PHOTOREACTION OF PSORALEN DERIVATIVES WITH STRUCTURALLY ORGANIZED DNA

Abstract— The DNA-photobinding process of a number of psoralen derivatives has been investigated using different nucleic acid structures, such as double helical DNA, nucleosomes, and chromatin under various ionic strength conditions. Important differences were observed using "free" vs organised DNA as the target macromolecule, which are related to conformational, stereochemical, ionic and competition effects. The furocoumarin chemical nature also plays a role; in particular, charged compounds are shown to be more reactive than uncharged analogues with free DNA at low salt concentration, whereas a levelling off in photobinding efficiency occurs on increasing ionic strength and nucleic acid complexity. These results allow an explanation for the photobiological effects of the examined psoralens.     

Trismaleimide Dendrimers: Helix‐to‐Superhelix Supramolecular Transition Accompanied by White‐Light Emission

Reported here are unprecedented fluorescent superhelices composed of primary, supramolecular polymers of the opposite helical twist. A new class of functional dendrimers was synthesized by amino‐ene click reactions, and they demonstrate an alternating OFF/ON fluorescence with generation growth. A peripherally alkyl‐modified dendrimer displays helix‐sense‐selective supramolecular polymerization, which predominantly forms right‐handed (or left‐handed) helical supramolecular polymers in the solution containing chiral solvents. With increasing the concentration, these primary helical supramolecular polymers spontaneously twist around themselves in the opposite direction to form superhelical structures. Atomic force microscopy and circular dichroism measurements were used to directly observe the helix‐to‐superhelix transition occurring with a reversal in the helical direction. Exceptional white‐light emission was observed during superhelix formation.     

Magnetic alignment of the chiral nematic phase of a cellulose microfibril suspension

Stable suspensions of tunicate cellulose microfibrils were prepared by acid hydrolysis of the cellulosic mantles of tunicin. They formed a chiral nematic phase above a critical concentration. External magnetic fields were applied to the chiral nematic phase in two different manners to control its phase structure. (i) Static magnetic fields ranging 1-28 T were used to align the chiral nematic axis (helical axis) in the field direction. (ii) A rotating magnetic field (5 T, 10 rpm) was applied to unwind the helices and to form a nematic phase. These phenomena were interpreted in terms of the anisotropic diamagnetic susceptibility of the cellulose microfibril. The diamagnetic susceptibility of the microfibril is smaller in the direction parallel (chi( parallel)) to the fiber axis than in the direction perpendicular (chi( perpendicular)) to the fiber axis, that is, chi( parallel) < chi( perpendicular) < 0. Because the helical axis coincides with the direction normal ( perpendicular) to the fiber axis, the helical axis aligned parallel to the applied field. On the other hand, the rotating magnetic field induced the uniaxial alignment of the smallest susceptibility axis, that is, chi( parallel) in the present case, and brought about unwinding of the helices.     

DNA cholesteric phases: the role of DNA molecular chirality and DNA-DNA electrostatic interactions

DNA molecules form dense liquid-crystalline twisted phases both in vivo and in vitro. How the microscopic DNA chirality is transferred into intermolecular twist in these mesophases and what is the role of chiral DNA-DNA electrostatic interactions is still not completely clear. In this paper, we first give an extended overview of experimental observations on DNA cholesteric phases and discuss the factors affecting their stability. Then, we consider the effects of steric and electrostatic interactions of grooved helical molecules on the sign of cholesteric twist. We present some theoretical results on the strength of DNA-DNA chiral electrostatic interactions, on DNA-DNA azimuthal correlations in cholesteric phases, on the value of DNA cholesteric pitch, and on the regions of existence of DNA chiral phases stabilized by electrostatic interactions. We suggest for instance that 146 bp long DNA fragments with stronger affinities for the nucleosome formation can form less chiral cholesteric phases, with a larger left-handed cholesteric pitch. Also, the value of left-handed pitch formed in assemblies of homologous DNA fragments is predicted to be smaller than that of randomly sequenced DNAs. We expect also the cholesteric assemblies of several-kbp-long DNAs to require higher external osmotic pressures for their stability than twisted phases of short nucleosomal DNA fragments at the same DNA lattice density.     

