Adjacent Strands Research Articles

Tuning the stability of DNA tetrahedra with base-stacking interactions.

DNA nanotechnology relies on programmable anchoring of regions of single-stranded DNA through base pair hybridization to create nanoscale objects such as polyhedra, tubes, sheets, and other desired shapes. Recent work from our lab measured the energetics of base-stacking interactions and suggested that terminal stacking interactions between two adjacent strands could be an additional design parameter for DNA nanotechnology. Here, we explore that idea by creating DNA tetrahedra held together with sticky ends that contain identical base pairing interactions but different terminal stacking interactions. Testing all 16 possible combinations, we found that the melting temperature of DNA tetrahedra varied by up to 10 °C from altering a single base stack in the design. These results can inform stacking design to control DNA tetrahedra stability in a substantial and predictable way. To that end, we show that a 4 bp sticky end with weak terminal stacking does not form stable tetrahedra, while strengthening the stacks confers high stability with a 46.8 ± 1.2 °C melting temperature, comparable to a 6 bp sticky end with weak stacking. The results likely apply to other types of DNA nanostructures and suggest that terminal stacking interactions play an integral role in formation and stability of DNA nanostructures.

Phosphoryl group wires stabilize pathological tau fibrils as revealed by multiple quantum spin counting NMR.

Hyperphosphorylation of the protein tau is one of the biomarkers of neurodegenerative diseases in the category of tauopathies. However, the molecular level, mechanistic, role of this common post-translational modification (PTM) in enhancing or reducing the aggregation propensity of tau is unclear, especially considering that combinatorial phosphorylation of multiple sites can have complex, non-additive, effects on tau protein aggregation. Since tau proteins stack in register and parallel to elongate into pathological fibrils, phosphoryl groups from adjacent tau strands with 4.8 Å separation must find an energetically favorable spatial arrangement. At first glance, this appears to be an unfavorable configuration due to the proximity of negative charges between phosphate groups from adjacent neighboring tau fibrils. However, this study tests a counterhypothesis that phosphoryl groups within the fibril core-forming segments favorably assemble into highly ordered, hydrogen-bonded, one-dimensionally extended wires under biologically relevant conditions. We selected two phosphorylation sites associated with neurodegeneration, serine 305 (S305p) and tyrosine 310 (Y310p), on a model tau peptide jR2R3-P301L (tau295-313) spanning the R2/R3 splice junction of tau, that readily aggregate into a fibril with characteristics of a seed-competent mini prion. Using multiple quantum spin counting (MQ-SC) by 31P solid-state NMR of phosphorylated jR2R3-P301L tau peptide fibrils, enhanced by dynamic nuclear polarization, we find that at least six phosphorous spins must neatly arrange in 1D within fibrils or in 2D within a protofibril to yield the experimentally observed MQ-coherence orders of four. We found that S305p stabilizes the tau fibrils and leads to more seeding-competent fibrils compared to jR2R3 P301L or Y310p. This study introduces a new concept that phosphorylation of residues within a core forming tau segment can mechanically facilitate fibril registry and stability due a hitherto unrecognized role of phosphoryl groups to form highly ordered, extended, 1D wires that stabilize pathological tau fibrils.

Functionalizing DNA Origami by Triplex-Directed Site-Specific Photo-Cross-Linking.

Here, we present a cross-linking approach to covalently functionalize and stabilize DNA origami structures in a one-pot reaction. Our strategy involves adding nucleotide sequences to adjacent staple strands, so that, upon assembly of the origami structure, the extensions form short hairpin duplexes targetable by psoralen-labeled triplex-forming oligonucleotides bearing other functional groups (pso-TFOs). Subsequent irradiation with UVA light generates psoralen adducts with one or both hairpin staples leading to site-specific attachment of the pso-TFO (and attached group) to the origami with ca. 80% efficiency. Bis-adduct formation between strands in proximal hairpins further tethers the TFO to the structure and generates "superstaples" that improve the structural integrity of the functionalized complex. We show that directing cross-linking to regions outside of the origami core dramatically reduces sensitivity of the structures to thermal denaturation and disassembly by T7 RNA polymerase. We also show that the underlying duplex regions of the origami core are digested by DNase I and thus remain accessible to read-out by DNA-binding proteins. Our strategy is scalable and cost-effective, as it works with existing DNA origami structures, does not require scaffold redesign, and can be achieved with just one psoralen-modified oligonucleotide.

