Unzipping Process Research Articles

A Novel Single Molecular Signature for Discriminating DNA Unzipping in a Nanopore

Using nanopore for DNA unzipping has been extensively studied. By measuring the voltage-dependent duration of current blocks produced by the unzipping process, one can evaluate the force and energy involved in the double strands hybridization. However, in the real-time biosensing, other molecules co-existing in the mixture may also produce blocks in similar amplitude and duration. Therefore a characteristic current signature is needed to discriminate the unzipping signal from other blockades. Here we identify a novel molecular signature that can reveal sequential steps in DNA unzipping in the nanopore.

Catalytic unzipping of carbon nanotubes to few-layer graphene sheets under microwaves irradiation

Catalytic unzipping of single-, double-, and multi-walled carbon nanotubes (SWNTs, DWNTs, and MWNTs), in the presence of Pd nanoparticles and an oxygen-containing liquid medium, to yield the few-layer graphene sheets, was performed under microwaves irradiation. In this unzipping process, the palladium particles act as a pair of scissors to cut the nanotube lengthways. Theoretical simulations with Reactive Forcefields confirm that the presence of Pd nanocatalysts and oxygen next to vacancies facilitate the unzipping process to form graphene from nanotube by significantly lowering the corresponding energy barrier. This synthesis method makes a link between nanotubes and graphene sheets, yielding a significant amount of graphene (between 4 and 8 wt.% with respect to the starting carbon material). Compared to previous methods, scaling-up can easily be achieved by increasing the number of synthesis reactors, leading to gram-amounts of graphene.

Transforming Carbon Nanotube Devices into Nanoribbon Devices

Reported here is an extension of the nanotube longitudinal unzipping process to convert electrode-bound multiwalled carbon nanotube (MWCNT) devices into graphene nanoribbon devices. Microscopy and Raman spectroscopy were used to monitor the conversion process. The electrical properties of the devices were characterized. The efficacy of the unzipping protocol on device-bound MWCNTs is demonstrated.

Mechanism of carbon nanotubes unzipping into graphene ribbons

The fabrication of graphene nanoribbons from carbon nanotubes (CNTs) treated with potassium permanganate in a concentrated sulfuric acid solution has been reported by Kosynkin et al. [Nature (London) 458, 872 (2009)]. Here we report ab initio density functional theory calculations of such unzipping process. We find that the unzipping starts with the potassium permanganate attacking one of the internal C-C bonds of the CNT, stretching and breaking it. The created defect weakens neighboring bonds along the length of the CNT, making them energetically prone to be attacked too.

The mechanism of DNA mechanical unzipping

The process of DNA double helix unzipping is considered to be a nonlinear dynamical process powered by an external force. In the course of unzipping the most probable pathway of the mechanical strands separation is determined. This pathway accounts for the structural organization of the double helix, the manner in which the external force is applied, and the kinetic parameters of the base pair opening in the double-stranded DNA chain. It is assumed in our model that the base pair unzipping includes the stretch of DNA complementary base pairs and the double helix torsion. For the description of the DNA unzipping the two-stage mechanism of the external force action is proposed. The mechanism explains the cooperative nature of the unzipping process under the physiological conditions and the threshold character of external force action. On the first stage the external force transforms the conformational state of the double helix and makes the unzipping possible. On the second stage the unzipping propagates along dsDNA. The boundary between the open and the closed parts of the helix (the so called ‘fork’) is demonstrated to move along the chain as a step-like excitation (kink soliton). It is shown that for stable unzipping propagation along DNA double helix, it is necessary to allow rotation of the DNA chain while keeping the velocity of the unzipping fork propagation small in comparison to the velocity of sound in the DNA. It is demonstrated that fluctuations of the external force at the constant velocity of unzipping and the fluctuations of the DNA unzipping length at the fixed force have the same origin: the heterogeneity of the DNA base pairs.

The effect of humidity on the degradation of Nafion ® membrane

Controlling the activity of water in the reactant streams is critical both to the design of fuel–cell systems and to the useable life of membrane separators. In this study, fuel–cell durability tests were conducted under different levels of relative humidity. The emission rates of various degradation products such as HF, SO 4 2− and TFA (trifluoroacetic acid) were determined as a function of water activity. The degradation of the membrane was accelerated as the level of water activity is reduced. The membranes become less conductive, more brittle and rigid after fuel–cell testing. ATR-FTIR investigations showed that the decomposition of the ether group in the middle of side chain corresponds well with the detection of a TFA product. Thermogravimetric analysis also showed a decrease in thermal stability after testing at lower humidity. Formation of cracks was observed in membranes degraded under conditions of low humidity. A model of membrane degradation based on the main chain unzipping process indicates that the mechanism changes with water activity. Finally, the representative reaction pathways in each degradation scheme were postulated.

Structural ultrafast dynamics of macromolecules: diffraction of free DNA and effect of hydration

Of special interest in molecular biology is the study of structural and conformational changes which are free of the additional effects of the environment. In the present contribution, we report on the ultrafast unfolding dynamics of a large DNA macromolecular ensemble in vacuo for a number of temperature jumps, and make a comparison with the unfolding dynamics of the DNA in aqueous solution. A number of coarse-graining approaches, such as kinetic intermediate structure (KIS) model and ensemble-averaged radial distribution functions, are used to account for the transitional dynamics of the DNA without sacrificing the structural resolution. The studied ensembles of DNA macromolecules were generated using distributed molecular dynamics (MD) simulations, and the ensemble convergence was ensured by monitoring the ensemble-averaged radial distribution functions and KIS unfolding trajectories. Because the order-disorder transition in free DNA implies unzipping, coiling, and strand-separation processes which occur consecutively or competitively depending on the initial and final temperature of the ensemble, DNA order-disorder transition in vacuo cannot be described as a two-state (un)folding process.

