DNA groove preference shift upon phosphorylation of a protamine-like cationic peptide.

Protamines, arginine-rich DNA-binding proteins, are responsible for chromatin compaction in sperm cells, but their DNA groove preference, major or minor, is not clearly identified. We herein study the DNA groove preference of a short protamine-like cationic peptide before and after phosphorylation, using all-atom molecular dynamics and umbrella sampling simulations. According to various thermodynamic and structural analyses, a peptide in its non-phosphorylated native state prefers the minor groove over the major groove, but phosphorylation of the peptide bound to the minor groove not only reduces its binding affinity but also brings a serious deformation of the minor groove, eliminating the minor-groove preference. As protamines are heavily phosphorylated before binding to DNA, we expect that the structurally disordered phosphorylated protamines would prefer major grooves to enter into DNA during spermatogenesis.

Corrosion-driven droplet wetting on iron nanolayers.

The classical Evans' drop describes a drop of aqueous salt solution, placed on a bulk metal surface where it displays a corrosion pit that grows over time producing further oxide deposits from the metal dissolution. We focus here on the corrosion-induced droplet spreading using iron nanolayers whose semi-transparency allowed us to monitor both iron corrosion propagation and electrolyte droplet behavior by simple optical means. We thus observed that pits grow under the droplet and merge into a corrosion front. This front reached the triple contact line and drove a non radial spreading, until it propagated outside the immobile droplet. Such chemically-active wetting is only observed in the presence of a conductive substrate that provides strong adhesion of the iron nanofilm to the substrate. By revisiting the classic Evan's drop experiment on thick iron film, a weaker corrosion-driven droplet spreading is also identified. These results require further investigations, but they clearly open up new perspectives on substrate wetting by corrosion-like electrochemical reactions at the nanometer scale.

DNA-protamine condensates under low salt conditions: molecular dynamics simulation with a simple coarse-grained model focusing on electrostatic interactions.

Protamine, a small, strongly positively-charged protein, plays a key role in achieving chromatin condensation inside sperm cells and is also involved in the formulation of nanoparticles for gene therapy and packaging of mRNA-based vaccines against viral infection and cancer. The detailed mechanisms of such condensations are still poorly understood especially under low salt conditions where electrostatic interaction predominates. Our previous study, with a refined coarse-grained model in full consideration of the long-range electrostatic interactions, has demonstrated the crucial role of electrostatic interaction in protamine-controlled reversible DNA condensation. Therefore, we herein pay our attention only to the electrostatic interaction and devise a coarser-grained bead-spring model representing the right linear charge density on protamine and DNA chains but treating other short-range interactions as simply as possible, which would be suitable for real-scale simulations. Effective pair potential calculations and large-scale molecular dynamics simulations using this extremely simple model reproduce the phase behaviour of DNA in a wide range of protamine concentrations under low salt conditions, again revealing the importance of the electrostatic interaction in this process and providing a detailed nanoscale picture of bundle formation mediated by a charge disproportionation mechanism. Our simulations also show that protamine length alters DNA overcharging and in turn redissolution thresholds of DNA condensates, revealing the important role played by entropies and correlated fluctuations of condensing agents and thus offering an additional opportunity to design tailored nanoparticles for gene therapy. The control mechanism of DNA-protamine condensates will also provide a better microscopic picture of biomolecular condensates, i.e., membraneless organelles arising from liquid-liquid phase separation, that are emerging as key principles of intracellular organization. Such condensates controlled by post-translational modification of protamine, in particular phosphorylation, or by variations in protamine length from species to species may also be responsible for the chromatin-nucleoplasm patterning observed during spermatogenesis in several vertebrate and invertebrate species.

Protic Ionic Liquids for Intrinsically Stretchable Conductive Polymers.

