Extended and dynamic linker histone-DNA Interactions control chromatosome compaction.

Chromatosomes play a fundamental role in chromatin regulation, but a detailed understanding of their structure is lacking, partially due to their complex dynamics. Using single-molecule DNA unzipping with optical tweezers, we reveal that linker histone interactions with DNA are remarkably extended, with the C-terminal domain binding both DNA linkers as far as approximately ±140 bp from the dyad. In addition to a symmetrical compaction of the nucleosome core governed by globular domain contacts at the dyad, the C-terminal domain compacts the nucleosome's entry and exit. These interactions are dynamic, exhibit rapid binding and dissociation, are sensitive to phosphorylation of a specific residue, and are crucial to determining the symmetry of the chromatosome's core. Extensive unzipping of the linker DNA, which mimics its invasion by motor proteins, shifts H1 into an asymmetric, off-dyad configuration and triggers nucleosome decompaction, highlighting the plasticity of the chromatosome structure and its potential regulatory role.

Visualizing Ribbon-to-Ribbon Heterogeneity of Chemically Unzipped Wide Graphene Nanoribbons by Silver Nanowire-Based Tip-Enhanced Raman Scattering Microscopy.

Graphene nanoribbons (GNRs), a quasi-one-dimensional form of graphene, have gained tremendous attention due to their potential for next-generation nanoelectronic devices. The chemical unzipping of carbon nanotubes is one of the attractive fabrication methods to obtain single-layered GNRs (sGNRs) with simple and large-scale production.  The authors recently found that unzipping from double-walled carbon nanotubes (DWNTs), rather than single- or multi-walled, results in high-yield production of crystalline sGNRs. However, details of the resultant GNR structure, as well as the reaction mechanism, are not fully understood due to the necessity of nanoscale spectroscopy. In this regard, silver nanowire-based tip-enhanced Raman spectroscopy (TERS) is applied for single GNR analysis and investigated ribbon-to-ribbon heterogeneity in terms of defect density and edge structure generated through the unzipping process.  The authors found that sGNRs originated from the inner walls of DWNTs showed lower defect densities than those from the outer walls. Furthermore, TERS spectra of sGNRs exhibit a large variety in graphitic Raman parameters, indicating a large variation in edge structures. This work at the single GNR level reveals, for the first time, ribbon-to-ribbon heterogeneity that can never be observed by diffraction-limited techniques and provides deeper insights into unzipped GNR structure as well as the DWNT unzipping reaction mechanism.

Single-molecule, hybridization-based strategies for short nucleic acids detection and recognition with nanopores.

DNA nanotechnology has seen large developments over the last 30 years through the combination of detection and discovery of DNAs, and solid phase synthesis to increase the chemical functionalities on nucleic acids, leading to the emergence of novel and sophisticated in features, nucleic acids-based biopolymers. Arguably, nanopores developed for fast and direct detection of a large variety of molecules, are part of a revolutionary technological evolution which led to cheaper, smaller and considerably easier to use devices enabling DNA detection and sequencing at the single-molecule level. Through their versatility, the nanopore-based tools proved useful biomedicine, nanoscale chemistry, biology and physics, as well as other disciplines spanning materials science to ecology and anthropology. This mini-review discusses the progress of nanopore- and hybridization-based DNA detection, and explores a range of state-of-the-art applications afforded through the combination of certain synthetically-derived polymers mimicking nucleic acids and nanopores, for the single-molecule biophysics on short DNA structures.

Structure and Dynamics of dsDNA in Cell-like Environments.

Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA's structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.

Possible scenarios of DNA double-helix unzipping process in single-molecule manipulation experiments.

