Antiparallel Orientation Research Articles

Interdependence of Filament Nucleation, Elongation and Crosslinking in Actin Bundle Assembly

A network of actin-binding proteins tightly regulates each stage of actin assembly, including filament nucleation, elongation and crosslinking. These processes are integrated together to assemble higher-order actin structures specialized for specific cellular roles. Actin bundles are composed of unbranched filaments that are crosslinked in parallel or anti-parallel orientations by bundling proteins. These structures form the basis of a number of cytoskeletal assemblies, including the contractile ring, stress fibers, and filopodia. Aberrant regulation of actin bundles and their associated proteins is linked to diseases such as focal segmental glomerulosclerosis and metastatic cancers. Yet despite their importance, the dynamic properties of actin bundles are not well understood. To gain insight into the mechanism of bundle assembly, we investigated how the processes of nucleation, elongation, and crosslinking influence each other. We utilized formins, which function as both nucleators and actin polymerases, to elucidate the interdependence between nucleation and elongation. We found that, whereas filament nucleation necessarily precedes and promotes filament elongation, the dependence of both processes on actin monomer availability gives rise to competition that ultimately favors nucleation over elongation. To investigate the relationship between elongation and crosslinking, we generated pools of actin filaments of uniform lengths and analyzed their kinetics of crosslinking by the bundling protein fascin. We found that fascin crosslinks short filaments more slowly than long filaments, suggesting that filament elongation plays a role in regulating filament bundling. We propose that elongating filaments undergo changes in curvature and rotational diffusion that modulate the probability of filament alignment and ultimately dictate the efficiency of fascin-mediated crosslinking. This work suggests that upregulation of fascin might alter the mechanical properties of bundled actin structures by promoting the incorporation of short filaments.

Pseudopeptide Amyloid Aggregation Inhibitors: In Silico, Single Molecule and Cell Viability Studies.

Neurodegeneration in Alzheimer’s disease (AD) is defined by pathology featuring amyloid-β (Aβ) deposition in the brain. Aβ monomers themselves are generally considered to be nontoxic, but misfold into β-sheets and aggregate to form neurotoxic oligomers. One suggested strategy to treat AD is to prevent the formation of toxic oligomers. The SG inhibitors are a class of pseudopeptides designed and optimized using molecular dynamics (MD) simulations for affinity to Aβ and experimentally validated for their ability to inhibit amyloid-amyloid binding using single molecule force spectroscopy (SMFS). In this work, we provide a review of our previous MD and SMFS studies of these inhibitors and present new cell viability studies that demonstrate their neuroprotective effects against Aβ(1–42) oligomers using mouse hippocampal-derived HT22 cells. Two of the tested SG inhibitors, predicted to bind Aβ in anti-parallel orientation, demonstrated neuroprotection against Aβ(1–42). A third inhibitor, predicted to bind parallel to Aβ, was not neuroprotective. Myristoylation of SG inhibitors, intended to enhance delivery across the blood-brain barrier (BBB), resulted in cytotoxicity. This is the first use of HT22 cells for the study of peptide aggregation inhibitors. Overall, this work will inform the future development of peptide aggregation inhibitors against Aβ toxicity.

Folding and fluorescence enhancement with strong odd-even effect for a series of merocyanine dye oligomers.

A series of merocyanine (MC) oligomers with a varying number of chromophores from two to six has been synthesized via a peptide synthesis strategy. Solvent-dependent UV/vis spectroscopic studies reveal folding processes for the MC oligomers driven by strong dipole–dipole interactions resulting in well-defined π-stacks with antiparallel orientation of the dyes. Whilst even-numbered tetramer 4 and hexamer 6 only show partial folding into dimeric units, odd-numbered trimer 3 and pentamer 5 fold into π-stacks of three and five MC units upon decreasing solvent polarity. In-depth 2D NMR studies provided insight into the supramolecular structure. For trimer 3, an NMR structure could be generated revealing the presence of a well-defined triple π-stack in the folded state. Concomitant with folding, the fluorescence quantum yield is increased for all MC oligomers in comparison to the single chromophore. Based on radiative and non-radiative decay rates, this fluorescence enhancement can be attributed to the rigidification of the chromophores within the π-stacks that affords a pronounced decrease of the non-radiative decay rates. Theoretical investigations for the double and triple dye stacks based on time-dependent density functional theory (TD-DFT) calculations indicate for trimer 3 a pronounced mixing of Frenkel and charge transfer (CT) states. This leads to significant deviations from the predictions obtained by the molecular exciton theory which only accounts for the Coulomb interaction between the transition dipole moments of the chromophores.