Inspired by the classic hard-soft acid-base theory and intrigued by a theoretical prediction of spontaneous ion exchange between poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) and hard-cation-soft-anion ionic liquid (IL), we treat PEDOT:PSS with a new IL composed of a protic (i.e., extremely hard) cation (3-methylimidazolium, p-MIM+) and an extremely soft anion (tetracyanoborate, TCB-). In fact, this protic IL (p-MIM:TCB) accomplishes the same levels of ion-exchange-mediated PEDOT-PSS separation, PEDOT-rich nanofibril formation, and electrical conductivity enhancement (∼2500 S/cm) as its aprotic counterpart (EMIM:TCB with 1-ethyl-3-methylimidazolium), the best IL used for this purpose so far. Furthermore, p-MIM:TCB significantly outperforms EMIM:TCB in terms of improving the stretchability (i.e., the highest tensile strain) of the PEDOT:PSS thin film. This enhancement is a result of the aromatic and protic cation p-MIM+, which acts as a molecular adhesive holding the exchanged ion pairs (PEDOT+:TCB----p-MIM+:PSS-) via ionic intercalation (at the surface of TCB--decorated PEDOT+ clusters) and hydrogen bonding (to PSS-), in which washing p-MIM+ out of the film degrades the stretchability while keeping the morphology. Our results offer molecular-level insight into the morphological, electrical, and mechanical properties of PEDOT:PSS and a molecular-interaction-based enhancement strategy that can be used for intrinsically stretchable conductive polymers.

Effect of phosphorylation of protamine-like cationic peptide on the binding affinity to DNA.

Protamines are more arginine-rich and more basic than histones and are responsible for providing a highly compacted shape to the sperm heads in the testis. Phosphorylation and dephosphorylation are two events that occur in the late phase of spermatogenesis before the maturation of sperms. In this work, we have studied the effect of phosphorylation of protamine-like cationic peptides using all-atom molecular dynamics simulations. Through thermodynamic analyses, we found that phosphorylation reduces the binding efficiency of such cationic peptides on DNA duplexes. Peptide phosphorylation leads to a less efficient DNA condensation, due to a competition between DNA-peptide and peptide-peptide interactions. We hypothesize that the decrease of peptide bonds between DNA together with peptide self-assembly might allow an optimal re-organization of chromatin and an efficient condensation through subsequent peptide dephosphorylation. Based on the globular and compact conformations of phosphorylated peptides mediated by arginine-phosphoserine H-bonding, we furthermore postulate that phosphorylated protamines could more easily intrude into chromatin and participate to histone release through disruption of histone-histone and histone-DNA binding during spermatogenesis.

A Molecular-Switch-Embedded Organic Photodiode for Capturing Images against Strong Backlight.

When the intensity of the incident light increases, the photocurrents of organic photodiodes (OPDs) exhibit relatively early saturation, due to which OPDs cannot easily detect objects against strong backlights, such as sunlight. In this study, this problem is addressed by introducing a light-intensity-dependent transition of the operation mode, such that the operation mode of the OPD autonomously changes to overcome early photocurrent saturation as the incident light intensity passes the threshold intensity. The photoactive layer is doped with a strategically designed and synthesized molecular switch, 1,2-bis-(2-methyl-5-(4-cyanobiphenyl)-3-thienyl)tetrafluorobenzene (DAB). The proposed OPD exhibits a typical OPD performance with an external quantum efficiency (EQE) of <100% and a photomultiplication behavior with an EQE of >100% under low-intensity and high-intensity light illuminations, respectively, thereby resulting in an extension of the photoresponse linearity to a light intensity of 434 mW cm-2 . This unique and reversible transition of the operation mode can be explained by the unbalanced quantum yield of photocyclization/photocycloreversion of the molecular switch. The details of the operation mechanism are discussed in conjunction with various photophysical analyses. Furthermore, they establish a prototype image sensor with an array of molecular-switch-embedded OPD pixels to demonstrate their extremely high sensitivity against strong light illumination.

Hard-Cation-Soft-Anion Ionic Liquids for PEDOT:PSS Treatment.