Single-molecule experiments on DNA unzipping are analyzed on the basis of the mobility of nucleic bases in complementary pairs. Two possible scenarios of DNA double-helix unzipping are proposed and studied, using the atom-atom potential function method. According to the first scenario, the base pairs transit into a 'preopened' metastable state and then fully open along the 'stretch' pathway. In this case, the DNA unzipping takes place slowly and as an equilibrium process, with the opening energies being similar to the energies obtained in thermodynamic experiments on DNA melting. The second scenario is characterized by higher opening forces. In this case, the DNA base pairs open directly along the 'stretch' pathway. It follows from our calculations that, in this scenario, the enthalpy difference between the A[Formula: see text]T and G[Formula: see text]C base pairs is much higher than in the first case. The features of the first unzipping scenario show that it can play a key role during the process of DNA genetic information transfer in vivo. It follows from our study that a peculiarity of the second scenario is that it can be used for the development of faster methods for reading genetic information in vitro.

A Cu(II)-anchored unzipped covalent triazine framework with peroxidase-mimicking properties for molecular imprinting-based electrochemiluminescent detection of sulfaquinoxaline.

The authors describe a method of electrochemiluminescent quantitation of the antibiotic sulfaquinoxaline (SQX). It relies on the use of a molecularly imprinted polymer and a Cu(II)-anchored unzipped covalent triazine framework (UnZ-CCTF) with excellent dispersibility, electrical conductivity, and peroxidaze-like activity. The framework was prepared by unzipping a covalent triazine framework under retention of basic triazine units. It was morphologically and structurally characterized by a range of instrumental techniques. The excellent peroxidase-mimicking effect of UnZ-CCTF on the electrochemiluminescence of the luminol/H2O2 system was exploited to design an ultrasensitive SQX assay with a 1.0-20 pM detection range and a detection limit of 0.76 pM (at 3δ/m). The technique was used for SQX quantitation in spiked milk samples, achieving recoveries of 94.0-104.8%. Graphical abstract Scheme of the sulfaquinoxaline molecularly imprinted electrochemiluminescence sensor based on Cu-anchored unzipped covalent triazine frameworks.

Ionic effects on the temperature-force phase diagram of DNA.

Double-stranded DNA (dsDNA) undergoes a structural transition to single-stranded DNA (ssDNA) in many biologically important processes such as replication and transcription. This strand separation arises in response either to thermal fluctuations or to external forces. The roles of ions are twofold, shortening the range of the interstrand potential and renormalizing the DNA elastic modulus. The dsDNA-to-ssDNA transition is studied on the basis that dsDNA is regarded as a bound state while ssDNA is regarded as an unbound state. The ground state energy of DNA is obtained by mapping the statistical mechanics problem to the imaginary time quantum mechanics problem. In the temperature-force phase diagram the critical force F c (T) increases logarithmically with the Na+ concentration in the range from 32 to 110 mM. Discussing this logarithmic dependence of F c (T) within the framework of polyelectrolyte theory, it inevitably suggests a constraint on the difference between the interstrand separation and the length per unit charge during the dsDNA-to-ssDNA transition.

Diffusive dynamics of DNA unzipping in a nanopore.

When an electric field is applied to an insulating membrane, movement of charged particles through a nanopore is induced. The measured ionic current reports on biomolecules passing through the nanopore. In this work, we explored the kinetics of DNA unzipping in a nanopore using our coarse-grained model (Stachiewicz and Molski, J. Comput. Chem. 2015, 36, 947). Coarse graining allowed a more detailed analysis for a wider range of parameters than all-atom simulations. Dependence of the translocation mode (unzipping or distortion) on the pore diameter was examined, and the threshold voltages were estimated. We determined the potential of mean force, position-dependent diffusion coefficient, and position-dependent effective charge for the DNA unzipping. The three molecular profiles were correlated with the ionic current and molecular events. On the unzipping/translocation force profile, two energy maxima were found, one of them corresponding to the unzipping, and the other to the translocation barriers. The unzipping kinetics were further explored using Brownian dynamics.

Physical origin of DNA unzipping.

In DNA transcription, the base pairs are unzipped in response to the enzymatic forces, separating apart two intertwined nucleotide strands. Consequently, the double-stranded DNA (dsDNA), in which two nucleotide strands wind about each other, transits structurally to the single-stranded DNA (ssDNA) in which two nucleotide strands are completely unwound and separated. The large interstrand separation is intimately related to the softening nucleotide strands. This conceptual framework is reinforced with the flow of the bending modulus toward zero under recursion relations derived from the momentum shell renormalization group. Interestingly, the stretch modulus remains the same under recursion relations. The renormalization of the bending modulus to zero has a profound implication that ssDNA has the shorter bending persistence length than does dsDNA in accordance with experiments.