Switching resonance character within merocyanine stacks and its impact on excited-state dynamics

Summary In this study, the optical properties and excited-state dynamics of the unique self-assembled donor-acceptor (DA) merocyanine dye stacks from dimer up to octamer, prepared via dipole-dipole interactions, are reported in terms of coherent exciton dynamics and formation of an excimer-like state. Our findings are based on the steady-state absorption/emission, time-resolved fluorescence, and transient absorption (anisotropy) measurements, including wavepacket analysis and quantum mechanical calculations. Coherent exciton of torsional motions-restricted dye stacks rapidly localizes into the weakly emissive excimer-like state, by shortening the inter-moiety distance and changing the bond-length alternation pattern. The inner merocyanine moiety, having two neighboring units, has a reversed resonance character (non-polar (N) Z) in the ground state. This difference has led to two conclusions: (1) tetramers and octamers exhibit different features of excimer-like state than the dimer, and (2) octamers exhibit slower localization dynamics due to the enhanced homogeneity (six inner-moieties) compared with tetramers (two inner moieties).

BeStSel: From Secondary Structure Analysis to Protein Fold Prediction by Circular Dichroism Spectroscopy.

Far-UV circular dichroism (CD) spectroscopy is a classical method for the study of the secondary structure of polypeptides in solution. It has been the general view that the α-helix content can be estimated accurately from the CD spectra. However, the technique was less reliable to estimate the β-sheet contents as a consequence of the structural variety of the β-sheets, which is reflected in a large spectral diversity of the CD spectra of proteins containing this secondary structure component. By taking into account the parallel or antiparallel orientation and the twist of the β-sheets, the Beta Structure Selection (BeStSel) method provides an improved β-structure determination and its performance is more accurate for any of the secondary structure types compared to previous CD spectrum analysis algorithms. Moreover, BeStSel provides extra information on the orientation and twist of the β-sheets which is sufficient for the prediction of the protein fold.The advantage of CD spectroscopy is that it is a fast and inexpensive technique with easy data processing which can be used in a wide protein concentration range and under various buffer conditions. It is especially useful when the atomic resolution structure is not available, such as the case of protein aggregates, membrane proteins or natively disordered chains, for studying conformational transitions, testing the effect of the environmental conditions on the protein structure, for verifying the correct fold of recombinant proteins in every scientific fields working on proteins from basic protein science to biotechnology and pharmaceutical industry. Here, we provide a brief step-by-step guide to record the CD spectra of proteins and their analysis with the BeStSel method.

Refined Force Field for Liquid Sulfolane with Particular Emphasis to Its Transport Characteristics.

An all-atom force field dedicated to capturing the properties of multifunctional sulfolane is necessary. In addition to being an excellent solvent and extractor, sulfolane is also a frequently investigated component for battery electrolytes in recent times. Given this, theoretically capturing its transport properties is essential. However, given the rather high shear viscosity of liquid sulfolane and its polar aprotic nature, formulating an appropriate non-polarizable force field for this compound remains a challenge. Starting from a generic force field, we report a refined force field for sulfolane which quantitatively captures its bulk properties, resulting in significantly improved estimates for self-diffusion constant and shear viscosity of sulfolane in comparison to force fields reported hitherto. Density, self-diffusion constant, and shear viscosity were determined between temperatures (303 and 398) K and at 1 bar pressure. All properties determined from the refined force field are in good agreement with experiments. The refined model employs atomic site charges obtained from the density-derived electrostatic and chemical (DDEC6) method for liquid sulfolane modeled using quantum density functional theory. Lennard-Jones parameters were refined using quantum potential energy scans. Despite possessing a large dipole moment, the large molecular size of sulfolane partially disrupts intermolecular dipolar ordering in liquid sulfolane. Molecular dipoles of near neighbor sulfolane, however, retain a partial preference for antiparallel orientation even at the highest temperatures investigated here.

