Right-handed Helix Research Articles

Dynamic regulation of Z-DNA in the mouse prefrontal cortex by the RNA-editing enzyme Adar1 is required for fear extinction.

DNA forms conformational states beyond the right-handed double-helix; however, the functional relevance of these non-canonical structures in the brain remains unknown. We show that, in the prefrontal cortex of mice, the formation of one such structure, Z-DNA, is involved in the regulation of extinction memory. Z-DNA is formed during fear learning, and reduced during extinction learning, which is mediated, in part, by a direct interaction between Z-DNA and the RNA editing enzyme Adar1. Adar1 binds to Z-DNA during fear extinction learning which leads to a reduction in Z-DNA at sites where Adar1 is recruited. Knockdown of Adar1 leads to an inability to modify a previously acquired fear memory and blocks activity-dependent changes in DNA structure and RNA state; effects that are fully rescued by the introduction of full-length Adar1. These findings suggest a novel mechanism of learning-induced gene regulation dependent on both proteins which recognize DNA structure, and the state.

A Novel Twist Sensor Based on Long-Period Fiber Grating Written in Side-Helical Polished Structure

We propose a novel method to write a long-period fiber grating in helical polished structure (HPLPFG) as a twist sensor. The helical structure is polished on one side of twisting fiber by CO2 laser following either right-hand or left-hand helix direction. The sensor can discriminate the twist direction and improve the twist sensitivity, due to its asymmetric and helical refractive index distribution. The twist and temperature characteristics of the sensor have been experimentally investigated. The twist sensitivities of the sensor (right-hand direction helix) are 0.199 nm/(rad/m) and 0.141 nm/(rad/m), and the twist sensitivities of the sensor (left-hand direction helix) are −0.119 nm/(rad/m) and −0.196 nm/(rad/m) in clockwise and anti-clockwise directions, respectively. The temperature sensitivities of the two sensors are 0.060 nm/°C and 0.063 nm/°C, respectively. The novel sensor has practical application potential in twist sensing.

Liquid Crystal Networks on Thermoplastics: Reprogrammable Photo-Responsive Actuators.

Arbitrary shape (re)programming is appealing for fabricating untethered shape‐morphing photo‐actuators with intricate configurations and features. We present re‐programmable light‐responsive thermoplastic actuators with arbitrary initial shapes through spray‐coating of polyethylene terephthalate (PET) with an azobenzene‐doped light‐responsive liquid crystal network (LCN). The initial geometry of the actuator is controlled by thermally shaping and fixing the thermoplastic PET, allowing arbitrary shapes, including origami‐like folds and left‐ and right‐handed helicity within a single sample. The thermally fixed geometries can be reversibly actuated through light exposure, with fast, reversible area‐specific actuation such as winding, unwinding and unfolding. By shape re‐programming, the same sample can be re‐designed and light‐actuated again. The strategy presented here demonstrates easy fabrication of mechanically robust, recyclable, photo‐responsive actuators with highly tuneable geometries and actuation modes.

Liquid Crystal Networks on Thermoplastics: Reprogrammable Photo‐Responsive Actuators

AbstractArbitrary shape (re)programming is appealing for fabricating untethered shape‐morphing photo‐actuators with intricate configurations and features. We present re‐programmable light‐responsive thermoplastic actuators with arbitrary initial shapes through spray‐coating of polyethylene terephthalate (PET) with an azobenzene‐doped light‐responsive liquid crystal network (LCN). The initial geometry of the actuator is controlled by thermally shaping and fixing the thermoplastic PET, allowing arbitrary shapes, including origami‐like folds and left‐ and right‐handed helicity within a single sample. The thermally fixed geometries can be reversibly actuated through light exposure, with fast, reversible area‐specific actuation such as winding, unwinding and unfolding. By shape re‐programming, the same sample can be re‐designed and light‐actuated again. The strategy presented here demonstrates easy fabrication of mechanically robust, recyclable, photo‐responsive actuators with highly tuneable geometries and actuation modes.