Understanding the Signatures of Secondary‐Structure Elements in Proteins with Raman Optical Activity Spectroscopy

A prerequisite for the understanding of functional molecules like proteins is the elucidation of their structure under reaction conditions. Chiral vibrational spectroscopy is one option for this purpose, but provides only indirect access to this structural information. By first‐principles calculations, we investigate how Raman optical activity (ROA) signals in proteins are generated and how signatures of specific secondary‐structure elements arise. As a first target we focus on helical motifs and consider polypeptides consisting of twenty alanine residues to represent α‐helical and 3₁₀‐helical secondary‐structure elements. Although ROA calculations on such large molecules have not been carried out before, our main goal is the stepwise reconstruction of the ROA signals. By analyzing the calculated ROA spectra in terms of rigorously defined localized vibrations, we investigate in detail how total band intensities and band shapes emerge. We find that the total band intensities can be understood in terms of the reconstructed localized vibrations on individual amino acid residues. Two different basic mechanisms determining the total band intensities can be established, and it is explained how structural changes affect the total band intensities. The band shapes can be rationalized in terms of the coupling between the localized vibrations on different residues, and we show how different band shapes arise as a consequence of different coupling patterns. As a result, it is demonstrated for the chiral variant of Raman spectroscopy how collective vibrations in proteins can be understood in terms of well‐defined localized vibrations. Based on our calculations, we extract characteristic ROA signatures of α helices and of 3₁₀‐helices, which our analysis directly relates to differences in secondary structure.     

Formation of triple helical nanofibers using self-assembling chiral benzene-1,3,5-tricarboxamides and reversal of the nanostructure's handedness using mirror image building blocks

Intertwining triple helical nanofibers with an overall handedness have been formed from self-assembling chiral benzene-1,3,5-tricarboxamides , and , whereas the achiral benzene-1,3,5-tricarboxamide upon self-association gives rise to straight nanofibers without any twist and transmission electron microscopy images of chiral compounds clearly demonstrate that the handedness of the triple helical nanofibers can be reversed by using the enantiomeric benzene-1,3,5-tricarboxamide building blocks.     

A chirality indicator for the walls and the surfaces of silica nanotubes

Single-handed helical silica nanotubes were prepared according to the literature procedures,using the self-assemblies of a pair of chiral cationic low-molecular-weight gelators as the templates.A chirality indicator,4,4’-bis(triethoxysilyl)-1,1’-biphenyl,was developed to determine the chirality of the silica nanotubes.The chirality of the surfaces and the bulky walls of the silica nanotubes were understood from the twist of the biphenylene rings.     

Synthesis and structure of a helical diindenophenanthrene with four congested phenyl substituents as a molecular spiral staircase

Treatment of 9 with potassium tert-butoxide produced 10 having a helical twist in a single operation. The X-ray structure of 10 shows that the four phenyl substituents are essentially parallel to one another but are virtually perpendicular to the helical axis of the diindenophenanthrene ring system. Viewing from the direction perpendicular to the helical axis, the structure of 10 resembles that of a segment of a spiral staircase having four parallel steps.     

Helical Mechanoclinic Deformation of Main‐Chain Chiral Smectic Elastomers

The helical mechanoclinic deformation of a main‐chain chiral smectic elastomer, which is prepared by a crosslinking reaction under twist deformation, is investigated. The twist deformation induces a layer tilt angle that depends on the handedness of twist. The layer tilt angle in the right‐handedly twisted elastomer, of which the handedness is consistent with that of the helix in the SmC* phase of the non‐crosslinked backbone polymer, is estimated to be up to 16° at room temperature, although that in the left‐handedly twisted elastomer is less than several degrees. The experiments provide evidence of chiral coupling between tilt and twist for helical mechanoclinic deformation in the chiral smectic system.