Heterodimeric Insecticidal Peptide Provides New Insights into the Molecular and Functional Diversity of Ant Venoms.

Ants use venom for predation, defense, and communication; however, the molecular diversity, function, and potential applications of ant venom remains understudied compared to other venomous lineages such as arachnids, snakes and cone snails. In this work, we used a multidisciplinary approach that encompassed field work, proteomics, sequencing, chemical synthesis, structural analysis, molecular modeling, stability studies, and in vitro and in vivo bioassays to investigate the molecular diversity of the venom of the Amazonian Pseudomyrmex penetrator ants. We isolated a potent insecticidal heterodimeric peptide Δ-pseudomyrmecitoxin-Pp1a (Δ-PSDTX-Pp1a) composed of a 27-residue long A-chain and a 33-residue long B-chain cross-linked by two disulfide bonds in an antiparallel orientation. We chemically synthesized Δ-PSDTX-Pp1a, its corresponding parallel AA and BB homodimers, and its monomeric chains and demonstrated that Δ-PSDTX-Pp1a had the most potent insecticidal effects in blowfly assays (LD50 = 3 nmol/g). Molecular modeling and circular dichroism studies revealed strong α-helical features, indicating its cytotoxic effects could derive from cell membrane pore formation or disruption. The native heterodimer was substantially more stable against proteolytic degradation (t 1/2 = 13 h) than its homodimers or monomers (t 1/2 < 20 min), indicating an evolutionary advantage of the more complex structure. The proteomic analysis of Pseudomyrmex penetrator venom and in-depth characterization of Δ-PSDTX-Pp1a provide novel insights in the structural complexity of ant venom and further exemplifies how nature exploits disulfide-bond formation and dimerization to gain an evolutionary advantage via improved stability, a concept that is highly relevant for the design and development of peptide therapeutics, molecular probes, and bioinsecticides.

Insights into the Microscopic Structure of RNF4-SIM-SUMO Complexes from MD Simulations

Post-translational modification with one of the isoforms of the small ubiquitin-like modifier (SUMO) affects thousands of proteins in the human proteome. The binding of SUMO to SUMO interacting motifs (SIMs) can translate the SUMOylation event into functional consequences. The E3 ubiquitin ligase RNF4 contains multiple SIMs and connects SUMOylation to the ubiquitin pathway. SIM2 and SIM3 of RNF4 were shown to be the most important motifs to recognize SUMO chains. However, the study of SIM-SUMO complexes is complicated by their typically low affinity and variable binding of the SIMs in parallel and antiparallel orientations. We investigated properties of complexes formed by SUMO3 with peptides containing either SIM2 or SIM3 using molecular dynamics simulations. The affinities of the complexes were determined using a state-of-the-art free energy protocol and were found to be in good agreement with experimental data, thus corroborating our method. Long unrestrained simulations allowed a new interpretation of experimental results regarding the structure of the SIM-SUMO interface. We show that both SIM2 and SIM3 bind SUMO3 in parallel and antiparallel orientations and identified main interaction sites for acidic residues flanking the SIM. We noticed unusual SIM-SUMO interfaces in a previously reported NMR structure (PDB: 2mp2) of a complex formed by a SUMO3 dimer with the bivalent SIM2-SIM3 peptide. Computational determination of the individual SIM-SUMO affinities based on these structural arrangements yielded significantly higher dissociation constants. To our knowledge, our approach adds new opportunities to characterize individual SIM-SUMO complexes and suggests that further studies will be necessary to understand these interactions when occurring in multivalent form.