III. Geometrical framework for thinking about globular proteins: Turns in proteins.

We have shown recently that the notion of poking pairwise interactions along a chain provides a unifying framework for understanding the formation of both secondary and the tertiary protein structure based on symmetry and geometry. α-helices and β-sheets are found to be special geometries that have systematic poking contacts in a repetitive manner with the contacts being local along the α-helix and non-local along a pair of adjacent strands within a β-sheet. Pairwise poking interactions also govern tertiary structure formation, but they are weaker and there are no special geometrical constraints as in secondary structure formation. Here we demonstrate that protein turns, the most prevalent non-repetitive structural element in proteins, are instances of local (as in α-helices) and isolated (non-repetitive) poking pairwise contacts for which the geometrical constraints are partially relaxed. This simple and purely geometrical definition of protein turns (also sometimes known as reverse turns, β-turns, β-bends, hairpin bends, 310 bends, kinks, widgets, etc.) provides a simple framework for unifying them. We present the results of a systematic analysis and identify their structural classes as well as their respective amino acid preferences.

Analysis, simulation and experimental research on the mechanisms of lantern-shaped strand defects in the conductor construction of transmission line

This paper focuses on theoretical, numerical simulation, and experimental research on the lantern-shaped strand defect that arises in tension stringing constructions of large-section conductors. Starting from considerations for factors such as the construction environment and the characteristics of the conductor passing through blocks, this paper presents the causes of conductor torque generation and analyzes the distribution of axial forces on the outmost layer strands and the outmost adjacent layer strands of the conductor when subjected to bending and twisting. Taking into account the contact forces between strands in different layers, this paper thoroughly examines the mechanical causes that lead to the occurrence of the lantern-shaped strand defect in conductors. It concludes that the axial compression and the external contact force acting on the outermost adjacent layer strands are crucial in the formation of the lantern-shaped strand defect. To numerically simulate the lantern-shaped defect, a finite element model is developed to replicate the passage of a 1250 mm2 large-section conductor through the block system. Furthermore, considering actual working conditions, a test equipment is designed and constructed to replicate the lantern-shaped defect. The shape and size of the lantern-shaped defect obtained from the tests exhibited a substantial agreement with the simulation results, suggesting concordance between theoretical analysis and real situation. This research methodology can be used to analyze defects in conductors with varying sections, serving as a theoretical foundation for the prevention and control of construction defects in conductors.

Laser beam heat treatment in large-scale additive manufacturing

Large-scale additive manufacturing (LSAM) has been developing a huge potential to address certain tasks in industrial applications over the last years. Particularly granule extrusion technologies enable the processing of an enormous variety of materials but also introduce new challenges in printing large-scale parts. Compared to fused layer modelling and due to larger nozzle diameters as well as higher extrusion rates strand geometry and consequently, process-related voids are enlarged. A promising approach to improve part quality is the integration of carbon dioxide laser (CO2) radiation into the additive manufacturing process to weld deposited strands by increasing the interface temperature. Experiments are conducted for polymethyl methacrylate (PMMA) and styrene-acrylonitrile (SAN) which are very good absorbers of the wavelength 10.6 µm. Due to the locally defined heat treatment, merely certain areas of the strands are heated to a desired temperature. This leads to a more complete diffusion. At the same time, temperature gradients in the overall part are avoided. By means of a thermographic camera, the temperatures at the re-melting process of deposited strands can be precisely monitored. Therefore, the relation between laser intensity and resulting temperature can be transferred into a repeatable process window. The interaction between laser and deposited material leads to a wider contact area between stacked strands. While flexural strength is not significantly affected, compared to specimens manufactured without any heat treatment bending force is increased by 66% (PMMA) and 48% (SAN), respectively. In addition, voids between adjacent strands are reduced by up to 57%.