Single-walled carbon nanotube absolute-handedness chirality assignment confirmation using metalized porphyrin's supramolecular structures via STM imaging technique.

This work reports confirmation of the experimental assignment of the absolute-handedness chirality of single-walled carbon nanotubes (SWNTs). This was achieved by applying the scanning tunneling microscopy (STM) imaging technique to a supramolecular composite consisting of a metalized porphyrin derivative (nickel-5,15-bisdodecylporphyrin [Ni-BDP]) affixed to the surfaces of chiral-concentrated SWNTs (with right-handed helix P- and left-handed helix M-). On the basis of the handedness chirality, different chiral supramolecular structures of Ni-BDP were observed on the surfaces of the two SWNT enantiomers. The incorporation of a metal center into the porphyrin ring did not significantly affect the SWNT absolute-handedness chirality assignment, the large pi-system porphyrin ring being the crucial factor. These findings will effectively pave the way towards the clear selective synthesis, separation, chemistry, and applications of SWNT enantiomers.

Towards focusing of a swarm of magnetic micro/nanomotors.

Magnetic micro- and nanoparticles propelled by a rotating magnetic field provide a new technology for targeted drug delivery. The therapeutic effect of the technology is achievable with the collective action of large groups (swarms) of the motors. Narrowing of the swarm width before it reaches the target or, vice versa, its expansion prior to deposition on the channel walls are of high importance. Here we show how such swarm tuning can be achieved using a combination of the in-plane rotating and static magnetic field acting in the same plane. Although for this asymmetric actuating field the steady synchronous solutions of the problem do not materialize, the developed approach admits an analytical consideration for the average motor orientation and propulsion. The unique property of an average motion in the actuation by an asymmetric magnetic field is the emergence of propeller's net drift in plane of the field rotation. The drift velocity can be comparable in magnitude to the propulsion velocity along the axis of the field rotation. The field-induced drift is studied in detail for achiral V-shaped and chiral helical propellers, depending on their magnetization. Finally, we suggest spatial configuration of the constant magnetic field capable of focusing/defocusing swarms of magnetic motors.

Kinetically controlled Ag+-coordinated chiral supramolecular polymerization accompanying a helical inversion.

We report kinetically controlled chiral supramolecular polymerization based on ligand–metal complex with a 3 : 2 (L : Ag+) stoichiometry accompanying a helical inversion in water. A new family of bipyridine-based ligands (d-L1, l-L1, d-L2, and d-L3) possessing hydrazine and d- or l-alanine moieties at the alkyl chain groups has been designed and synthesized. Interestingly, upon addition of AgNO3 (0.5–1.3 equiv.) to the d-L1 solution, it generated the aggregate I composed of the d-L1AgNO3 complex (d-L1 : Ag+ = 1 : 1) as the kinetic product with a spherical structure. Then, aggregate I (nanoparticle) was transformed into the aggregate II (supramolecular polymer) based on the (d-L1)3Ag2(NO3)2 complex as the thermodynamic product with a fiber structure, which led to the helical inversion from the left-handed (M-type) to the right-handed (P-type) helicity accompanying CD amplification. In contrast, the spherical aggregate I (nanoparticle) composed of the d-L1AgNO3 complex with the left-handed (M-type) helicity formed in the presence of 2.0 equiv. of AgNO3 and was not additionally changed, which indicated that it was the thermodynamic product. The chiral supramolecular polymer based on (d-L1)3Ag2(NO3)2 was produced via a nucleation–elongation mechanism with a cooperative pathway. In thermodynamic study, the standard ΔG° and ΔHe values for the aggregates I and II were calculated using the van't Hoff plot. The enhanced ΔG° value of the aggregate II compared to that of the formation of aggregate I confirms that aggregate II was thermodynamically more stable. In the kinetic study, the influence of concentration of AgNO3 confirmed the initial formation of the aggregate I (nanoparticle), which then evolved to the aggregate II (supramolecular polymer). Thus, the concentration of the (d-L1)3Ag2(NO3)2 complex in the initial state plays a critical role in generating aggregate II (supramolecular polymer). In particular, NO3− acts as a critical linker and accelerator in the transformation from the aggregate I to the aggregate II. This is the first example of a system for a kinetically controlled chiral supramolecular polymer that is formed via multiple steps with coordination structural change.