Rational Modulation of pH-Triggered Macromolecular Poration by Peptide Acylation and Dimerization.

The synthetically evolved pH-dependent delivery (pHD) peptides are a unique family that bind to membranes, fold into α-helices, and form macromolecule-sized pores at low concentration at pH < 6. These peptides have potential applications in drug delivery and tumor targeting. Here, we show how pHD peptide activity can be modulated without changing the amino acid sequence. We increased the hydrophobicity of a representative peptide, pHD108 (GIGEVLHELAEGLPELQEWIHAAQQLGC-amide), by coupling hydrophobic acyl groups of 6-16 carbons and by forming dimers. Unlike the parent peptide, almost all variants showed activity at pH 7. This was due to strong partitioning into phosphatidylcholine vesicle bilayers and induced helix formation. The dimer maintained some pH sensitivity while being the most active peptide studied in this work, with macromolecular poration occurring at 1:2000 peptide:lipid at pH 5. These results confirm that membrane binding, rather than pH, is the determining factor in activity, while also showing that acylation and dimerization are viable methods to modulate pHD108 activity. We propose a possible toroidal pore architecture with peptides in a parallel or mixed parallel/antiparallel orientation without strong electrostatic interactions between peptides in the pore as evidenced by a lack of dependence of activity on either pH or salt concentration.

Robustness of chiral symmetry in atomic nuclei with reflection-asymmetric shapes

Abstract Nearly degenerate quantum states arise from fundamental symmetries, which are often broken in finite many-body systems like atomic nuclei. Chirality can be static, like in molecules composed of more than four atoms, or dynamic, like in particle physics distinguishing between parallel and antiparallel orientation of the spin with respect to the momentum of massless fermions. Frauendorf and Meng.

Nearly complete 1H, 13C and 15N chemical shift assignment of monomeric form of N-terminal domain of Nephila clavipes major ampullate spidroin 2.

Spider dragline silk is well recognized due to its excellent mechanical properties. Dragline silk protein mainly consists of two proteins, namely, major ampullate spidroin 1 (MaSp1) and major ampullate spidroin 2 (MaSp2). The MaSp N-terminal domain (NTD) conformation displays a strong dependence on ion and pH gradients, which is crucial for the self-assembly behavior of spider silk. In the spider major ampullate gland, where the pH is neutral and concentration of NaCl is high, the NTD forms a monomer. In contrast, within the spinning duct, where pH becomes more acidic (to pH ~ 5) and the concentration of salt is low, NTD forms a dimer in antiparallel orientation. In this study, we report near-complete backbone and side chain chemical shift assignment of the monomeric form of NTD of MaSp2 from Nephila clavipes at pH 7 in the presence of 300mM NaCl. Our NMR data demonstrate that secondary structure of monomeric form of NTD MaSp2 consists of five helix regions.

Donor strand sequence, rather than donor strand orientation, determines the stability and non-equilibrium folding of the type 1 pilus subunit FimA

FimA is the main structural subunit of adhesive type 1 pili from uropathogenic Escherichia coli strains. Up to 3000 copies of FimA assemble to the helical pilus rod through a mechanism termed donor strand complementation, in which the incomplete immunoglobulin-like fold of each FimA subunit is complemented by the N-terminal extension (Nte) of the next subunit. The Nte of FimA, which exhibits a pseudo-palindromic sequence, is inserted in an antiparallel orientation relative to the last β-strand of the preceding subunit in the pilus. The resulting subunit-subunit interactions are extraordinarily stable against dissociation and unfolding. Alternatively, FimA can fold to a self-complemented monomer with anti-apoptotic activity, in which the Nte inserts intramolecularly into the FimA core in the opposite, parallel orientation. The FimA monomers, however, show dramatically lower thermodynamic stability compared with FimA subunits in the assembled pilus. Using self-complemented FimA variants with reversed, pseudo-palindromic extensions, we demonstrate that the high stability of FimA polymers is primarily caused by the specific interactions between the side chains of the Nte residues and the FimA core and not by the antiparallel orientation of the donor strand alone. In addition, we demonstrate that nonequilibrium two-state folding, a hallmark of FimA with the Nte inserted in the pilus rod-like, antiparallel orientation, only depends on the identity of the inserted Nte side chains and not on Nte orientation.