Clean WS2 and MoS2 Nanoribbons Generated by Laser-Induced Unzipping of the Nanotubes.

The preparation of 1D WS(2) and MoS(2) flexible nanoribbons by laser-induced unzipping of the nanotubes is reported. The nanoribbons are of high quality, uniform width, and devoid of surface contamination. The zig-zag edges in WS(2) nanoribbons give rise to ferromagnetism at room temperature.

DNA Y structure: a versatile, multidimensional single molecule assay.

Optical trapping is a powerful single molecule technique used to study dynamic biomolecular events, especially those involving DNA and DNA-binding proteins. Current implementations usually involve only one of stretching, unzipping, or twisting DNA along one dimension. To expand the capabilities of optical trapping for more complex measurements would require a multidimensional technique that combines all of these manipulations in a single experiment. Here, we report the development and utilization of such a novel optical trapping assay based on a three-branch DNA construct, termed a "Y structure". This multidimensional assay allows precise, real-time tracking of multiple configurational changes. When the Y structure template is unzipped under both force and torque, the force and extension of all three branches can be determined simultaneously. Moreover, the assay is readily compatible with fluorescence, as demonstrated by unzipping through a fluorescently labeled, paused transcription complex. This novel assay thus allows for the visualization and precision mapping of complex interactions of biomechanical events.

All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.

The SNARE complex, consisting of three proteins (VAMP2, syntaxin, and SNAP-25), is thought to drive membrane fusion by assembling into a four-helix bundle through a zippering process. In support of the above zippering model, a recent single-molecule optical tweezers experiment by Gao et al. revealed a sequential unzipping of SNARE along VAMP2 in the order of the linker domain → the C-terminal domain → the N-terminal domain. To offer detailed structural insights to this unzipping process, we have performed all-atom and coarse-grained steered molecular dynamics (sMD) simulations of the forced unfolding pathways of SNARE using different models and force fields. Our findings are summarized as follows: First, the sMD simulations based on either an all-atom force field (with an implicit solvent model) or a coarse-grained Go model were unable to capture the forced unfolding pathway of SNARE as observed by Gao et al., which may be attributed to insufficient simulation time and inaccurate force fields. Second, the sMD simulations based on a reparameterized coarse-grained model (i.e., modified elastic network model) were able to predict a sequential unzipping of SNARE in good agreement with the findings by Gao et al. The key to this success is to reparameterize the intrahelix and interhelix nonbonded force constants against the pair-wise residue-residue distance fluctuations collected from all-atom MD simulations of SNARE. Therefore, our finding supports the importance of accurately describing the inherent dynamics/flexibility of SNARE (in the absence of force), in order to correctly simulate its unfolding behaviors under force. This study has established a useful computational framework for future studies of the zippering function of SNARE and its perturbations by point mutations with amino-acid level of details, and more generally the forced unfolding pathways of other helix bundle proteins.

Controlled fabrication of intermolecular junctions of single-walled carbon nanotube/graphene nanoribbon.

Intramolecular junctions can be formed in single-walled carbon nanotubes (SWNTs) by introducing a pentagon and/or heptagon into the hexagonal carbon lattice. The realization of these carbon-based molecular electronics is still quite challenging. Here, it is reported that nickel or cobalt catalyzed etching can be applied to partially unzip an SWNT into an intermolecular junction of SWNT/graphene nanoribbon, directly confirmed by atomic force microscopy and Raman spectroscopy.

Development of a Ratiometric Tension Sensor Exclusively Responding to Integrin Tension Magnitude in Live Cells.

