Multiscale mechanical models of DNA nanotubes: A theoretical basis for the design and tuning of DNA nanocarriers

DNA nanostructures are one of potential candidates for drug carriers due to their good biocompatibility and non-specificity in vivo. A reliable prediction about mechanical properties of artificial DNA structures is desirable to improve the efficiency of DNA drug carriers, however there is only a handful of information on mechanical functionalities of DNA nanotubes (DNTs). This paper focuses on quantifying the multiscale correlations among DNT deformation, packaging conditions and surrounding factors to tune mechanical properties of DNTs. By combining WLC statistical mechanics model, Parsegian's mesoscopic liquid crystal model and Euler's continuum beam theory, we developed a multiscale DNA-frame model; then theoretically characterize the initial packed states of DNTs for the first time, and reveal the diversity mechanism in mechanical properties of DNTs induced by interchain interactions and initial packed states. Moreover, the study of parameters, such as packaging conditions and environmental factors, provides a potential control strategy for tuning mechanical properties of DNTs. These conclusions provide a theoretical basis for accurately controlling the property and deformation of DNT in various DNT dynamic devices, such as DNA nanocarriers.

Shear-Thinning in Oligomer Melts—Molecular Origins and Applications

We investigate the molecular origin of shear-thinning in melts of flexible, semiflexible and rigid oligomers with coarse-grained simulations of a sheared melt. Entanglements, alignment, stretching and tumbling modes or suppression of the latter all contribute to understanding how macroscopic flow properties emerge from the molecular level. In particular, we identify the rise and decline of entanglements with increasing chain stiffness as the major cause for the non-monotonic behaviour of the viscosity in equilibrium and at low shear rates, even for rather small oligomeric systems. At higher shear rates, chains align and disentangle, contributing to shear-thinning. By performing simulations of single chains in shear flow, we identify which of these phenomena are of collective nature and arise through interchain interactions and which are already present in dilute systems. Building upon these microscopic simulations, we identify by means of the Irving–Kirkwood formula the corresponding macroscopic stress tensor for a non-Newtonian polymer fluid. Shear-thinning effects in oligomer melts are also demonstrated by macroscopic simulations of channel flows. The latter have been obtained by the discontinuous Galerkin method approximating macroscopic polymer flows. Our study confirms the influence of microscopic details in the molecular structure of short polymers such as chain flexibility on macroscopic polymer flows.

Coexistence of Spin Canting and Metamagnetism in a One-Dimensional Mn(II) Compound Bridged by Alternating Double End-to-End and Double End-On Azido Ligands and the Analog Co(II) Compound

Two new compounds of general formula [M(N3)2(dmbpy)] in which dmbpy = 5,5′-dimethyl-2,2′-bipyridine, and M = Mn(II) or Co(II), have been solvothermally synthesized and characterized structurally and magnetically. The structures consist of zig-zag polymeric chains with alternating bis-µ(azide-N1)2M and bis-µ(azide-N1,N3)2M units in which the cis-octahedrally based coordination geometry is completed by the N,N’-chelating ligand dmbpy. The molecular structures are basically the same for each metal. The Mn(II) compound has a slightly different packing mode compared to the Co(II) compound, resulting from their different space groups. Interestingly, relatively weak interchain interactions are present in both compounds and this originates from π–π stacking between the dmbpy rings. The magnetic properties of both compounds have been investigated down to 2 K. The measurements indicate that the manganese compound shows spin-canted antiferromagnetic ordering with a Néel temperature of TN = 3.4 K and further, a field-induced magnetic transition of metamagnetism at temperatures below the TN. This finding affords the first example of an 1D Mn(II) compound with alternating double end-on (EO) and double end-to-end (EE) azido-bridged ligands, showing the coexistence of spin canting and metamagnetism. The cobalt compound shows a weak ferromagnetism resulting from a spin-canted antiferromagnetism and long-range magnetic ordering with a critical temperature, TC = 16.2 K.

Negatively Charged Ions to Probe Self-Assembled Monolayers Reorganization Driven by Interchain Interactions

A combined cyclic voltammetry (CV) and grazing angle – attenuated total reflectance (GA-ATR) IR study on the interchain interaction driven reorganization of self-assembled monolayers (SAMs) in an electric field, is...

Effect of Face-to-Face and Side-to-Side Interchain Interactions on the Electron Transport in Emeraldine Salt Polyaniline

Polyaniline (PANI) is a conductive polymer that has been studied intensively due to its high conductivity, ease of synthesis, fascinating doping mechanism, and a broad spectrum of applications. Polyaniline doped...

Static all-atom energetic mappings of the SARS-Cov-2 spike protein and dynamic stability analysis of “Up” versus “Down” protomer states

The SARS-CoV-2 virion responsible for the current world-wide pandemic COVID-19 has a characteristic Spike protein (S) on its surface that embellishes both a prefusion state and fusion state. The prefusion Spike protein (S) is a large trimeric protein where each protomer may be in a so-called Up state or Down state, depending on the configuration of its receptor binding domain (RBD) within its distal, prefusion S1 domain. The Up state is believed to allow binding of the virion to ACE-2 receptors on human epithelial cells, whereas the Down state is believed to be relatively inactive or reduced in its binding behavior. We have performed detailed all-atom, dominant energy landscape mappings for noncovalent interactions (charge, partial charge, and van der Waals) of the SARS-CoV-2 Spike protein in its static prefusion state based on two recent and independent experimental structure publications. We included both interchain interactions and intrachain (domain) interactions in our mappings in order to determine any telling differences (different so-called “glue” points) between residues in the Up and Down state protomers. The S2 proximal, fusion domain demonstrated no appreciable energetic differences between Up and Down protomers, including interchain as well as each protomer’s intrachain, S1-S2 interactions. However, the S1 domain interactions across neighboring protomers, which include the RBD-NTD cross chain interactions, showed significant energetic differences between Up-Down and Down-Down neighboring protomers. This included, for example, a key RBD residue ARG357 in the Up-Down interaction and a three residue sequence ALA520-PRO521-ALA522, associated with a turn structure in the RBD of the Up state protomer, acting as a stabilizing interaction with the NTD of its neighbor protomer. Additionally, our intra chain dominant energy mappings within each protomer, identified a significant “glue” point or possible “latch” for the Down state protomer between the S1 subdomain, SD1, and the RBD domain of the same protomer that was completely missing in the Up state protomer analysis. Ironically, this dominant energetic interaction in the Down state protomer involved the backbone atoms of the same three residue sequence ALA520-PRO521-ALA522 of the RBD with the amino acid R-group of GLN564 in the SD1 domain. Thus, this same three residue sequence acts as a stabilizer of the RBD in the Up conformation through its interactions with its neighboring NTD chain and a kind of latch in the Down state conformation through its interactions with its own SD1 domain. The dominant interaction energy residues identified here are also conserved across reported variations of SARS-CoV-2, as well as the closely related virions SARS-Cov and the bat corona virus RatG13. We conducted preliminary molecular dynamics simulations across 0.1 μ seconds to see if this latch provided structural stability and indeed found that a single point mutation (Q564G) resulted in the latch releasing transforming the protomer from the Down to the Up state conformation. Full trimeric Spike protein studies of the same mutation across all protomers, however, did not exhibit latch release demonstrating the critical importance of interchain interactions across the S1 domain, including RBD-NTD neighboring chain interactions. Therapies aimed at disrupting these noncovalent interactions could be a viable route for the physico-chemical mitigation of this deadly virion.