Asymmetric valley polarization and photoluminescence in MoS2/MoO3 heterostructure.

We investigate circularly polarized photoluminescence (PL) in the MoS2/MoO3 heterostructure, which was fabricated by transferring MoS2 monolayer to cover the MoO3 few layers on the SiO2/Si substrate. It is shown that the PL with the same helicity as the excitation light is dominant due to the inherent chiral optical selectivity, which allows exciting one of the valleys in MoS2 monolayer. The degree of polarization (DP), which characterizes the intensity difference of two chiral components of PL, is unequal for the right-handed and left-handed circularly polarized excitations in the MoS2/MoO3 heterostructure. This effect is different from the one in pristine MoS2. Our Raman spectra results together with ab initio calculations indicate the p-doped features of the MoS2 when it covers the MoO3 layers. Thus the possible explanation of the unequal DP is that the p-doping process generates a built-in voltage and therefore brings the difference of electron-hole overlaps between K and K' valleys. Namely the asymmetric valley polarization may be obtained in the MoS2/MoO3 heterostructure. Consequently, the circularly polarized PL caused by the electron-hole recombination at K and K' valleys manifests unequal DP for the right-handed and left-handed helix excitations. This asymmetric effect is further enhanced by decreasing the temperature in the MoS2/MoO3 heterostructure. Our investigation provides a unique platform for developing novel two-dimensional valleytronic devices.

Evidence Falsifying the Double Helix Model

Through more than 40 years of reading, thinking, searching, and experimentation, we have found that the double helix model carries some defects or incorrect information. Evidence gleaned from the literature clearly indicates that the two strands of DNA are coiled ambidextrously, rather than plectonemically. It is likely that the linking number of native chromosomal Escherichia coli (E. coli) DNA is less than 960. Presently, a clear voice is necessary to break the ice formed from decades of misleading media, questionable textbooks, and expediency. For the sake of science, we are responsible and willing to share our hard-earned knowledge, experience, and knack with the public. A promising research plan is provided for the additional falsification of the right-handed double helix model. It would be a precision hit at the Achilles’ heel of the double helix model. An appropriate conceptual shift will hopefully lead to new knowledge on the secondary structure of DNA and improve understanding of its biological functions.

Sodium [N,N′-ethylenebis(D-penicillaminato)]indate(III) tetrahydrate

The asymmetric unit of the title compound {systematic name: sodium [2-({2-[(1-carboxylato-2-methyl-2-sulfanidylpropyl)amino]ethyl}amino)-3-methyl-3-sulfanidylbutanoato-κ4 S,N,N′,S′]indate(III) tetrahydrate}, Na[In(C12H20N2O4S2)]·4H2O, contains four indate(III) complex anions {[In(D-ebp)]−; D-H4ebp = N,N′-ethyelenebis(D-penicillamine)], four sodium(I) cations and sixteen water molecules. The indate(III) anions and sodium cations are alternately connected through coordination bonds between Na+ ions and the carboxylate groups of the complex anions, forming an infinite sixfold right-handed helix along the c-axis direction. In the crystal, the helices are linked by O—H...O hydrogen bonds between water molecules bound to Na+ ions and carboxylate groups. The crystal studied was twinned via a twofold axis about [001].