     

Helical Graphitic Carbon Nitrides with Photocatalytic and Optical Activities

Graphitic carbon nitride can be imprinted with a twisted hexagonal rod‐like morphology by a nanocasting technique using chiral silicon dioxides as templates. The helical nanoarchitectures promote charge separation and mass transfer of carbon nitride semiconductors, enabling it to act as a more efficient photocatalyst for water splitting and CO₂ reduction than the pristine carbon nitride polymer. This is to our knowledge a unique example of chiral graphitic carbon nitride that features both left‐ and right‐handed helical nanostructures and exhibits unique optical activity to circularly polarized light at the semiconductor absorption edge as well as photoredox activity for solar‐to‐chemical conversion. Such helical nanostructured polymeric semiconductors are envisaged to hold great promise for a range of applications that rely on such semiconductor properties as well as chirality for photocatalysis, asymmetric catalysis, chiral recognition, nanotechnology, and chemical sensing.     

New types of multifunctional liquid crystalline photochromic copolymers for optical data recording and storage

A new family of multifunctional chiral‐photochromic liquid crystalline (LC) copolymers containing mesogenic, chiral and photoactive groups were synthesized. The new principles of photo‐regulation of the helical supramolecular structure and optical properties of the binary and ternary chiral‐photochromic LC polymers based on the change of helical twisting power of the chiral‐photochromic monomer units, the dual photochromism and photochemical spectral gap burning were developed. It was shown, that the introduction of small amount of low‐molar‐mass chiral‐photochromic dopants in chiral LC copolymers having different helix signs followed by light irradiation permits one to twist or untwist the helical supramolecular structure. The synthesized polymers are shown to be promising candidates for colour data recording and storage.     

Helical structures induced by laterally-connected chiral twin molecules

Abstract

A novel chiral twin material, (R)-bis[5-octyloxy-2-(4-octyloxyphenoxycarbonyl)phenyl] 3-methyladipate, has been prepared, where two mesogenic parts are connected laterally by a spacer possessing a chiral centre. A weaker helical structure, in particular in the chiral smectic C (S?_c) phase, was found to be induced by the laterally-connected twin material than by the analogous terminally-connected twin material. If laterally-connected chiral twin molecules prefer to stay in the smectic layer structure so that the two mesogenic parts exist in the same smectic layer, the twist interaction between adjacent layers cannot be produced by direct correlation of motion and directions of two mesogenic parts. Thus, the helical structure in the S?_c phase induced by laterally-connected chiral twin molecules becomes weak. An analogous laterally-branched ‘monomeric’ compound, (S)-5-octyloxy-2-(4-octyloxyphenoxycarbonyl)phenyl 3-methyl-pentanoate, has also been prepared, and the induced helical structures compared.     

Ferroelectric properties of smectic C liquid crystals with induced helical structure

Ferroelectricity has been observed in liquid crystalline mixtures of chiral smectic C type with a helical structure induced by chiral guest molecules (pitch p ≈ 100 μm). Samples of thickness d?p form monodomains with finite zero-field electric polarization because the spontaneous polarization of the smectic layers is not compensated by the helical twist. The temperature dependence of the spontaneous polarization has been studied near the phase transition smectic C→ smectic A.     

Distinct Helical Molecular Orbitals through Conformational Lock**

Several theoretical studies have proposed strategies to generate helical molecular orbitals (Hel-MOs) in [n]cumulenes and oligoynes. While chiral even-[n] cumulenes feature Hel-MOs, odd-[n] cumulenes may also present them if the terminal groups lie in different planes. However, the proposed systems have been either experimentally unfeasible or resulted in opposite pseudo-degenerated Hel-MOs. We hereby demonstrate the introduction of a remarkable energy difference between helical orbitals of opposite twist by fixing the torsion angle between the terminal groups in butadiyne fragments. To experimentally lock the conformation of the terminal groups, we designed and synthesized cyclic architectures by combining acetylenes with chiral spirobifluorenes. The high stability of these systems with distinct helical orbitals allowed their isolation and full characterization. In our view, these results constitute a step further in the development of real systems presenting helical molecular orbitals.     