Factors influencing flexoelectric polarization in liquid crystals

The work experimentally investigated the factors affecting the formation and physical parameters of flexoelectric polarization in liquid crystals (LC) with nematic as well as smectic A- and C-phases. Factors such as the heating temperature of the sample, orientation effects near the nematic – isotropic state (N-I) phase transition, and the initial orientation of LC molecules were studied. The thickness of the studied layers is from 10 to 100 μm, the frequency of exposure is 1000 Hz. It was found that the flexosignal takes maximum value in homeotropically oriented samples in the nematic phase. When approaching the N-I phase transition, the magnitude of the flex signal increases, which is associated with an increase in the deviation angle of the director of the LC. As the dipole moment grows, the quadrupole moment also increases. This is due to the tendency of LC molecules to form dipole pairs with antiparallel orientation of electric moments. The estimate of the flexural value U1ω yielded (for example, for MBBA) with a planar orientation 3 times less than with a homeotropic one. The presence of the second harmonic U2ω is a consequence of the orientational instability of surface polarization. The rapid growth of U2ω is associated with an increase in the square of the director deviation angle .

Some Features of Surfactant Organization in DNA Solutions at Various NaCl Concentrations.

The photosensitive azobenzene-containing surfactant C4-Azo-OC6TMAB is a promising agent for reversible DNA packaging in a solution. The simulation of the trans-isomer surfactant organization into associates in a solution with and without salt as well as its binding to DNA at different NaCl concentrations was carried out by molecular dynamics. Experimental data obtained by spectral and hydrodynamic methods were used to verify the results of simulation. It was shown that head-to-tail aggregates with close to antiparallel orientation of surfactant molecules were formed at certain NaCl and surfactant concentrations (below critical micelle concentration). Such aggregates have two positively charged ends, and therefore, they can be attracted to negatively charged DNA phosphates far located along the chain, as well as those that belong to different molecules. This contributes to the formation of intermolecular DNA–DNA contacts, and this way, the experimentally observed precipitation of DNA can be explained.

Field-driven spin reorientation in SmMnO3 polycrystalline powders

The SmMnO3 perovskite system shows interesting magnetic properties and making them an attractive material for specific technological application. However, these materials on nanosized dimension display properties that can be significantly different from their bulk dimension. In this regard, using the sol-gel method, the successful synthesis of SmMnO3 polycrystalline powders is herein reported. The structure, morphology, vibrational and magnetic properties of the as-produced sample have been investigated. X-ray diffraction pattern shows a single-perovskite SmMnO3 crystalline phase structure, with a crystalline size of ∼70 nm. The room temperature Raman spectrum confirms the formation of the perovskite SmMnO3 crystalline structure observed by XRD. DC magnetic measurements show an antiferromagnetic-like transition at 60 K (TN ≈ 60 K), attributed to the antiferromagnetic ordering of the Mn3+ spins, magnetic measurements also reveal a temperature-induced magnetization reversal phenomenon characterized by the magnetic compensation temperature (Tcomp ≈ 6 K), attributed to antiparallel orientation of weak ferromagnetic Mn3+- and Sm3+-ion magnetic moments induced by Sm3+-Mn3+ exchange interaction. Magnetization loops, recorded from the as-synthesized SmMnO3 sample contain some singularity compared to previous studies of SmMnO3, which are assigned to small particle size and single domain character of the particles, which are characterized by two well-defined anomalies, both connected with the spin inversion phenomena: one at low fields showing increasing and decreasing branches intersecting each other; another at high fields revealing sudden jumps. The study of a Schottky anomaly in the specific heat measurements recorded at low temperatures (below 10 K) under DC magnetic fields (in the range 5–14 T), is consistent with the presence of a field-driven spin reorientation, from antiferromagnetic to a net ferromagnetic order.