Integrin tensions are critical for cell mechanotransduction. By converting force to fluorescence, molecular tension sensors image integrin tensions in live cells with a high resolution. However, the fluorescence signal intensity results collectively from integrin tension magnitude, tension dwell time, integrin density, sensor accessibility, and so forth, making it highly challenging to specifically monitor the molecular force level of integrin tensions. Here, a ratiometric tension sensor (RTS) was developed to exclusively monitor the integrin tension magnitude. The RTS consists of two tension-sensing units that are coupled in series and always subject to the same integrin tension. These two units are activated by tension to fluoresce in separate spectra and with different activation rates. The ratio of their activation probabilities, reported by fluorescence ratiometric measurement, is solely determined by the local integrin tension magnitude. RTS responded sensitively to the variation of integrin tension magnitude in platelets and focal adhesions due to different cell plating times, actomyosin inhibition, or vinculin knockout. At last, RTS confirmed that integrin tension magnitude in platelets and focal adhesions decreases monotonically with the substrate rigidity, verifying the rigidity dependence of integrin tensions in live cells and suggesting that integrin tension magnitude could be a key biomechanical factor in cell rigidity sensing.

Tunable Hybridized Morphologies Obtained through Flash Joule Heating of Carbon Nanotubes.

Hybrid carbon nanomaterials, such as those that incorporate carbon nanotubes into graphene sheets, have been found to display interesting mechanical and electrical properties because of their covalent bonding and π-π stacking domains. However, synthesis of these hybrid materials is limited by the high energetic cost of techniques like chemical vapor deposition. Here, we demonstrate the solvent- and gas-free synthesis of a 2D carbon nanotube/graphene network through flash Joule heating of pristine carbon nanotubes. The relative proportion of each morphology in the hybrid material can be tuned by varying the pulse time, as confirmed by Raman spectroscopy and microscopy. Triboindentation of epoxy composites made with the hybrid material shows increases of 162% and 64% to the hardness and Young's modulus, respectively, compared with the neat epoxy. These results demonstrate that flash Joule heating can be used to inexpensively convert carbon nanotubes into a hybrid network of nanotubes and graphene for use as an effective reinforcing additive in epoxy composites.

A pH-sensitive switch activates virulence in Salmonella.

The transcriptional regulator SsrB acts as a switch between virulent and biofilm lifestyles of non-typhoidal Salmonella enterica serovar Typhimurium. During infection, phosphorylated SsrB activates genes on Salmonella Pathogenicity Island-2 (SPI-2) essential for survival and replication within the macrophage. Low pH inside the vacuole is a key inducer of expression and SsrB activation. Previous studies demonstrated an increase in SsrB protein levels and DNA-binding affinity at low pH; the molecular basis was unknown (Liew et al., 2019). This study elucidates its underlying mechanism and in vivo significance. Employing single-molecule and transcriptional assays, we report that the SsrB DNA-binding domain alone (SsrBc) is insufficient to induce acid pH-sensitivity. Instead, His12, a conserved residue in the receiver domain confers pH sensitivity to SsrB allosterically. Acid-dependent DNA binding was highly cooperative, suggesting a new configuration of SsrB oligomers at SPI-2-dependent promoters. His12 also plays a role in SsrB phosphorylation; substituting His12 reduced phosphorylation at neutral pH and abolished pH-dependent differences. Failure to flip the switch in SsrB renders Salmonella avirulent and represents a potential means of controlling virulence.

Maturation of siRNA by strand separation: Steered molecular dynamics study.

RNA interference, particularly siRNA induced gene silencing is becoming an important avenue of modern therapeutics. The siRNA is delivered to the cells as short double helical RNA which becomes single stranded for forming the RISC complex. Significant experimental evidence is available for most of the steps except the process of the separation of the two strands. We have attempted to understand the pathway for double stranded siRNA (dsRNA) to single stranded (ssRNA) molecules using steered molecular dynamics simulations. As the process is completely unexplored we have applied force from all possible directions restraining all possible residues to convert dsRNA to ssRNA. We found pulling one strand along the helical axis direction restraining the far end of the other strand demands excessive force for ssRNA formation. Pulling a central residue of one strand, in a direction perpendicular to the helix axis, while keeping the base paired residue fixed requires intermediate force for strand separation. Moreover, we found that in this process the force requirement is quite high for the first bubble formation (nucleation energy) and the bubble propagation energies are quite small. We believe the success rate of the design of siRNA sequences for gene silencing may increase if this mechanistic knowledge is utilized for such a design process.Communicated by Ramaswamy H. Sarma.