Synthesis and Light‐Mediated Structural Disruption of an Azobenzene‐Containing Helical Poly(isocyanide)

Helical poly(isocyanide)s are an important class of synthetic polymers possessing a static helical structure. Since their initial discovery, numerous examples of these helices have been fabricated. In this contribution, the synthesis of a chiral, azobenzene (azo)-containing isocyanide monomer is reported. Upon polymerization with nickel(II) catalysts, a well-defined circular dichroism (CD) trace is obtained, corresponding to the formation of a right-handed polymeric helix. The helical polymer, dissolved in chloroform and irradiated with UV light (365 nm), undergoes a cis to trans isomerization of the azobenzene side-chains. After the isomerization, a change in conformation of the helix occurs, as evidenced by CD spectroscopy. When the solution is irradiated with LED light, the polymer returns to a right-handed helical conformation. To open up the possibility for chain-end post-polymerization modification of this light-responsive system, an alkyne-functionalized nickel(II) catalyst is also used in the polymerization of the azobenzene monomer, resulting in a stimuli-responsive, terminal-alkyne-containing helical poly(isocyanide).

Solvent steers chiral synthesis

Organic chemists who want to make only one of a molecule’s two enantiomers typically use chiral catalysts to steer the synthesis in the right direction. Now, researchers have shown that chiral solvents can act as the sole source of handedness in catalytic reactions that preferentially produce a single enantiomer (ACS Cent. Sci. 2019, DOI: 10.1021/acscentsci.9b00330). The method works by passing the chirality of the solvent, (R)-limonene, to a copolymer, poly(quinoxaline-2,3-diyl), or PQX, which twists into a right-handed helix. Then the helix binds a palladium catalyst, creating a chiral structure that can control the symmetry of a reaction. Michinori Suginome of Kyoto University and colleagues created the catalyst and tested it in the Suzuki-Miyaura reaction, which forms a carbon-carbon bond by coupling an aryl bromide to an aryl boronic acid. It produced the S enantiomer of the coupling product almost exclusively, with an enantiomeric excess of 98% (a 99:1 mixture of

Ligand-Rearrangement-Induced Transformation from a 3D Supramolecular Network to a Discrete Octanuclear Cluster: A Good Detector for Pb2+ and Cr2O7 2.

A three-dimensional supramolecular framework containing both left- and right-handed helixes, {[Zn(TTPA)Cl2]·1.63H2O}n (1), has been converted to a novel octanuclear cluster containing a metal–organic framework, [Zn8(ptptp)6Cl2](ClO4)2·4CH3OH·2H2O (1b), induced by ligand rearrangement during a solvothermal process. The luminescent properties of 1b indicate that the material can act as a selective probe toward Pb2+ and Cr2O72–.

Perspectives for Applying G-Quadruplex Structures in Neurobiology and Neuropharmacology.

The most common form of DNA is a right-handed helix or the B-form DNA. DNA can also adopt a variety of alternative conformations, non-B-form DNA secondary structures, including the DNA G-quadruplex (DNA-G4). Furthermore, besides stem-loops that yield A-form double-stranded RNA, non-canonical RNA G-quadruplex (RNA-G4) secondary structures are also observed. Recent bioinformatics analysis of the whole-genome and transcriptome obtained using G-quadruplex–specific antibodies and ligands, revealed genomic positions of G-quadruplexes. In addition, accumulating evidence pointed to the existence of these structures under physiologically- and pathologically-relevant conditions, with functional roles in vivo. In this review, we focused on DNA-G4 and RNA-G4, which may have important roles in neuronal function, and reveal mechanisms underlying neurological disorders related to synaptic dysfunction. In addition, we mention the potential of G-quadruplexes as therapeutic targets for neurological diseases.

