Unzipping Process Research Articles

Localization and discrimination of GG mismatch in duplex DNA by synthetic ligand-enhanced protein nanopore analysis.

Mismatched base pairs in DNA are the basis of single-nucleotide polymorphism, one of the major issues in genetic diseases. However, the changes of physical and chemical properties of DNA caused by single-site mismatches are often influenced by the sequence and the structural flexibility of the whole duplex, resulting in a challenge of direct detection of the types and location of mismatches sensitively. In this work, we proposed a synthetic ligand-enhanced protein nanopore analysis of GG mismatch on DNA fragment, inspired by in silico investigation of the specific binding of naphthyridine dimer (ND) on GG mismatch. We demonstrated that both the importing and unzipping processes of the ligand-bound DNA duplex can be efficiently slowed down in α-hemolysin nanopore. This ligand-binding induced slow-down effect of DNA in nanopore is also sensitive to the relative location of the mismatch on DNA duplex. Especially, the GG mismatch close to the end of a DNA fragment, which is hard to be detected by either routine nanopore analysis or tedious nanopore sequencing, can be well differentiated by our ND-enhanced nanopore experiment. These findings provide a promising strategy to localize and discriminate base mismatches in duplex form directly at the single-molecule level.

Chemical Recycling of Poly(cyclohexene carbonate)s via Synergistic Catalysis.

Chemical recycling of polymers to the corresponding monomers offers a valuable solution to address the current plastics crisis for creating an ideal and circular polymer economy. Here, we present a bimetallic synergistic depolymerization of the widely studied CO2-based polycarbonates, poly(cyclohexene carbonate)s, to epoxide monomers efficiently. The bimetallic CrIII-complex-mediated highly selective depolymerization and repolymerization was achieved via the regulation of reaction temperature, thus closing the circular loop of poly(cyclohexene carbonate)s in situ. Mechanistic investigation has revealed that the formation of epoxides undergoes a direct chain-end unzipping process. A bimetallic catalysis involving a nucleophilic attack of the metal-alkoxide species toward the methine carbon atom bound with an adjacent carbonyl that is activated by the other metal center features a lower energy barrier in DFT calculations, which promotes the epoxide extrusion.

Effect of reaction temperature and concentration of H2SO4 acid in the unzipping process of carbon nanotubes to form graphene nanoribbons

Unzipping carbon nanotubes (CNTs) is one of the methods to produce graphene nanoribbons. In this research, we investigated the effect of reaction temperature and concentration of H2SO4 acid on graphene nanoribbons (GNRs) formation. By increasing the reaction temperature, the transformation of CNTs to form GNRs is getting better. The results showed that the unzipping process was strongly affected by temperature. At 100 °C temperature, GNRs obtained 100% yield with a purity of +99%C and surface area of 250 m2/g. Furthermore, H2SO4 acid is the only environment for the wet chemical reaction, it doesn’t affect GNRs quality so the low concentration of acid will be utilized and contribute to reducing the environmental impact in the world. The GNRs will be a potential material for both anode and cathode in batteries and supercapacitors to get higher energy density and fast charging properties.

Force-induced unzipping of DNA in the presence of solvent molecules

The melting of double-stranded DNA (dsDNA) in the presence of solvent molecules is a fundamental process with significant implications for understanding the thermal and mechanical behavior of DNA and its interactions with the surrounding environment. The solvents play an essential role in the structural transformation of DNA subjected to a pulling force. In this study, we simulate the thermal and force induced denaturation of dsDNA and elucidate the solvent dependent melting behavior, identifying key factors that influence the stability of DNA melting in presence of solvent molecules. Using a statistical model, we first find the melting profile of short heterogeneous DNA molecules in the presence of solvent molecules in Force ensemble. We also investigate the effect of solvent's strengths on the melting profile of DNA. In the force ensemble, we consider two homogeneous DNA chains and apply the force on different locations along the chain in the presence of solvent molecules. Different pathways manifest the melting of the molecule in both ensembles, and we found several interesting features of melting DNA in a constant force ensemble, such as lower critical force when the chain is pulled from the base pair close to a solvent molecule. The results provide new insights into the force-induced unzipping of DNA and could be used to develop new methods for controlling the unzipping process. By providing a better understanding of melting and unzipping of dsDNA in the presence of solvent molecules, this study provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA nanostructures.

