Topotactic Conversion of β‐Helix‐Layered Silicate into AST‐Type Zeolite through Successive Interlayer Modifications

AST‐type zeolite with a plate morphology can be synthesized by topotactic conversion of a layered silicate (β‐helix‐layered silicate; HLS) by using N,N‐dimethylpropionamide (DPA) to control the layer stacking of silicate layers and the subsequent interlayer condensation. Treatment of HLS twice with 1) hydrochloric acid/ethanol and 2) dimethylsulfoxide (DMSO) are needed to remove interlayer hydrated Na ions and tetramethylammonium (TMA) ions in intralayer cup‐like cavities (intracavity TMA ions), both of which are introduced during the preparation of HLS. The utilization of an amide molecule is effective for the control of the stacking sequence of silicate layers. This method could be applicable to various layered silicates that cannot be topotactically converted into three‐dimensional networks by simple interlayer condensation by judicious choice of amide molecules.     

Enantioselective Assembly of a Ruthenium(II) Polypyridyl Complex into a Double Helix

Evolution can increase the complexity of matter by self‐organization into helical architectures, the best example being the DNA double helix. One common aspect, apparently shared by most of these architectures, is the presence of covalent bonds within the helix backbone. Here, we report the unprecedented crystal structures of a metal complex that self‐organizes into a continuous double helical structure, assembled by non‐covalent building blocks. Built up solely by weak stacking interactions, this alternating tread stairs‐like double helical assembly mimics the DNA double helix structure. Starting from a racemic mixture in aqueous solution, the ruthenium(II) polypyridyl complex forms two polymorphic structures of a left‐handed double helical assembly of only the Λ‐enantiomer. The stacking of the helices is different in both polymorphs: a crossed woodpile structure versus a parallel columnar stacking.     

An ab initio molecular orbital study on the stacking interaction between nucleic acid bases: Dependence on the sequence and relation to the conformation

The stacking interaction energies between nucleic acid bases in A DNA and B DNA are calculated by means of the ab initio molecular orbital method. The calculated values agree well with the experimental values of stacking enthalpy changes. The stacking interaction energy is shown to be highly sequence dependent, particularly when the sequence includes guanine or cytosine. The possibility is shown that the conformation of a DNA double helix fragment is determined by the constituent stacking interaction. Electrostatic energy is the cause of the sequence dependency of the stacking energy, while charge transfer and dispersion energies contribute to the overall stability.     

双核三螺旋铁配合物的合成和结构

本文选择了2-羟基-1-萘醛与水合肼形成的席夫碱,[(HO)(C₁₀H₆)CH=N-N=CH(C₁₀H₆)(OH)],作为配体,设计组装了双核三螺旋的三价铁配合物。配合物中每一个铁离子以准八面体的配位方式分别与三个NO双齿单元配位, 三个配体分别桥联两个金属形成特定的三螺旋构型。分子内和分子间的π-π堆积作用对螺旋体的形成和堆积方式起着十分重要的作用。作为对照,本文还报道了配体的晶体结构。     

H-Bonded complexes of adenine with Rebek imide receptors are stabilised by cation-pi interactions and destabilised by stacking with perfluoroaromatics

A series of Rebek imide receptors with naphthalene or heteroaromatic platforms attached by amide or ester linkers have been prepared from the corresponding acyl chloride or anhydride; the X-ray crystal structure of the receptor-derived anhydride reveals a supramolecular H-bonded helix formation in the crystal; the complexes of adenine bound to the receptors by Hoogsteen H-bonding are found to be stabilised by stacking with a methylquinolinium ion, but destabilised by stacking with a perfluorinated naphthalene.     

Supramolecular Self-Assembly of β3-Peptides Mediated by Janus-Type Recognition Units

To gain mechanistic insights, natural systems with biochemical relevance are inspiring for the creation of new biomimetics with unique properties and functions. Despite progress in rational design and protein engineering, folding and intramolecular organization of individual components into supramolecular structures remains challenging and requires controlled methods. Foldamers, such as β-peptides, are structurally well defined with rigid conformations and suitable for the specific arrangement of recognition units. Herein, we show the molecular arrangement and aggregation of β³-peptides into a hexameric helix bundle. For this purpose, β-amino acid side chains were modified with cyanuric acid and triamino-s-triazine as complementary recognition units. The pre-organization of the β³-peptides leads these Janus molecule pairs into a hexameric arrangement and a defined rosette nanotube by stacking. The helical conformation of the subunits was indicated by circular dichroism spectroscopy, while the supramolecular arrangement was detected by dynamic light scattering and confirmed by high-resolution electrospray ionization mass spectrometry (ESI-HRMS).     

A homochiral triple helix constructed from an axially chiral bipyridine

A homochiral triple helix was self-assembled from an axially chiral bipyridine and a linear metal-connecting point, which further assembles into a 2D network via infinite pi...pi stacking interactions and acts as a host for the inclusion of guest molecules.     