A promising conducting polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) experiences significant conductivity enhancement when treated with proper ionic liquids (ILs). Based on the hard-soft-acid-base principle, we propose a combination of a hydrophilic hard cation A+ (instead of the commonly used 1-ethyl-3-methyl imidazolium, EMIM+) and a hydrophobic soft anion X- (such as tetracyanoborate, TCB-) as the best ILs for this purpose. Such ILs would decouple hydrophilic-but-insulating PSS- from conducting-but-hydrophobic PEDOT+ most efficiently by strong interactions with hydrophilic A+ and hydrophobic X-, respectively. Such a favorable ion exchange between PEDOT+:PSS- and A+:X- ILs would allow the growth of conducting PEDOT+ domains decorated by X-, not disturbed by PSS- or A+. Using density functional theory calculations and molecular dynamics simulations, we demonstrate that a protic cation- (aliphatic N-alkyl pyrrolidinium, in particular) combined with the hydrophobic anion TCB- indeed outperforms EMIM+ by promptly leaving hydrophobic TCB- and strongly binding to hydrophilic PSS-.

Effect of Bulky Atom Substitution on Backbone Coplanarity and Electrical Properties of Cyclopentadithiophene-Based Semiconducting Polymers.

The effect of atomic substitution on the optoelectronic properties of a coplanar donor-acceptor (D-A) semiconducting polymer (SPs), prepared using cyclopentadithiophene (CDT) and 2,1,3-benzothiadiazole (BT) moieties, is investigated. By substituting a carbon atom in the BT unit with CF or C-Cl, two random D-A SPs are prepared, and their optoelectronic properties are thoroughly investigated. Density functional theory calculations demonstrate that the fluorinated polymer has a slightly smaller dihedral angle (Ï´ = 0.6°) than the pristine polymer (Ï´ = 1.9°) in its lowest-energy conformation, implying efficient charge transport through the coplanar backbone of the fluorinated polymer. However, the chlorinated polymer shows the lowest energy at a relatively larger dihedral angle (Ï´ = 139°) due to the steric hindrance induced by bulky chlorine atoms in the backbone, thereby leading to thin-film morphology, which is unfavorable for charge transport. Consequently, the fluorinated polymer yields the highest field-effect mobility (µ) of 0.57 cm2 V-1 s-1 , slightly higher than that of the pristine polymer (µ = 0.33 cm2 V-1 s-1 ), and the extended device lifetime of organic field-effect transistors over 12 d without any encapsulation layers. The results of this study provide design guidelines for air-stable D-A SPs.

DNA-assisted assembly of cationic gold nanoparticles: Monte Carlo simulation.

DNA-assisted assembly of ligand-stabilized gold nanoparticles is studied using Monte Carlo simulations with coarse-grained models for DNA and AuNP. Their interaction in a periodic simulation box is described by a combination of electrostatic and pairwise hard core potentials. We first probe the self-assembly of AuNPs resulting in an ordered distribution on a single fixed DNA strand. Subsequently, the effective force calculated between a pair of parallel DNA in the presence of AuNPs shows the attraction between them at short distance associated to a stable equilibrium position. Finally, the osmotic pressure calculated in a compact DNA-AuNP lattice with various amounts of monovalent salt ions shows that an increasing amount of salt prevents aggregate formation.

Protamine-Controlled Reversible DNA Packaging: A Molecular Glue.

Packaging paternal genome into tiny sperm nuclei during spermatogenesis requires 106-fold compaction of DNA, corresponding to a 10-20 times higher compaction than in somatic cells. While such a high level of compaction involves protamine, a small arginine-rich basic protein, the precise mechanism at play is still unclear. Effective pair potential calculations and large-scale molecular dynamics simulations using a simple idealized model incorporating solely electrostatic and steric interactions clearly demonstrate a reversible control on DNA condensates formation by varying the protamine-to-DNA ratio. Microscopic states and condensate structures occurring in semidilute solutions of short DNA fragments are in good agreement with experimental phase diagram and cryoTEM observations. The reversible microscopic mechanisms induced by protamination modulation should provide valuable information to improve a mechanistic understanding of early and intermediate stages of spermatogenesis where an interplay between condensation and liquid-liquid phase separation triggered by protamine expression and post-translational regulation might occur. Moreover, recent vaccines to prevent virus infections and cancers using protamine as a packaging and depackaging agent might be fine-tuned for improved efficiency using a protamination control.