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.

First-principles investigation of interaction between the atomic oxygen species and carbon nanostructures

• The following trends in the value of adsorption energies of triplet oxygen atoms on the carbon nanostructures were identified: diamond-like structures (sp 3 ) < graphene-like structures (sp 2 ) < fullerenes & nanotubes (sp 2 , pentagons, high curvature). • For the graphene flake and fullerene structures there are common precursors for carbon desorption in the form of CO/CO 2 molecules: (1) ether-ether-epoxy precursor and (2) epoxy-ether-epoxy. • Etching of sp 3 hybridized carbon structures can proceed faster than etching of sp 2 structures. • For graphene structure, unzipping process is more favorable than reduction process at lower temperatures. In this work we perform a systematic theoretical study of oxidation process of different carbon nanomaterials by atomic oxygen. In order to understand the atomistic mechanism of interaction between atomic oxygen and carbon nanostructures and to explain experimental results on their oxygen treatment, first-principles calculations were performed. Influence of spin state of the atomic oxygen on its interaction with different carbon nanostructures (finite size graphene flake, carbon nanotube, fullerene, diamondoid) was investigated. We found that the structure and stability of the adsorption complexes are determined by the oxygen spin state and depend on the carbon nanostructure morphology and hybridization. The atomistic mechanisms of chemical transformations driven by high local oxygen coverage, such as CO/CO 2 desorption and graphene unzipping, were investigated. Calculated barriers of CO 2 desorption allow to explain experimental data on thermal reduction of the oxidized carbon structures. In case of graphene, competition between channels resulting in CO 2 desorption and plane unzipping was observed. We found that for the temperatures ~400 K and lower unzipping process is favorable, since CO 2 desorption precursor formation proceeds through higher activation barrier (1.3 eV) and requires temperatures above 450 K.

Catalyst and substrate-free synthesis of graphene nanosheets by unzipping C60 fullerene clusters using a pulse current method

Transformation of carbon nanomaterials to different allotropes is a very promising approach for preparing a variety of carbon nanomaterials. Herein, we present the catalyst and substrate-free synthesis of graphene (G) nanosheets from fullerene (C60) clusters. G nanosheets were formed from an unzipping process of fullerene clusters using a direct pulse current via a pulsed current sintering method, in which carbon atoms were evaporated from fullerenes as a result of generation of locally high temperatures. Fullerene clusters and G nanosheets were analyzed by different characterization tools and it was demonstrated that G can be successfully synthesized using transformation of fullerenes as starting materials without the need for catalyst or substrate.

Current pulse signature of native kanamycin aptamer and its implication for molecular interactions on a single protein nanopore sensing interface

Due to the pore size limitation of single α-hemolysin (α-HL) nanopore sensing interface, ssDNA with secondary conformations can only pass through the nanopore after unzipping as linear ssDNA. For hairpin DNA, a tail with 15–50 bases was usually added to the stem terminal (5′ or 3′) to facilitate the capture rate and unzipping process, and the typical translocation signal behaves as a square wave with a short dip at the end of the pulse. In this work, the pulse signal of native kanamycin aptamer, a hairpin DNA without the added long tail, was investigated with the single nanopore sensing interface, and different current pulse pattern was observed. The pulse signal exhibited two precise current levels with significantly extended duration of the second, and both duration of the two levels correlate to the interaction of the aptamer to kanamycin. Moreover, the pulse signal not only reveals the selectivity of the aptamer to its target, but also sensitive to the loop sequence change of the aptamer. This work shows that a single nanopore sensing interface could be used as a unique alternative means for interaction investigation of hairpin DNA aptamer without labeling or adding the extra-long tail.