Prebiotic competition and evolution in self-replicating polynucleotides can explain the properties of DNA/RNA in modern living systems

BackgroundWe hypothesize prebiotic evolution of self-replicating macro-molecules (Alberts, Molecular biology of the cell, 2015; Orgel, Crit Rev Biochem Mol Biol 39:99-123, 2004; Hud, Nat Commun 9:5171) favoured the constituent nucleotides and biophysical properties observed in the RNA and DNA of modern organisms. Assumed initial conditions are a shallow tide pool, containing a racemic mix of diverse nucleotide monomers (Barks et al., Chembiochem 11:1240-1243, 2010; Krishnamurthy, Nat Commun 9:5175, 2018; Hirao, Curr Opin Chem Biol 10:622-627), subject to day/night thermal fluctuations (Piccirilli et al., Nature 343:33-37, 1990). Self-replication, like Polymerase Chain Reactions, followed as higher daytime thermal energy “melted” inter-strand hydrogen bonds causing strand separation while solar UV radiation increased prebiotic nucleobase formation (Szathmary, Proc Biol Sci 245:91-99, 1991; Materese et al., Astrobiology 17:761-770, 2017; Bera et al., Astrobiology 17:771-785, 2017). Lower night energies allowed free monomers to form hydrogen bonds with their template counterparts leading to daughter strand synthesis (Hirao, Biotechniques 40:711, 2006).ResultsEvolutionary selection favoured increasing strand length to maximize auto-catalytic function in RNA and polymer stability in double stranded DNA (Krishnamurthy, Chemistry 24:16708-16715, 2018; Szathmary, Nat Rev Genet 4:995-1001, 2003). However, synthesis of the full daughter strand before daytime temperatures produced strand separation, longer polymer length required increased speed of self-replication. Computer simulations demonstrate optimal polynucleotide autocatalytic speed is achieved when the constituent nucleotides possess a left-right asymmetry that decreases the hydrogen bond kinetic barrier for the free nucleotide attachment to the template on one side and increases bond barrier on the other side preventing it from releasing prior to covalent bond formation. This phenomenon is similar to asymmetric kinetics observed during polymerization of the front and the back ends of linear cytoskeletal proteins such as actin and microtubules (Orgel, Nature 343:18-20, 1990; Henry, Curr Opin Chem Biol 7:727-733, 2003; Walker et al., J Cell Biol 108:931-937, 1989; Crevenna et al., J Biol Chem 288:12102-12113, 2013). Since rotation of the nucleotide would disrupt the asymmetry, the optimal nucleotides must form two or more hydrogen bonds with their counterpart on the template strand. All nucleotides in modern RNA and DNA have these predicted properties. Our models demonstrate these constraints on the properties of constituent monomers result in biophysical properties found in modern DNA and RNA including strand directionality, anti-parallel strand orientation, homochirality, quadruplet alphabet, and complementary base pairing. Furthermore, competition between RNA and DNA auto-replicators for 3 nucleotides in common permit states coexistence and possible cooperative interactions that could be incorporated into nascent living systems.ConclusionOur findings demonstrate the molecular properties of DNA/RNA could have emerged from Darwinian competition among macromolecular replicators that selected nucleotide monomers that maximized the speed of autocatalysis.