Book Religion? The Role of the Scroll in Deuteronomy

ABSTRACT This essay engages with Kåre Berge’s reflections on book religion in Deuteronomy. It first elaborates upon the concepts of religion and book religion and considers aspects of the literary and rhetorical anatomy of Deuteronomy. Then it argues that the salient point in Deuteronomy is not the text of the Torah as such, but the doing of what that text says. This orientation towards religious practice is squarely similar to adjacent strands of ancient Hebrew religion. Deuteronomy, however, adds certain religious practices, all of which required the use of (oral or written) texts. The essay argues that Deuteronomy had little potential to generate common religious change, but it could be seen as a force towards changes in religious leadership. Finally, the essay considers the concept of book religion—as a classificatory concept and as an analytical perspective.

Unexpected essential surfaces among exteriors of twisted torus knots

The twisted torus knots K(p, q; r, s) are obtained by performing a sequence of s full twists on r adjacent strands of (p, q)-torus knots. Morimoto asked whether all twisted torus knots with essential tori in the exterior fit into one of two families. We prove that the answer to this question is no, by finding two different new families of toroidal twisted torus knots.

A large HIV gp41 construct with trimer-of-hairpins structure exhibits V2E mutation-dominant attenuation of vesicle fusion and helicity very similar to V2E attenuation of HIV fusion and infection and supports: (1) hairpin stabilization of membrane apposition with larger distance for V2E; and (2) V2E dominance by an antiparallel β sheet with interleaved fusion peptide strands from two gp41 trimers

There is complete attenuation of fusion and infection mediated by HIV gp160 with gp41 subunit with V2E mutation, and also V2E dominance with WT/V2E mixtures. V2E is at the N-terminus of the ∼25-residue fusion peptide (Fp) which likely binds the target membrane. In this study, large V2E attenuation and dominance were observed for vesicle fusion induced by FP_HM, a large gp41 ectodomain construct with Fp followed by hyperthermostable hairpin with N- and C-helices, and membrane-proximal external region (Mper). FP_HM is a trimer-of-hairpins, the final gp41 structure during fusion. Vesicle fusion and helicity were measured for FP_HM using trimers with different fractions (f's) of WT and V2E proteins. Reductions in FP_HM fusion and helicity vs. fV2E were quantitatively-similar to those for gp160-mediated fusion and infection. Global fitting of all V2E data supports 6 WT gp41 (2 trimers) required for fusion. These data are understood by a model in which the ∼25 kcal/mol free energy for initial membrane apposition is compensated by the thermostable hairpin between the Fp in target membrane and Mper/transmembrane domain in virus membrane. The data support a structural model for V2E dominance with a membrane-bound Fp with antiparallel β sheet and interleaved strands from the two trimers. Relative to fV2E = 0, a longer Fp sheet is stabilized with small fV2E because of salt-bridge and/or hydrogen bonds between E2 on one strand and C-terminal Fp residues on adjacent strands, like R22. A longer Fp sheet results in shorter N- and C-helices, and larger separation during membrane apposition which hinders fusion.

Tuning Xanthan Viscosity by Directed Random Coil-to-Helix Transition.

Xanthan gum is a polysaccharide that is widely used as a thickening agent in numerous food, cosmetic, and technical applications. Therefore, the knowledge of the molecular interplay that builds up and stabilizes water-binding networks is crucial for the optimization of xanthan thickening performance. Using atomic force microscopy, rheometry, and inductively coupled plasma optical emission spectroscopy, we show a clear correlation between xanthan thickening properties and the ability to form characteristic secondary structures as well as the valence and amount of cations coordinated at the polysaccharide side chain. Based on these findings and the Debye-Hückel theory, we derive an ion-interaction model in which divalent cations mediate bridging of adjacent single polymer strands due to chelate-like coordination building stable secondary structures. We furthermore demonstrate in a cation exchange assay that xanthan secondary structures can be modified in a directed and reversible manner, which, in turn, alters its thickening properties.