Predicting the rapid devolatilization of mineral-free cellulose

This paper extends the validation of a reaction mechanism for the devolatilization of mineral-free cellulose called “cel-FC.” A single set of model parameters accurately interprets the partitioning of raw cellulose into oil, noncondensables, and solid residue and oil molecular weight distributions (MWDs) for temperatures to 600 °C, heating rates from 60 to 6000°C/s, contact times to 120 s, and pressures of vacuum and 0.1 MPa. The analysis incorporates depolymerization via random scission and unzipping from chain ends; charring via monomer decomposition, spontaneous charring, and thermal annealing; fragmentation statistics, and the flash distillation analogy. Random depolymerization is responsible for the induction of primary cellulose devolatilization and eventually generates chains short enough to vaporize. The accompanying surge in the relative concentrations of chain ends activates the unzipping process. The fastest oil production rates are driven by scission plus unzipping and mediated by flash distillation. Whenever vaporization of longer oil precursors is limited, unzipping delivers monomer derivatives into the oil. Whenever longer volatile chains can freely vaporize they are no longer subject to unzipping or scission, so there are necessarily fewer monomers in oil. This is why ultimate oil yields are essentially the same across broad ranges of heating rate, temperature (given sufficient contact time at low temperatures), and pressure, and why oil MWDs shift toward heavier molecular weights for progressively faster heating rates, hotter temperatures, and lower pressures. Cel-FC interprets the optimal primary products - 94 wt% oil plus a mixture of light oxygenates, CO2, and CO in H2O – as the limit of depolymerization via scission and unzipping without any charring reactions. Monomer decomposition and spontaneous charring produce hardly any bio-char from mineral-free cellulose but are major sources of noncondensable gases and responsible for greater gas yields for slower heating rates, hotter temperatures, and higher pressures.

Photoluminescent Semiconducting Graphene Nanoribbons via Longitudinally Unzipping Single-Walled Carbon Nanotubes.

The lack of a sizeable band gap has so far prevented graphene from building effective electronic and optoelectronic devices despite its numerous exceptional properties. Intensive theoretical research reveals that a band gap larger than 1 eV can only be achieved in sub-3 nm wide graphene nanoribbons (GNRs), but real fabrication of such ultranarrow GNRs still remains a critical challenge. Herein, we demonstrate an approach for the synthesis of ultranarrow and photoluminescent semiconducting GNRs by longitudinally unzipping single-walled carbon nanotubes. Atomic force microscopy reveals the unzipping process, and the resulting 2.2 nm wide GNRs are found to emit strong and sharp photoluminescence at ∼685 nm, demonstrating a very desirable semiconducting nature. This band gap of 1.8 eV is further confirmed by follow-up photoconductivity measurements, where a considerable photocurrent is generated, as the excitation wavelength becomes shorter than 700 nm. More importantly, our fabricated GNR field-effect transistors (FETs), by employing the hexagonal boron nitride-encapsulated heterostructure to achieve edge-bonded contacts, demonstrate a high current on/off ratio beyond 105 and carrier mobility of 840 cm2/V s, approaching the theoretical scattering limit in semiconducting GNRs at room temperature. Especially, highly aligned GNR bundles with lengths up to a millimeter are also achieved by prepatterning a template, and the fabricated GNR bundle FETs show a high on/off ratio reaching 105, well-defined saturation currents, and strong light-emitting properties. Therefore, GNRs produced by this method open a door for promising applications in graphene-based electronics and optoelectronics.

Transformation from antiferromagnetic target skyrmion to antiferromagnetic skyrmion by unzipping process through a confined nanostructure

The manipulation of magnetic skyrmion has been attracting considerable attention for the fundamental physical perspective and promising applications in spintronics, ascribed to their nontrivial topology and emergent electrodynamics. However, there is a hindrance to the transmission of a skyrmion in the racetrack memory due to the skyrmion Hall effect (SHE). Antiferromagnetic (AFM) materials provide a possibility to overcome the SHE in high-velocity data writing. Herein, we systematically investigate the generation and motion of an AFM target skyrmion under the spin-polarized current. We found that the AFM target skyrmion can reach a velocity of 1088.4 m s−1 under the current density of 8 × 1012 A m−2, which is lower than 1269.8 m s−1 for the AFM skyrmion. This slowdown can be ascribed to the deformation of AFM target skyrmion in the process of motion on a nanotrack. In addition, we observed a transformation from AFM target skyrmion to AFM skyrmion by the unzipping process through a constricted nanostructure which is mediated by the formation of AFM domain wall. Two energy barriers need to be overcome in this dynamic process, i.e. 2.93 × 104 eV from AFM target skyrmion to AFM domain wall, and 7.625 × 103 eV from AFM domain wall to AFM skyrmion. Our results provide guidance for future target skyrmion-based devices.