Molecular Dynamics of PEDOT:PSS Treated with Ionic Liquids. Origin of Anion Dependence Leading to Cation Design Principles.

Conductivity enhancement of PEDOT:PSS via the morphological change of PEDOT-rich domains has been achieved by introducing a 1-ethyl-3-methylimidazolium (EMIM)-based ionic liquid (IL) into its aqueous solution, and the degree of such change varies drastically with the anion coupled to the EMIM cation constituting the IL. We carry out a series of molecular dynamics simulations on various simple model systems for the extremely complex mixtures of PEDOT:PSS and EMIM:X IL in water, varying the anion X, the IL concentration, the oligomer model of PEDOT:PSS, and the size of the model systems. The common characteristic found in all simulations is that although planar hydrophobic anions X are the most efficient for ion exchange between PEDOT:PSS and EMIM:X, they tend to bring together planar EMIM cations to PEDOT-rich domains, disrupting PEDOT π-stacks with PEDOT-X-EMIM intercalating layers. Nonplanar hydrophobic anions, which leave most of EMIM cations in water, are efficient for both ion exchange and the formation of extended PEDOT π-stacks, as observed in experiments. Based on such findings, we propose a design principle for new cations replacing EMIM; nonplanar hydrophilic cations combined with hydrophobic anions should improve IL efficiency for PEDOT:PSS treatment.

Protamine Binding Site on DNA: Molecular Dynamics Simulations and Free Energy Calculations with Full Atomistic Details.

Protamine, an arginine-rich basic protein, compacts DNAs in sperm nuclei to densities higher than those in somatic cells. The mechanism of this compaction in sperm cells is even less clear than in somatic cells. Even the preferred binding site, if any, of protamine on DNA is not clearly identified. In this work, we carry out fully atomistic (or all-atom) molecular dynamics simulations to estimate the relative stabilities of protamine binding sites on DNA. Free energy calculated with umbrella sampling on a short arginine stretch bound to the major and minor grooves suggests that a short arginine stretch would prefer the DNA major groove as its binding site. Complementary umbrella sampling simulations where an arginine stretch or a whole protamine is transferred from the major to the minor groove also lead to the same conclusion. We find that the protamine located in the major groove better utilizes the DNA backbone as the binding site and represents the best compromise between enthalpy and entropy gain.

Ionic Liquid for PEDOT:PSS Treatment. Ion Binding Free Energy in Water Revealing the Importance of Anion Hydrophobicity.

Water solubility of PEDOT:PSS conducting polymer is achieved by PSS at the expense of disturbing the crystallinity and electron mobility of PEDOT. Recently, PEDOT crystallinity and electron mobility have been improved by treating the PEDOT:PSS aqueous solution with 1-ethyl-3-methylimidazolium- (EMIM-) based ionic liquids (IL) EMIM:X. The amount of such improvement varies drastically with the anion X coupled to EMIM cation in the IL. Herein, using umbrella-sampling molecular dynamics simulations on the aqueous solutions of a minimal model of PEDOT:PSS mixed with various EMIM:X ILs, we show that the solvation of each ion in water plays a major role in the free energies of ion binding and exchange. Anions X efficient for the improvement are weakly stabilized by hydration (i.e., hydrophobic) and prefer binding to hydrophobic PEDOT than to hydrophilic EMIM, favoring the ion exchange. In order to fulfill our design principle, a quantitative criterion based on hydration free energy is proposed to select efficient hydrophobic anions X.

Mass spectrometry imaging of untreated wet cell membranes in solution using single-layer graphene.

We report a means by which atomic and molecular secondary ions, including cholesterol and fatty acids, can be sputtered through single-layer graphene to enable secondary ion mass spectrometry (SIMS) imaging of untreated wet cell membranes in solution at subcellular spatial resolution. We can observe the intrinsic molecular distribution of lipids, such as cholesterol, phosphoethanolamine and various fatty acids, in untreated wet cell membranes without any labeling. We show that graphene-covered cells prepared on a wet substrate with a cell culture medium reservoir are alive and that their cellular membranes do not disintegrate during SIMS imaging in an ultra-high-vacuum environment. Ab initio molecular dynamics calculations and ion dose-dependence studies suggest that sputtering through single-layer graphene occurs through a transient hole generated in the graphene layer. Cholesterol imaging shows that methyl-ß-cyclodextrin preferentially extracts cholesterol molecules from the cholesterol-enriched regions in cell membranes.