Ribbonlength of twisted torus knots

The ribbonlength Rib[Formula: see text] of a knot [Formula: see text] is the infimum of the ratio of the length of any flat knotted ribbon with core [Formula: see text] to its width. A twisted torus knot [Formula: see text] is obtained from the torus knot [Formula: see text] by twisting [Formula: see text] adjacent strands [Formula: see text] full twists. In this paper, we show that the ribbonlength of [Formula: see text] is less then or equal to [Formula: see text] where [Formula: see text] and [Formula: see text] are positive. Furthermore, if [Formula: see text], then the ribbonlength of [Formula: see text] is less then or equal to [Formula: see text].

Effects of a rotary shear field on the interlayer bond and mechanical properties of polylactide fabricated using fused filament fabrication

Polylactide (PLA) is a kind of distinct semicrystalline polymer and widely applied for fused filament fabrication (FFF), because of its low price and high mechanical properties. But the bad interface of FFF printed PLA parts and their high mechanical anisotropy limit their industrial application deeply. In this work, an innovative FFF 3D printer with a rotary shear head was developed to control the interface and crystallization of FFF printed PLA parts. Compared with traditional FFF, the tensile strength of specimen fabricated via the rotary shear field increases from 21.1 MPa to 59.3 MPa, and the degree of mechanical anisotropy decreases from 0.41 to 0.09. As indicated by the meso-structure morphologies, not only the triangular voids between adjacent strands were disappeared, but also the randomly-distributed shish-kebab structure crystals and fibrils were obtained by the rotary shear field treatment. And the DSC results showed a high crystallinity value of 26.1% of specimen with the rotary shear field treatment. Therefore, the good interface, randomly-distributed crystals and high crystallinity contribute the effort to increase the tensile strength and decrease the degree of mechanical anisotropy of FFF printed PLA parts.

Synergies of Adjacent Sites in Atomically Dispersed Ruthenium toward Achieving Stable Hydrogen Evolution.

It is a challenge to fabricate atomically dispersed metal clusters in polymeric carbon nitride (PCN) for durable photocatalytic reactions owing to the thermodynamic stability limitation. Herein, atomically dispersed Ru clusters are implanted into the PCN skeleton matrix based on an ionic diffusion and coordination (IDC) strategy, the stability of which is improved owing to the robust Ru-N bonds in the formed RuN4 and RuN3 configurations. Additionally, RuN4 and RuN3 as charge transport bridges between two adjacent melon strands efficaciously conquer hydrogen bond restriction in the skeleton to facilitate the in-plane mobility and separation of charge carriers. Moreover, the synergistic effect of adjacent Ru atoms is triggered on the assembled RuN3-RuN4 and RuN3-RuN3 in the atomically dispersed Ru clusters to significantly decrease hydrogen adsorption energy. As a result, the optimal PCN-Ru photocatalyst achieves nearly 6 times higher than the photocatalytic hydrogen evolution (PHE) rate of the Pt/PCN benchmark and maintains the long-term stable running for 104 h of 26 cycles; its overall PHE performance is far superior to the most of single atoms supported on g-C3N4 photocatalysts reported. The findings here gain new insight into the preparation strategy, structure configuration, and reaction mechanism for atomically dispersed metal clusters supported on PCN, which further stimulates the intensive investigations toward developing more efficient and stable PCN-like photocatalytic materials.

Structural insights into a spindle-shaped archaeal virus with a sevenfold symmetrical tail

Archaeal viruses with a spindle-shaped virion are abundant and widespread in extremely diverse environments. However, efforts to obtain the high-resolution structure of a spindle-shaped virus have been unsuccessful. Here, we present the structure of SSV19, a spindle-shaped virus infecting the hyperthermophilic archaeon Sulfolobus sp. E11-6. Our near-atomic structure reveals an unusual sevenfold symmetrical virus tail consisting of the tailspike, nozzle, and adaptor proteins. The spindle-shaped capsid shell is formed by seven left-handed helical strands, constructed of the hydrophobic major capsid protein, emanating from the highly glycosylated tail assembly. Sliding between adjacent strands is responsible for the variation of a virion in size. Ultrathin sections of the SSV19-infected cells show that SSV19 virions adsorb to the host cell membrane through the tail after penetrating the S-layer. The tailspike harbors a putative endo-mannanase domain, which shares structural similarity to a Bacteroides thetaiotaomicro endo-mannanase. Molecules of glycerol dibiphytanyl glycerol tetraether lipid were observed in hydrophobic clefts between the tail and the capsid shell. The nozzle protein resembles the stem and clip domains of the portals of herpesviruses and bacteriophages, implying an evolutionary relationship among the archaeal, bacterial, and eukaryotic viruses.