Profiling selective binding to promoter CpG islands by a single-DNA mechanical footprinting assay

Profiling selective binding to promoter CpG islands by a single-DNA mechanical footprinting assay

Rational structure design for enhanced uranium(VI) capture and beyond: From carbon nanotubes to graphene oxide nanoribbons

Graphene oxide nanoribbons (GONRs) that are derived from chemical unzipping of multi-walled carbon nanotubes (MWCNTs) for uranium capture have been reported, but little is known about the complex chemical interactions between uranium(VI) and GONRs with different unzipping level. An unzipping process from MWCNTs to GONRs was identified using field emission scanning electron microscopy (FE-SEM), Raman spectroscopy, X-ray powder diffraction (XRD), Fourier transformed infrared (Ft-IR) spectroscopy and X-ray photoelectron spectroscopy (XPS). The uranium(VI) adsorption performances of GONRs with different unzipping level were investigated, and the enhanced U(VI) capture was closely related to their structures and surface oxygen-containing functional groups. The interaction mechanism at the molecular level demonstrated that UO22+ mainly complexed with carboxyl and hydroxyl groups at the edges of the GONRs. In addition, further functionalization has been proposed for expanding the potential applications of GONRs.

Kinetics and coupled dynamics of dewetting and chemical reaction in Si/$$\hbox {SiO}_2$$/Si system

We report on the observation of a coupling between the dewetting of a Si layer on $$\hbox {SiO}_{{2}}$$ induced by surface/interface energy minimization and the etching between both materials due to the $$\hbox {Si}+\hbox {SiO}_{2}\longrightarrow 2$$ $$\hbox {SiO}^\uparrow _g$$ reaction. In the limit of a thin $$\hbox {SiO}_{{2}}$$ layer ( $$\le 10 \,\hbox {nm}$$ ) sandwiched between a Si layer and a Si handle wafer, the front of Si dewetting and the front of $$\hbox {SiO}_{{2}}$$ etching coexist in a narrow region. The interplay between both phenomena gives rise to specific morphologies. We show that extended Si fingers formed by dewetting are stabilized with respect to Rayleigh–Plateau-type instability over tenth of microns thanks to a localized etching of the $$\hbox {SiO}_{{2}}$$ layer. The breakup of this structure occurs abruptly by an unzipping process combining dewetting and etching phenomena. We also put in evidence that Si rings are created with a thin $$\hbox {SiO}_{{2}}$$ layer in the center. These processes are thermally activated with an activation energy of $$2.4\pm 0.5 \,\hbox {eV}$$ and $$4.0\pm 0.5 \,\hbox {eV}$$ , respectively, for dewetting and the etching reaction. All these results highlight the respective roles of wetting and etching in Si/ $$\hbox {SiO}_{{2}}$$ /Si system dynamics and could be a stepping stone for the development of advanced processes based on Silicon-On-Insulator technology.

Long-Range Ordered Water Correlations between A–T/C–G Nucleotides

Summary The interactions between complementary base pairs are crucial to the helical duplex structure of DNA. Although base-base interactions have been widely reported, the study of long-range interactions in the base-pairing processes is still a major challenge in this field. Here, we first study the long-range interactions between the base pairs by atomic force microscopy-based single-molecule force spectroscopy (SMFS). The SMFS results of A–T/C–G imply that there are weak long-range interactions between them, which have a range of 15–25 nm. Raman spectroscopy results imply that these weak interactions can be attributed to multiplex hydrogen bond interaction of ordered water structure between A–T/C–G nucleotides. In addition, the theoretical calculations deduce that the ideal structure of these water molecules exhibits a specific helical structure. Our findings might open up a new understanding of biological assembly processes and provide helpful strategies for bio-nanotechnology.