Manganese(II) and zinc(II) coordination polymers based on 2-(5-bromo-pyridin-3-yl)-1H-imidazole-4,5-dicarboxylic acid: synthesis, structure and properties

Two metal–organic frameworks based on a multifunctional ligand 2-(5-bromo-pyridin-3-yl)-1H-imidazole-4,5-dicarboxylic acid (H3L), [Mn(HL)(C2H5OH)]n (1) and {[Zn(HL)(H2O)2]·H2O}n (2), have been hydro/solvothermally synthesized and characterized by IR, elemental analyses, X-ray powder and single-crystal diffractions, and thermogravimetric analyses. In 1, (HL)2– ligands adopt the μ3-kN,O:kN′,O′:kN′′ coordination mode and use their imidazoledicarboxylates to bis-chelate MnII into left- and right-handed helixes which are further bridged into a mesolayer structure with (4·82) topology through the coordination of their pyridyl groups. In 2, (HL)2– ligands only use their imidazoledicarboxylates to bis-chelate ZnII into linear chains which are further linked into a 2D supramolecular framework through interchain hydrogen–bonding interactions. Interestingly, the structures of 1 and 2 are mainly dominated by the bis-N,O-chelation of the imidazoledicarboxylate in (HL)2–. As for the formation of the imidazoledicarboxylate-bridged helical chains in 1 or straight chains in 2, it largely depends on the cis- or trans-chelation of two imidazoledicarboxylates around the same metal center. Magnetostructural analysis of 1 discloses that the bis-N,O-chelating imidazoledicarboxylate of (HL)2– transmits antiferromagnetic interactions along the imidazoledicarboxylate-bridged helical chain with the spin-coupling constant of –0.71 cm–1. Additionally, 2 emits greatly enhanced blue fluorescence mainly originating from the intraligand charge transition.

Groove binding between ferulic acid and calf thymus DNA: spectroscopic methodology combined with chemometrics and molecular docking studies

Ferulic acid (FA), a dietary phenolic acid compound, is proved to possess numerous biological activities. Hence, this study was devoted to explore the interaction between FA and calf thymus DNA (ctDNA) by UV − vis absorption, fluorescence, circular dichroism (CD) spectroscopy combined with multivariate curve resolution-alternating least-squares (MCR − ALS) and molecular docking studies. The concentration curves and the pure spectra of compositions (FA, ctDNA and FA − ctDNA complex) were obtained by MCR − ALS approach to verify and monitor the interaction of FA with ctDNA. The groove binding mode between FA and ctDNA was confirmed by the results of melting analysis, viscosity measurements, single-stranded DNA experiments, and competitive studies. The binding constant of FA − ctDNA complex was 4.87 × 104 L mol−1 at 298 K. The values of enthalpy (ΔH°) and entropy (ΔS°) changes in the interaction were −16.24 kJ mol−1 and 35.02 J mol−1 K−1, respectively, indicating that the main binding forces were hydrogen bonds and hydrophobic interactions. The result of CD spectra suggested that a decrease in right-handed helicity of ctDNA was induced by FA and the DNA conformational transition from the B-form to the A-form. The results of docking indicated that FA binding with ctDNA in the minor groove. These findings may be conducive to understand the interaction mechanism of FA with ctDNA and the pharmacological effects of FA. Communicated by Ramaswamy H. Sarma

Сhiral and Racemic Fields Concept for Understanding of the Homochirality Origin, Asymmetric Catalysis, Chiral Superstructure Formation from Achiral Molecules, and B-Z DNA Conformational Transition

The four most important and well-studied phenomena of mirror symmetry breaking of molecules were analyzed for the first time in terms of available common features and regularities. Mirror symmetry breaking of the primary origin of biological homochirality requires the involvement of an external chiral inductor (environmental chirality). All reviewed mirror symmetry breaking phenomena were considered from that standpoint. A concept of chiral and racemic fields was highly helpful in this analysis. A chiral gravitational field in combination with a static magnetic field (Earth’s environmental conditions) may be regarded as a hypothetical long-term chiral inductor. Experimental evidences suggest a possible effect of the environmental chiral inductor as a chiral trigger on the mirror symmetry breaking effect. Also, this effect explains a conformational transition of the right-handed double DNA helix to the left-handed double DNA helix (B-Z DNA transition) as possible DNA damage.