The effect of the position of the methyl group on the helical twisting powers of aldol condensation products of methyl cyclohexanones

The four aldol condensation products of methylcyclohexanone isomers and 4-(4-hexyloxybenzoyloxy)benzaldehyde have been prepared. These chiral products were either obtained with high enantiomeric excess or the enantiomers were separated by means of chiral HPLC. In all cases only the E-isomer was obtained. UV irradiation was used to isomerize the E-isomers to the Z-isomers. Comparison of the helical twisting powers (HTP) of the E-isomers revealed that the derivative in which the methyl group is directly next to the double bond exhibits the highest value. Although the other three E-isomers have lower HTP values, they show large HTP changes and reversal of the helical twist sense upon irradiation. Of these compounds, the one derived from the commercially available (R)-3-methylcyclohexanone is an interesting candidate for use as an alternative to compounds derived from menthone for realizing photochemically induced twist changes in twisted nematic and cholesteric materials.     

A Disulfide Switch Providing Absolute Handedness Control in Double Helices via Conversion from the Antiparallel to Parallel Helical Pattern

A strategy to reversibly switch the parallel/antiparallel helical conformation of aromatic double helices through the formation/breakage of a disulfide bond is presented. Single-crystal X-ray structures, NMR, and circular dichroism spectroscopy demonstrate that the double helices with terminal thiol groups favor an antiparallel helical arrangement both in the solid state and in solution, while the P/M bias of helicity induced by chiral segments from another extremity of the sequence is weak in this structural motif. The antiparallel helices can be rearranged to parallel helices through the disulfide connection of the sequences. This change enhances the bias of helical handedness and results in absolute chirality control of the double helices. The handedness-mediated process can be governed by the oxidation-reduction cycle, thereby switching the structural arrangement and the enhancement of chiral bias. In addition, we find that the sequences can dimerize into an intermolecular double helix with the disulfide connection. And the helical handedness is also fully controlled due to the head-to-head structural motif.     

NMR spectra of chiral smectic liquid crystals differing in helical parameters

Chiral liquid crystals with three-ring rigid core were examined. The method based on the selectively reflected light was used to determine the helical pitch. The helical twist sense was worked out using the polarimetry method. ¹H and ¹³C NMR measurements were performed. The influence of three molecular structure parameters: the type of chiral centre, the length of non-chiral chain and substitution of benzene ring by fluorine atoms, on helical pitch, handedness of helical structure and values of chemical shift in proton and carbon spectra was determined. The change of the length of non-chiral terminal chain has the most significant influence on the temperature dependence of helical pitch. All tested parameters have the biggest influence on the values of chemical shift of atoms in the chiral centre.     

Novel Ligands Incorporating Phosphinoxide Groups as Particularly Efficient Sensitizers for Lanthanide Emission

Helical molecular assemblies of bile acids and their derivatives were systematically investigated. These molecules have a common asymmetric structure with three different directions, and form characteristic inclusion crystals with the following hierarchical structure. First, such molecules arrange along their helical axes to yield the helical tapes with a definite direction. Second, the helical tapes are combined in a parallel fashion by using their side-chains through hydrogen bonds to produce chiral sheets. Third, the sheets stack together through van der Waals forces in a parallel or antiparallel fashion. Fourth, there exist chiral spaces for including guests among their sheets. Such hierarchical structure enables us to explain a role of the side-chains with different hydrogen bonding groups and length.     

Direct Observation of Dynamic Interactions between Orientation-Controlled Nucleosomes in a DNA Origami Frame

The nucleosome is one of the most fundamental units involved in gene expression and consequent cell development, differentiation, and expression of cell functions. We report here a method to place reconstituted nucleosomes into a DNA origami frame for direct observation using high-speed atomic-force microscopy (HS-AFM). By using this method, multiple nucleosomes can be incorporated into a DNA origami frame and real-time movement of nucleosomes can be visualized. The arrangement and conformation of nucleosomes and the distance between two nucleosomes can be designed and controlled. In addition, four nucleosomes can be placed in a DNA frame. Multiple nucleosomes were well accessible in each conformation. Dynamic movement of the individual nucleosomes were precisely monitored in the DNA frame, and their assembly and interaction were directly observed. Neither mica surface modification nor chemical fixation of nucleosomes is used in this method, meaning that the DNA frame not only holds nucleosomes, but also retains their natural state. This method offers a promising platform for investigating nucleosome interactions and for studying chromatin structure.