Long-Term Exposure of MoS2 to Oxygen and Water Promoted Armchair-to-Zigzag-Directional Line Unzippings.

Understanding the long-term stability of MoS2 is important for various optoelectronic applications. Herein, we show that the long-term exposure to an oxygen atmosphere for up to a few months results in zigzag (zz)-directional line unzipping of the MoS2 basal plane. In contrast to exposure to dry or humid N2 atmospheres, dry O2 treatment promotes the initial formation of line defects, mainly along the armchair (ac) direction, and humid O2 treatment further promotes ac line unzipping near edges. Further incubation of MoS2 for a few months in an O2 atmosphere results in massive zz-directional line unzipping. The photoluminescence and the strain-doping plot based on two prominent bands in the Raman spectrum show that, in contrast to dry-N2-treated MoS2, the O2-treated MoS2 primarily exhibits hole doping, whereas humid-O2-treated MoS2 mainly exists in a neutral charge state with tension. This study provides a guideline for MoS2 preservation and a further method for generating controlled defects.

Secondary-Heteroatom-Doping-Derived Synthesis of N, S Co-Doped Graphene Nanoribbons for Enhanced Oxygen Reduction Activity.

The rareness and weak durability of Pt-based electrocatalysts for oxygen reduction reactions (ORRs) have hindered the large-scale application of fuel cells. Here, we developed an efficient metal-free catalyst consisting of N, S co-doped graphene nanoribbons (N, S-GNR-2s) for ORRs. GNRs were firstly synthesized via the chemical unzipping of carbon nanotubes, and then N, S co-doping was conducted using urea as the primary and sulfourea as the secondary heteroatom sources. The successful incorporation of nitrogen and sulfur was confirmed by elemental mapping analysis as well as X-ray photoelectron spectroscopy. Electrochemical testing revealed that N, S-GNR-2s exhibited an Eonset of 0.89 V, E1/2 of 0.79 V and an average electron transfer number of 3.72, as well as good stability and methanol tolerance. As a result, N, S-GNR-2s displayed better ORR property than either N-GNRs or N, S-GNRs, the control samples prepared with only a primary heteroatom source, strongly clarifying the significance of secondary-heteroatom-doping on enhancing the catalytic activity of carbon-based nanomaterials.

Adsorption of Cisplatin on Oxidized Graphene Nanoribbons for Improving the Uptake in Non-small Cell Lung Carcinoma Cell Line A549.

BACKGROUND: Graphene nanoribbons are nanosized strips of graphene with unique physicochemical properties like higher drug loading capacity and affinity for tumor cells. OBJECTIVE: The principal objective of this research was to develop oxidized graphene nanoribbons (O-GNRs)-based delivery system for cisplatin against non-small cell lung carcinoma cell line A549 by selective endocytosis. METHODS: The O-GNRs prepared using various synthetic steps like oxidative unzipping were evaluated for various parameters like morphology, Fourier Transform Infrared (FTIR) study, % adsorption efficacy, Differential scanning colometric (DSC) study and in-vitro efficacy studies. RESULTS: Graphene nanoribbons with the length of 200-250 nm and width of 20-40 nm were obtained. The FTIR spectrum of drug-loaded O-GNRs exhibited a characteristic peak at 1550 cm-1 (- N-H group) of cisplatin. The DSC indicated the presence of sharp endothermic peaks at 59°C (PEG), 254°C (-C-NH3) and 308.6°C (-C-Pt). The % adsorption efficiency was found to be 74.56 ± 0.798% with in-vitro release in controlled manner (63.36% ± 0.489%) for 24 h. CONCLUSION: The nanoformulation showed an average inhibition of 22.72% at a lower dose of cisplatin (> 25%) by passive targeting on cell line A549 by DNA alkylation. In the near future, graphene-based systems will establish potential nanosystems in cancer treatment due to the additive effect of graphene with various therapeutic agents.