Heterostructured Titanium Oxynitride-Manganese Cobalt Oxide Nanorods as High-Performance Electrode Materials for Supercapacitor Devices.

Metal oxynitrides have been considered recently as emerging electrode materials for supercapacitors. Herein, we converted titanate nanotubes into a series of titanium oxynitride (TiON) nanorods at nitridation temperatures of 800, 900, and 1000 °C in ammonia gas and tested them as supercapacitor electrodes. TiON-800, TiON-900, and TiON-1000 showed capacities of 60, 140, and 71 F g-1, respectively, at a current density of 1 A g-1. However, because of TiON's low capacity, a heterostructure (TiON-900/MnCo2O4) was designed based on the optimized TiON with MnCo2O4 (MCO). The heterostructure TiON-900-MCO and MCO electrode materials showed specific capacities of 515 and 381 F g-1, respectively, at a current density of 1 A g-1. The cycling stability retention of TiON-900 and MCO were 75 and 68%, respectively; moreover, the heterostructure of TiON-900-MCO reached 78% at a current density of 5 A g-1 over 5000 cycles. The increased capacity and sustained cycling stability retention are attributable to the synergistic effect of TiON-900 and MCO. A coin cell (CC)-type symmetric supercapacitor prototype of TiON-900-MCO was fabricated and tested in the voltage range of 0.0-2.0 V in 1 M LiClO4 in propylene carbonate/dimethyl carbonate electrolyte, and a 79% cycling retention capacity of TiON-900-MCO-CC was achieved over 10 000 cycles at a current density of 250 mA g-1. We demonstrated a prototypical single cell of TiON-900-MCO-CC as a sustained energy output by powering a red-light emitting diode that indicated TiON-900-MCo electrode materials' potential application in commercial supercapacitor devices.

Liquid crystal ordering of nucleic acids.

Several analytical calculations and computer simulations propose that cylindrical monodispersive rods having an aspect ratio (ratio of length to diameter) greater than 4 can exhibit liquid crystal (LC) ordering. But, recent experiments demonstrated the signature of LC ordering in systems of 4- to 20-base pair (bp) long nucleic acids (NAs) that do not satisfy the shape anisotropy criterion. Mechanisms of end-to-end adhesion and stacking have been proposed to explain this phenomenon. In this study, using all-atom molecular dynamics (MD) simulation, we explicitly verify the end-to-end stacking of double-stranded RNA (dsRNA) and demonstrate the LC ordering at the microscopic level. Using umbrella sampling (US) calculation, we quantify the potential of mean force (PMF) between two dsRNAs for various reaction coordinates (RCs) and compare our results with previously reported PMFs for double-stranded DNA (dsDNA). The PMF profiles demonstrate the anisotropic nature of inter-NA interaction. We find that, like dsDNA, dsRNA also prefers to stack on top of each other while repelling sideways, leading to the formation of supra-molecular-columns that undergo LC ordering at high NA volume fraction (φ). We also demonstrate and quantify the nematic ordering of the RNAs using several hundred nanosecond-long MD simulations that remain almost invariant for different initial configurations and under different external physiological conditions.

Orientation Dependence of Inter-NCP Interaction: Insights into the Behavior of Liquid Crystal Phase and Chromatin Fiber Organization.

We report equilibrium and nonequilibrium molecular dynamics (MD) simulations of two nucleosome core particles (NCPs) stacked with their dyad axes oriented in parallel or antiparallel fashion. From the equilibrium trajectories, we determine the bridging behavior of different histone tails and observe that different sets of histone tails play important roles in the two orientations in stabilizing the NCP stack. While the H4 and H2A tails play important intermediary roles in the parallel stack, the H3 and H2B tails are important in the antiparallel stack. We use steered MD simulations to unstack the two NCPs and find a stark difference in their unstacking pathways. While the average rupture force was found to be higher for the parallel stack, the work done for complete unstacking was similar for both orientations. We use Jarzynski equality to determine the PMF profiles along the unstacking pathway, relate our findings to the behavior of NCP mesophases, and derive insights into the enigmatic nucleosomal organization in the chromatin fiber.