(Invited) Towards a FRET Based DNA SAM Biosensor for Detection of Nucleic Acids

Rapid and sensitive detection of nucleic acids is an essential tool in many medical and clinical settings, that allows for fast diagnosis of bacterial and viral infections. Here, we present a DNA FRET-based biosensor to detect a hybridization event on a DNA SAM on gold surface. The monolayer was prepared by a potential assisted thiol exchange deposition, which provides better control over the surface coverage and its uniformity1. Our approach relies on a change in FRET (Förster Resonance Energy Transfer) signal caused by variations in distance between fluorophores. FRET imaging is a well-known, very sensitive technique, used commonly in many areas of chemistry and microbiology. FRET signal depends strongly on the distance between an acceptor and a donor fluorophore. It is an excellent tool to analyze small changes in DNA distance between adjacent strands and the surface2. Metal quenching also plays a major role, since fluorescence is strongly dependent on the distance from the metal surface3, which is an efficient quencher. Fluorophores, both acceptor and donor, are quenched significantly by the gold surface, this however, decreases substantially as the distance increases between the surface and fluorophore. As DNA is binding its complementary strands, the distance between the surface and the fluorophore labelled end increases.Using a self-assembly property of thiols on gold surface, we show that mixed ssDNA SAM composed of two strands of thiolated ssDNA, each labelled with a different FRET fluorophore, gives an 8-to-10-fold signal enhancement, upon DNA hybridization (see figure 1). Binding of a complementary strand rigidifies the adsorbed DNA structure, and as a result we observe the increase in signal due to weaker gold quenching and shorter distance between FRET participating fluorophores. Moreover, by utilizing a single crystal electrode, we can study different surface concentration regimes and fluorescence signal increases, based on surface crystallography and the electrode potential.(1) Leung, K. K.; Gaxiola, A. D.; Yu, H.-Z.; Bizzotto, D. Tailoring the DNA SAM Surface Density on Different Surface Crystallographic Features Using Potential Assisted Thiol Exchange. Electrochim. Acta 2018, 261, 188–197. https://doi.org/https://doi.org/10.1016/j.electacta.2017.12.114.(2) Verhaven, A.; Doneux, T.; Bizzotto, D. Application of FRET Microscopy to the Study of the Local Environment and Dynamics of DNA SAMs on Au Electrodes. Langmuir 2018, 34 (49), 14802–14810. https://doi.org/10.1021/acs.langmuir.8b02131.(3) Casanova-Moreno, J.; Yu, Z. L.; Massey-Allard, J.; Ditchburn, B.; Young, J. F.; Bizzotto, D. Luminescence in Electrochemistry; Springer International Publishing: Cham, 2017; pp 21– 77. Figure 1

Domino Effect in Allosteric Signaling of Peptide Binding

While being a thoroughly studied model of dynamic allostery in a small protein, the pathway of signal transduction in the PDZ3 domain has not been fully determined. Here, we investigate peptide binding to the PDZ3 domain by conventional and fully data-driven analyses of molecular dynamics simulations. First, we identify isoleucine 37 as a key residue by widely used computational procedures such as cross-correlation and community network analysis. Simulations of the Ile37Ala mutant show disruption of the coordinated movements of spatially close regular elements of secondary structure. Then, we employ a recently developed unsupervised, data-driven procedure to determine an optimized reaction coordinate (slowest-relaxation eigenvector) of peptide binding. We use this reaction coordinate to improve sampling by restarting additional simulations from the transition state region. Significant differences in the distributions of some of the pairwise residue distances in the bound and unbound states emerge from the projection onto the optimized reaction coordinate. The unsupervised analysis shows that allosteric signaling is transduced from the β2 strand, which forms part of the peptide binding site, to the spatially adjacent β3 and β4 strands, and from there to the α3 helix. The domino-like transmission of a (peptide binding) signal along β strands and α helices that are close in three-dimensional space is likely to be a general mechanism of allostery in single-domain proteins.