Highly efficient sers performance from the silver nanoparticles/graphene nanoribbons/ cellulose paper

Introduction: Metal/graphene heterojunction structure has been one of the most crucial tools in the growth of high-performance Surface-enhanced Raman spectroscopy (SERS) platform, which is appropriate for sensing applications. In this research, we developed a SERS platform, graphene nanoribbons (GNRs) decorated silver nanoparticles (AgNPs) on cellulose paper substrate, in which GNRs was synthesized by wet chemical based on unzipping process of Multi-walled carbon nanotubes (MWCNTs), then GNRs hybridized with AgNPs through magnetron sputtering method.&#x0D; Methods: The morphology of graphene nanoribbons coated-Ag (AgNPs@GNRs) was analyzed by field emission scanning electronic microscopy (FESEM) and transmission electron microscopy (TEM). The quality and thermal stability of GNRs were characterized using thermogravimetric analysis. Besides, its structure and quality were also characterized by Raman spectroscope.&#x0D; Results: The results show that the unzipping process of MWCNTs to form GNRs was strongly affected by dispersing time and stirring temperature. The suitable condition creating the Graphene Nanoribbons using MWCNTs was the dispersing time of 10 mins in an acid environment, stirring in 30 mins at room temperature and in 45 min at 100°C. Moreover, SERS platform of AgNPs@GNRs exhibit the outstanding SERS signal enhancement with rhodamine 6G (R6G) low concentration of 10-5 M compared with pristine graphene and silver thin film. This could be attributed to the synergistic effect between AgNPs, GNRs and analyze molecules based on the enhancement of electromagnetic mechanism (EM) and chemical mechanism (CM), which plays a vital role in promoting the improvement SERS behavior.&#x0D; Conclusion: Ag NPs assembled onto graphene nanoribbons/ cellulose paper substrate could also serve as SERS active substrates for practical applications in various fields at trace levels.

Collapse mechanism analysis of the FIU pedestrian bridge based on the improved structural vulnerability theory (ISVT)

On Mar 152018, a pedestrian bridge on the campus of Florida International University (FIU bridge) collapsed during construction, and 6 victims were identified in this disaster event. This paper investigates the collapse mechanism of the FIU bridge through improved structural vulnerability theory (ISVT). A topological hierarchy model of the FIU bridge is established by the clustering process of the ISVT, and various possible collapse modes are identified by the unzipping process. Besides, the damage event that vibration effects by crane is considered in the computing work. By comparing the collapse mode identified by ISVT and the actual collapse scenario of the FIU bridge, it is found that ISVT could effectively identify the weakness and predicts the possible collapse modes of the FIU bridge by an quantitative vulnerability index. Then, parametric analyses are conducted for the bridge to different unforeseen damage events, and the collapse mechanism of the failure characteristics of the FIU bridge is also revealed by the ISVT. Finally, some suggestions are recommended for the structural design of rigid frame bridge like the FIU bridge.

CO2/NIR light dual-controlled nanoparticles for dsDNA unzipping

Both of carbon dioxide (CO2) and near-infrared (NIR) light as triggers for non-invasive remotely control are attracting wide attentions due to their good biocompatibility and easy operation. Here, CO2/NIR light dual controlled nanoparticles are proposed to remotely regulate the unzipping of dsDNA by using imidazole functionalized conjugated polymer nanoparticles (imidazole-CPNs). The dsDNA successfully coats on the shell of imidazole-CPNs to form imidazole-CPNs/dsDNA assembly due to intensively electrostatic interaction triggered by CO2. Furthermore, the unzipping process of dsDNA is remotely controlled by NIR light based on the photothermal effect, and it can be readily monitored by the fluorescence intensity of ethidium bromide (EB) and CD spectra of dsDNA. Thus, dual stimulation responsive imidazole-CPNs effectively control dsDNA unzipping under CO2 stimulus and NIR light, promising a new direction in the biological applications of DNA, such as the treatments of diseases caused by gene duplication abnormality.

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

The original article was published with the following errors.

Fatigue crack growth behaviour in single-colony lamellar structure of Ti–6Al–4V

Microstructural fatigue crack growth in Ti–6Al–4V lamellar colonies was examined using small compact-tension specimens, with post-fatigue-test transmission electron microscopy for a mechanistic understanding of the anisotropy. In colonies oriented favourably for prismatic slip in the α phase, the crack grew by alternating shearing on two symmetrically arranged prismatic slip planes (unzipping process). Interlamellar decohesion along the α/β interface significantly increased the crack growth rate, which depended on the lamellar orientation. When the colony was loaded along [0001], deflected crack growth was accompanied by basal slip and < c + a > pyramidal slip gliding, and the crack growth rates slightly exceeded those during unzipping.