Sequence-dependent effects in A-DNA double helices

To date, more than ten different A-DNA structures have been analyzed at near atomic resolution by X-ray methods. This structural information enables us for the first time, to begin to discover the rules which govern the conformation of the double helix in the A form.A detailed analysis of the various helical conformations show that local structural changes are induced by base-pair stacking interactions. Variations in stacking geometry are sequence dependent. For pyrimidine-purine sites, the stacking mode is determined by the nature of the base-pair doublet only, whereas for purine-pyrimidine and homopolymer sites the identity of neighboring base pairs is important as well.     

Strain-dependence of the electronic properties in periodic quadruple helical G4-wires

The electronic structure of periodic quadruple helix guanine wires, which mimic G4-DNA molecules, was studied as a function of the stacking distance between consecutive planes, by means of first principles density functional theory calculations. We show that, whereas for the native DNA interplane separation of 3.4 A the HOMO- and LUMO-derived bands are poorly dispersive, the bandwidths can be significantly increased when compressive strain is applied along the helical axis. Our findings indicate that efficient band conduction for both holes and electrons can be supported by such wires for stacking distances below 2.6 A, which imply a huge axial deformation with respect to double and quadruple helices in solutions and in crystals.     

SCF CI MO calculations on the base–base interactions in dinucleoside monophosphates

In order to elucidate further details of RNA conformations we have studied base stacking in dinucleoside monophosphates (DNP's) using UV difference spectra and the hypochromic effect. SCF CI MO calculations according to PPP and MIM approximations were carried out for six pyrimidine-containing DNP's in each of several stacking geometries. The calculated and plotted difference spectra were fitted to the experimental spectra. Different DNP's showed distinct geometries in the range of the helix angle of 35°. From our results we conclude that there is a microstructure in the helix. This would imply an additional content of information in this macromolecule, a higher precision in nucleic acid interactions, and make possible the prediction of the conformation of polynucleotides.     

Control of helix sense in protein-mimicking backbone by the noncovalent chiral effect

We have reviewed our previous work regarding induction or control of a peptide helix sense through chiral stimulus to the peptide chain terminus. An optically inactive 3(10)-helix designed mainly with unusual alpha-amino acid residues was commonly employed. Such an N-terminal-free peptide generates a preferred helix sense by chiral acid molecule. A helix sense pre-directed in chiral sequence is also influenced or controlled by the chiral sign of such external molecule. Here free amide groups in the 3(10)-helical N-terminus participate in the formation of a multipoint coordinated complex. The terminal asymmetry produces the noncovalent chiral domino effect (NCDE) to influence the whole helix sense. The NCDE-mediated control of helicity provides the underlying chiral nature of protein-mimicking helical backbones: notably, chiral recognition at the terminus and modulation of helical propensity through chiral stimulus. The above items from our previous reports have been outlined and reviewed together with their significance in biopolymer science and chiral chemistry.     

Molecular Spring‐like Triple‐Helix Coordination Polymers as Dual‐Stress and Thermally Responsive Crystalline Metal–Organic Materials

Elastic metal–organic materials (MOMs) capable of multiple stimuli‐responsiveness based on dual‐stress and thermally responsive triple‐helix coordination polymers are presented. The strong metal‐coordination linkage and the flexibility of organic linkers in these MOMs, rather than the 4 Å stacking interactions observed in organic crystals, causes the helical chain to act like a molecular spring and thus accounts for their macroscopic elasticity. The thermosalient effect of elastic MOMs is reported for the first time. Crystal structure analyses at different temperatures reveal that this thermoresponsiveness is achieved by adaptive regulation of the triple‐helix chains by fine‐tuning the opening angle of flexible V‐shaped organic linkers and rotation of its lateral conjugated groups to resist possible expansion, thus demonstrating the vital role of adaptive reorganization of triple‐helix metal–organic chains as a molecular spring‐like motif in crystal jumping.     

Communication between the active site and the allosteric site in class A beta-lactamases

Bacterial production of beta-lactamases, which hydrolyze beta-lactam type antibiotics, is a common antibiotic resistance mechanism. Antibiotic resistance is a high priority intervention area and one strategy to overcome resistance is to administer antibiotics with beta-lactamase inhibitors in the treatment of infectious diseases. Unfortunately, beta-lactamases are evolving at a rapid pace with new inhibitor resistant mutants emerging every day, driving the design and development of novel beta-lactamase inhibitors. Here, we examined the inhibitor recognition mechanism of two common beta-lactamases using molecular dynamics simulations. Binding of beta-lactamase inhibitor protein (BLIP) caused changes in the flexibility of regions away from the binding site. One of these regions was the H10 helix, which was previously identified to form a lid over an allosteric inhibitor binding site. Closer examination of the H10 helix using sequence and structure comparisons with other beta-lactamases revealed the presence of a highly conserved Trp229 residue, which forms a stacking interaction with two conserved proline residues. Molecular dynamics simulations on the Trp229Ala mutants of TEM-1 and SHV-1 resulted in decreased stability in the apo form, possibly due to loss of the stacking interaction as a result of the mutation. The mutant TEM-1 beta-lactamase had higher H10 fluctuations in the presence of BLIP, higher affinity to BLIP and higher cross-correlations with BLIP. Our results suggest that the H10 helix and specifically W229 are important modulators of the allosteric communication between the active site and the allosteric site.     

Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC

CeNA oligonucleotides consist of a phosphorylated backbone where the deoxyribose sugars are replaced by cyclohexene moieties. The X-ray structure determination and analysis of a fully modified octamer sequence GTGTACAC, which is the first crystal structure of a carbocyclic-based nucleic acid, is presented. This particular sequence was built with left-handed building blocks and crystallizes as a left-handed double helix. The helix can be characterized as belonging to the (mirrored) A-type family. Crystallographic data were processed up to 1.53 A, and the octamer sequence crystallizes in the space group R32. The sugar puckering is found to adopt the 3H2 half-chair conformation which mimics the C3'-endo conformation of the ribose sugar. The double helices stack on top of each other to form continuous helices, and static disorder is observed due to this end-to-end stacking.     

Enantiodifferentiating Photodimerization of a 2,6‐Disubstituted Anthracene Assisted by Supramolecular Double‐Helix Formation with Chiral Amines

A novel 2,6‐anthrylene‐linked bis(m‐terphenylcarboxylic acid) strand ( 1 ) self‐associates into a racemic double‐helix. In the presence of chiral mono‐ and diamines, either a right‐ or left‐handed double‐helix was predominantly induced by chiral amines sandwiched between the carboxylic acid strands with accompanying stacking of the two prochiral anthracene linker units in an enantiotopic face‐selective way, as revealed by circular dichroism and NMR spectral analyses. The photoirradiation of the optically active double helices complexed with chiral amines proceeded in a diastereo‐ (anti or syn) and enantiodifferentiating way to afford the chiral anti‐photodimer with up to 98 % enantiomeric excess when (R)‐phenylethylamine was used as a chiral double‐helix inducer. The resulting optically active anti‐photodimer can recognize the chirality of amines and diastereoselectively complex with chiral amines.     

Self-assembly of nucleoamphiphiles: investigating nucleosides effect and the mechanism of micrometric helix formation

A new family of self-assembling systems based on nucleoamphiphiles is described. Nano to micrometric left-handed helix formation in aqueous solution was induced simply by complexing a GMP or an AMP with a nonchiral monocationic amphiphile. The assembling behavior such as micellar formation, monolayer at air-water interface, as well as the aggregates in solution of these nucleoamphiphiles are strongly influenced by the presence of nucleosides in solution. The observed effects depend on the properties of complexed nucleotides and nucleosides with a complex mixture of pi stacking, hydrophobicity of the bases, and hydrogen bonding.     

Triple Helix Formation in a Topologically Controlled DNA Nanosystem

In the present study, we demonstrate single‐molecule imaging of triple helix formation in DNA nanostructures. The binding of the single‐molecule third strand to double‐stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson–Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high‐speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace.     

Variation of molecular stacking with different length of alkyl chain: synthesis, structure determination, and mesogenic study of N,N-disubstituted aminophenylazo-(4)-p-alkylbenzenes

To help understand the influence of polarity and length of the terminal alkyl chain of a molecule on the molecular stacking of a liquid crystal and on its mesogenic behaviour, four new aminophenylazo-(4)-p-alkylbenzenes were prepared and one of them was further studied by single crystal structure determination. The molecular stacking based on this crystallographic data was established, and compared with that of two previously reported homologues. The mesogenic behaviour of this series of compounds was also investigated.     

Analysis of the ethidium bromide bound to DNA by photoacoustic and FTIR spectroscopy.

Under physiological conditions B-form DNA is an exceedingly stable structure. However, experimental evidences obtained through nuclear magnetic resonance and fluorescence anisotropy suggest that the structure of the double helix fluctuates substantially. We describe photoacoustic phase modulation frequency measurements of ethidium bromide (Eb) with calf thymus DNA. As in fluorescence phase modulation measurements, we used an intercalating dye as a probe; however, we monitored the triplet excited state lifetime at different ionic strengths. The triplet lifetime of Eb varied from about 0.30 ms, with no DNA present, to 20 ms (at a DNA:Eb molar ratio of 5). With salt titration, this value falls to about 2.0 ms. This result suggests a strong coupling between the phenantridinium ring of the ethidium and the base pairs because of the stacking movement of the DNA molecule under salt effect. This effect may be understood considering DNA as a polyelectrolyte. The counterions in the solution shield the phosphate groups, reducing the electrostatic repulsion force between them, hence compacting the DNA molecule. The results from Fourier transform infrared demonstrated two important bands: 3187 cm-1 corresponding to the symmetric stretching of the NH group of the bases and 1225 cm-1 corresponding to the asymmetric stretching of phosphate groups shifted toward higher wavenumbers, suggesting a proximity between the intercalant and base pairs and a modification of the DNA backbone state, both induced by salt accretion.