Evolutionary advantage of anti-parallel strand orientation of duplex DNA

DNA in all living systems shares common properties that are remarkably well suited to its function, suggesting refinement by evolution. However, DNA also shares some counter-intuitive properties which confer no obvious benefit, such as strand directionality and anti-parallel strand orientation, which together result in the complicated lagging strand replication. The evolutionary dynamics that led to these properties of DNA remain unknown but their universality suggests that they confer as yet unknown selective advantage to DNA. In this article, we identify an evolutionary advantage of anti-parallel strand orientation of duplex DNA, within a given set of plausible premises. The advantage stems from the increased rate of replication, achieved by dividing the DNA into predictable, independently and simultaneously replicating segments, as opposed to sequentially replicating the entire DNA, thereby parallelizing the replication process. We show that anti-parallel strand orientation is essential for such a replicative organization of DNA, given our premises, the most important of which is the assumption of the presence of sequence-dependent asymmetric cooperativity in DNA.

X-ray detection of ultrashort spin current pulses in synthetic antiferromagnets

We explore the ultrafast generation of spin currents in magnetic multilayer samples by applying fs laser pulses to one layer and measuring the magnetic response in the other layer by element-resolved x-ray spectroscopy. In Ni(5 nm)/Ru(2 nm)/Fe(4 nm), the Ni and Fe magnetization directions couple antiferromagnetically due to the Ruderman–Kittel–Kasuya–Yosida interaction but may be oriented parallel through an applied magnetic field. After exciting the top Ni layer with a fs laser pulse, we also find that the Fe layer underneath demagnetizes, with a 4.1±1.9% amplitude difference between parallel and antiparallel orientation of the Ni and Fe magnetizations. We attribute this difference to the influence of a spin current generated by the fs laser pulse that transfers angular momentum from the Ni into the Fe layer. Our results confirm that superdiffusive spin transport plays a role in determining the sub-ps demagnetization dynamics of synthetic antiferromagnetic layers, but also evidence large depolarization effects due to hot electron dynamics, which are independent of the relative alignment of the magnetization in Ni and Fe.

Stacking Domains and Dislocation Networks in Marginally Twisted Bilayers of Transition Metal Dichalcogenides.

We apply a multiscale modeling approach to study lattice reconstruction in marginally twisted bilayers of transition metal dichalcogenides (TMD). For this, we develop density functional theory parametrized interpolation formulae for interlayer adhesion energies of MoSe_{2}, WSe_{2}, MoS_{2}, and WS_{2}, combine those with elasticity theory, and analyze the bilayer lattice relaxation into mesoscale domain structures. Paying particular attention to the inversion asymmetry of TMD monolayers, we show that 3R and 2H stacking domains, separated by a network of dislocations develop for twist angles θ^{∘}<θ_{P}^{∘}∼2.5° and θ^{∘}<θ_{AP}^{∘}∼1° for, respectively, bilayers with parallel (P) and antiparallel (AP) orientation of the monolayer unit cells and suggest how the domain structures would manifest itself in local probe scanning of marginally twisted P and AP bilayers.

Symmetry in Nucleic-Acid Double Helices

In nature and in the test tube, nucleic acids occur in many different forms. Apart from single-stranded, coiled molecules, DNA and RNA prefer to form helical arrangements, in which the bases are stacked to shield their hydrophobic surfaces and expose their polar edges. Focusing on double helices, we describe the crucial role played by symmetry in shaping DNA and RNA structure. The base pairs in nucleic-acid double helices display rotational pseudo-symmetry. In the Watson–Crick base pairs found in naturally occurring DNA and RNA duplexes, the symmetry axis lies in the base-pair plane, giving rise to two different helical grooves. In contrast, anti-Watson–Crick base pairs have a dyad axis perpendicular to the base-pair plane and identical grooves. In combination with the base-pair symmetry, the syn/anti conformation of paired nucleotides determines the parallel or antiparallel strand orientation of double helices. DNA and RNA duplexes in nature are exclusively antiparallel. Watson–Crick base-paired DNA or RNA helices display either right-handed or left-handed helical (pseudo-) symmetry. Genomic DNA is usually in the right-handed B-form, and RNA double helices adopt the right-handed A-conformation. Finally, there is a higher level of helical symmetry in superhelical DNA in which B-form double strands are intertwined in a right- or left-handed sense.