtained. In Ćø29 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)Ā12G1-1-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
Ć
, exhibiting a four-strata 2<sub>1</sub> 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 Ā°C/min to 1 Ā°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>)āFamilies 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 AB<sub>3</sub> 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 Ā°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
(Cl<sub>4</sub>PBI), naphthalene (NBI), and pyromellitic (PMBI) bisimides
functionalized with environmentally friendly AB<sub>3</sub> 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, Cl<sub>4</sub>PBI and NBI with <i>m</i> = 0. Unexpectedly, assemblies
of twisted Cl<sub>4</sub>PBIs 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 Cl<sub>4</sub>PBI 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 Ć
ĻāĻ 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
āSingleāSingleā 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 āsingleāsingleā 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 āsingleāsingleā 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