On the effect of strand damage on the operating margin of a Nb3Sn Rutherford cable

Degradation of performance in superconducting magnets can be a major concern when a brittle material like Nb3Sn is employed. Indeed, degradation can significantly alter the transport properties of a cable if, e.g. an excessive stress is applied during coil and magnet manufacturing. In this paper, we study the limiting case of a strand in a Rutherford type cable that, at a given location, does not carry any current. We refer to such strand simplistically as the ‘broken strand’, regardless of the actual cause disrupting the current carrying capability. To this aim, a model was developed using the code THEA, to describe the electric and thermal properties of the Rutherford cable of the HL-LHC 11 T dipole magnet. First, we studied the current distribution in the cable, considering a uniform current in each strand at the boundaries, namely with single strands behaving as current generators, or zero-resistance joints, namely equipotential boundaries. We concluded that the two adjacent strands to the broken strand play the most significant role in the distribution of current out of the broken strand. A similar situation was found when a strand of the cable suddenly goes normal, i.e. it quenches. We then derived the characteristic times and lengths for the current redistribution in the case of an instantaneous strand breakage. We describe in detail the procedure to extract such quantities from the simulation results, and we demonstrate a good agreement between the numerically derived characteristic times and the analytical calculation from a previous theoretical work. The results of this study help to shed light on the repercussions of degradation in brittle materials such as Nb3Sn. This subject is indeed crucial for the next generation of accelerator coils and magnets for high-energy physics projects.

Modulation of beta-amyloid aggregation using ascorbic acid

Studies have shown that the level of ascorbic acid (AA) is reduced in the brain of Alzheimer's disease (AD) patients. However, its effect on amyloid-β 1–42 (Aβ42) aggregation has not yet been elucidated. Here we investigated for the first time the effect of AA on Aβ42 aggregation using fluorescence assay, circular dichroism, atomic force microscopy, isothermal titration calorimetry, ligand docking, and molecular dynamics. Our results showed that the fibril content decreases in the growth phase when the peptides are co-incubated with AA. AA molecules bind to Aβ42 peptides with high binding affinity and a binding site for AA between the β-strands of Aβ42 oligomers prevents the stack of adjacent strands. We demonstrate the inhibitory effect of AA on the aggregation of Aβ42 and its molecular interactions, which can contribute to the development of an accessible therapy for AD and also to the design of novel drugs for other amyloidogenic diseases.

Nanomechanics combined with HDX reveals allosteric drug binding sites of CFTR NBD1

Cystic fibrosis (CF) is a frequent genetic disease in Caucasians that is caused by the deletion of F508 (ΔF508) in the nucleotide binding domain 1 (NBD1) of the CF transmembrane conductance regulator (CFTR). The ΔF508 compromises the folding energetics of the NBD1, as well as the folding of three other CFTR domains. Combination of FDA approved corrector molecules can efficiently but incompletely rescue the ΔF508-CFTR folding and stability defect. Thus, new pharmacophores that would reinstate the wild-type-like conformational stability of the ΔF508-NBD1 would be highly beneficial. The most prominent molecule, 5-bromoindole-3-acetic acid (BIA) that can thermally stabilize the NBD1 has low potency and efficacy. To gain insights into the NBD1 (un)folding dynamics and BIA binding site localization, we combined molecular dynamics (MD) simulations, atomic force spectroscopy (AFM) and hydrogen-deuterium exchange (HDX) experiments. We found that the NBD1 α-subdomain with three adjacent strands from the β-subdomain plays an important role in early folding steps, when crucial non-native interactions are formed via residue F508. Our AFM and HDX experiments showed that BIA associates with this α-core region and increases the resistance of the ΔF508-NBD1 against mechanical unfolding, a phenomenon that could be exploited in future developments of folding correctors.

Torus knots obtained by negatively twisting torus knots

Twisted torus knots are torus knots with some full twists added along some number of adjacent strands. There are infinitely many known examples of twisted torus knots which are actually torus knots. We give eight more infinite families of such twisted torus knots with a single negative twist.