Molecular Engineering of a Donor-Acceptor Polymer To Realize Single Band Absorption toward a Red-Selective Thin-Film Organic Photodiode.

Herein, we explore the strategy of realizing a red-selective thin-film organic photodiode (OPD) by synthesizing a new copolymer with a highly selective red-absorption feature. PCZ-Th-DPP, with phenanthrocarbazole (PCZ) and diketopyrrolopyrrole (DPP) as donor and acceptor units, respectively, was strategically designed/synthesized based on a time-dependent density functional theory calculation, which predicted the significant suppression of the band II absorption of PCZ-Th-DPP due to the extremely efficient intramolecular charge transfer. We demonstrate that the synthesized PCZ-Th-DPP exhibits not only a high absorption coefficient within the red-selective band I region, as theoretically predicted, but also a preferential face-on intermolecular structure in the thin-film state, which is beneficial for vertical charge extraction as an outcome of a glancing incidence X-ray diffraction study. By employing PCZ-Th-DPP as a photoactive layer of Schottky OPD, to fully match its absorption characteristic to the spectral response of the red-selective OPD, we demonstrate a genuine red-selective specific detectivity in the order of 1012 Jones while maintaining a thin active layer thickness of ∼300 nm. This work demonstrates the possibility of realizing a full color image sensor with a synthetic approach to the constituting active layers without optical manipulation.

Correlational Effects of the Molecular-Tilt Configuration and the Intermolecular van der Waals Interaction on the Charge Transport in the Molecular Junction.

Molecular conformation, intermolecular interaction, and electrode-molecule contacts greatly affect charge transport in molecular junctions and interfacial properties of organic devices by controlling the molecular orbital alignment. Here, we statistically investigated the charge transport in molecular junctions containing self-assembled oligophenylene molecules sandwiched between an Au probe tip and graphene according to various tip-loading forces ( FL) that can control the molecular-tilt configuration and the van der Waals (vdW) interactions. In particular, the molecular junctions exhibited two distinct transport regimes according to the FL dependence (i.e., FL-dependent and FL-independent tunneling regimes). In addition, the charge-injection tunneling barriers at the junction interfaces are differently changed when the FL ≤ 20 nN. These features are associated to the correlation effects between the asymmetry-coupling factor (η), the molecular-tilt angle (θ), and the repulsive intermolecular vdW force ( FvdW) on the molecular-tunneling barriers. A more-comprehensive understanding of these charge transport properties was thoroughly developed based on the density functional theory calculations in consideration of the molecular-tilt configuration and the repulsive vdW force between molecules.

Sub-nanometer pore formation in single-molecule-thick polyurea molecular-sieving membrane: a computational study.

A polymeric network of 1-(4-tritylphenyl)urea (TPU) built via layer-by-layer cross-linking polymerization has been proposed to be an excellent mesh equipped with single-molecule-thick pores (i.e., cyclic poly-TPU rings), which can sieve glucose (∼0.7 nm) out of its mixture with urea for hemodialysis applications. Monte Carlo search for the lowest-energy conformation of various sizes of poly-TPU rings unravels the origin of narrow pore size distribution, which is around the sizes of dimer and trimer rings (0.3-0.8 nm). Flexible rings larger than the dimer and trimer rings, in particular tetramer rings, prefer a twisted conformation in the shape of the infinity symbol (∞, which looks like two dimer rings joined together) locked by a hydrogen bond between diphenylurea linker groups facing each other. Translocation energy profiles across these TPU rings reveal their urea-versus-glucose sieving mechanism: glucose is either too large (to enter dimers and twisted tetramers) or too perfectly fit (to exit trimers), leaving only a dimer-sized free space in the ring, whereas smaller-sized urea and water pass through these effective dimer-sized rings (bare dimers, twisted tetramers, and glucose-filled trimers) without encountering a substantial energy barrier or trap.