Three-State Switchable Chiral Stationary Phase Based on Helicity Control of an Optically Active Poly(phenylacetylene) Derivative by Using Metal Cations in the Solid State.

An unprecedented three-state switchable chiral stationary phase (CSP) for high-performance liquid chromatography (HPLC) was developed using a helical poly(phenylacetylene) bearing a chiral ( R)-α-methoxyphenylacetic acid residue as the pendant (poly-1). The left- and right-handed helical conformations were induced in poly-1-based CSP upon coordination with a catalytic amount of soluble sodium and cesium tetrakis[3,5-bis(trifluoromethyl)phenyl]borate salts (MBArF), respectively, which are soluble in the HPLC conditions [hexane-2-propanol (95:5, v/v)]. The switch between the two different helical states of poly-1 can be easily achieved by rinsing the poly-1-based CSP with MeOH and the subsequent addition of the proper MBArF salt. Using this dynamic helical CSP, we demonstrate how changes on the orientation of the secondary structure of a chiral polymer (right-handed, left-handed, and racemic helices) can alter and even invert the elution order of the enantiomers. This study was done without adding chiral additives or changing the mobile phase, which could produce changes on the retention times and make it more difficult to determine the role of the secondary structure during the chiral recognition process.

3D morphological analysis of spiral intestine morphogenesis in the little skate, Leucoraja erinacea.

The evolution of organ asymmetries is less explored than the field of organ morphology and coiling. The digestive tract of elasmobranchs provides a fascinating model for studying the evolution of morphological asymmetries. Unique to elasmobranchs and all basal fishes is the spiral intestine, which may represent an intermediate morphology in evolution from the straight gut of lamprey to the elongated coils of higher vertebrates. The short spiral allows for a large absorptive surface area that can fit into a restrictive abdominal space. Using histology and high resolution microCT, we provide the first 3D morphometric analysis of the spiral intestine during development in the little skate, Leucoraja erinacea. Spiral formation is initiated by asymmetric growth in the mesenchyme, causing a bulging fold that protrudes into the lumen of the gut. As development proceeds, the fold elongates and spirals into a right-handed helix. Spiraling progresses along the anterior-posterior axis and is likely the result of mechanical forces driven by the asymmetric growth of surrounding tissues. After initial asymmetric growth, radial constraints from within the gut tube create constrictive forces further propagating spiraling. We propose a model for potential biophysical mechanisms that direct the morphogenesis of the spiral intestine.

Comparable investigation of in vitro interactions between three ruthenium(II) arene complexes with curcumin analogs and ctDNA

Ruthenium(II) arene complexes with curcumin analogs possessing different structures have attracted huge attentions in several areas. Herein, in vitro interactions between three ruthenium(II) arene complexes with curcumin analogs and calf thymus DNA (ctDNA) were comparably investigated by viscosity measurement, multi-spectroscopic techniques, and electrochemical methods. Three complexes caused the red shift of absorption peak and weak hypochromic effect of ctDNA. These complexes increased the melting temperature but decreased the relative viscosity of ctDNA to different content. Three complexes all intercalated into the G–C base pairs of ctDNA by hydrogen bonding and van der Waals interactions, which did not affect the right-handed B-form helicity of ctDNA significantly. The intercalative binding interactions between three complexes and ctDNA were further proved by electrochemical methods. The polarity and the space steric hindrance effect of these complexes were responsible for their differences in their intercalative binding interactions with ctDNA. Complex 1 with higher polarity and less steric hindrance effect exhibited the strongest intercalative binding ability with ctDNA. These results revealed the molecular mechanisms of the intercalative binding interactions between three ruthenium(II) arene complexes with curcumin analogs and DNA, which provided new insight into the biological applications of these complexes in the future.