The Chemistry of Fuel Cell Membrane Chemical Degradation

A detailed thermochemical and kinetic analysis of PFSA ionomers and the reactive oxygen species formed in an operating fuel cell is reported. The analysis reveals that hydroxyl radical is the only oxygen species capable of abstracting a hydrogen atom from carboxylic acid intermediates, thereby propagating the PFSA main chain unzipping process. Two chemically specific, main chain scission mechanisms are proposed. The first involves formation of sulfonyl radicals under dry conditions and the second invokes the action of hydrogen atoms formed from hydrogen gas and hydroxyl radical. The thermochemical analysis provides a strong basis from which to rationalize the results from a broad range of in-situ and ex-situ fuel cell degradation studies.

Synthesis and degradation behavior of poly(ethyl cyanoacrylate)

Poly(ethyl cyanoacrylate) was synthesized using N, N′-dimethyl- p-toluidine as an initiator through an anionic/zwitterionic pathway. The degradability and the degradation mechanism of the prepared polymer were examined from various viewpoints. A combination of TGA and GPC analysis allowed us to confirm that the thermal degradation of this polymer was predominantly due to an unzipping depolymerization process initiated from the polymer chain terminus. The polymer was inherently unstable and exhibited interesting degradation behavior in solution with basic reagents. The degradation in solution was also found to be attributed to the unzipping of the monomer from the chain end. However, the degradation behavior of the polymer could be controlled by changing solvents, temperatures, and additives. These findings give an insight into the degradation behavior of poly(alkyl cyanoacrylate)s, which is a crucial point in utilizing these polymer homologues for various applications.

Rheological Behavior and Modeling of Thermal Degradation of Poly(∊-Caprolactone) and Poly(L-Lactide)

Abstract Growing environmental concerns have led to the development of alternative biodegradable polymers with properties comparable to the conventional poly(ethylene), poly(propylene) or poly(ethylene terephthalate). In this paper the thermal degradation of poly(∊-caprolactone) (PCL) and poly(L-lactide) (PLLA) melts was investigated by rheometry and thermogravimetry under different temperatures and inert atmosphere. The chain scission process was modeled to explain the phenomenon. The analysis suggests that PLLA is degraded by an unzipping depolymerization process from the hydroxyl end of the polymer chains. In contrast, the thermal degradation behavior of PCL was very complex because various reactions occurred concurrently: post-polymerization, loss of structural regularities and random chain scissions.

Merrifield-like resin beads by acid catalyzed incorporation of benzyl chloride into dehydrochlorinated PVC

A method is presented for preparing Merrifield-like resin beads starting from poly (vinyl chloride) (PVC) in spherical bead form. In this method, first, PVC is partially dehydrochlorinated in boiling methanolic KOH (20%) solution to create minute amounts of allylic carbon centers. Those centers trigger the un-zipping process and make further dehydrochlorination possible at relatively low temperatures (180–200 °C), while retaining the bead shapes. Acid catalyzed reaction of the dehydrochlorinated PVC particles with benzyl chloride at 180 °C yields crosslinked spherical bead polymers possessing chloromethyl benzene functions as high as 3.4 mmol g −1. Experiments showed that, high yields of benzyl chloride insertions can be attained by using PVC samples with 40–50% of unsaturations. In the study transformation yields in each step were followed by conventional analytical methods and IR spectrometry. It was also demonstrated that modification of the chloromethyl groups either with KCN or sodium acetate proceeds with nearly quantitative yields, as in the case for chloromethylated styrene-divinyl benzene resins.

Oxygen-Driven Unzipping of Graphitic Materials

Optical microscope images of graphite oxide (GO) reveal the occurrence of fault lines resulting from the oxidative processes. The fault lines and cracks of GO are also responsible for their much smaller size compared with the starting graphite materials. We propose an unzipping mechanism to explain the formation of cracks on GO and cutting of carbon nanotubes in an oxidizing acid. GO unzipping is initiated by the strain generated by the cooperative alignment of epoxy groups on a carbon lattice. We employ two small GO platelets to show that through the binding of a new epoxy group or the hopping of a nearby existing epoxy group, the unzipping process can be continued during the oxidative process of graphite. The same epoxy group binding pattern is also likely to be present in an oxidized carbon nanotube and cause its breakup.

What Governs the Unzipping Process of Double-Stranded DNA

The unzipping process of double-stranded DNA is analysed using adiscrete model at the base level [Chin. Phys. Lett. 22 (2005) 1540]. The numerical results are consistent with theexperimental observations on the force-displacement behaviour includingthe sequence-dependence. We find that the hydrogen bond interaction in abase pair is crucially important to the force–displacement profile.

Single Molecule Unzipping of Coiled Coils: Sequence Resolved Stability Profiles

We use a high resolution atomic force microscopy technique to mechanically unzip and rezip single coiled-coil proteins. This allows us to read off the complete stability profile of the protein turn by turn. We investigated three coiled coils with different length as well as a point mutation and find force fluctuations between 9 and 15 pN that can be directly related to the amino-acid sequences. An equilibrium model previously applied to DNA fully describes the mechanical unzipping process including free-energy contributions of the individual turns and seed formation energy.

Pause Point Spectra in DNA Constant-Force Unzipping

Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the locations of pause points can be extracted in the form of a pause point spectrum. A simple theoretical model of DNA constant-force unzipping is presented, which generates theoretical pause point spectra through Monte Carlo simulation of the unzipping process. The locations of peaks in the experimental and theoretical pause point spectra are found to be nearly coincident below 6000 basepairs for unzipping the bacteriophage λ-genome. The model only requires the sequence, temperature, and a set of empirical basepair binding and stacking energy parameters, and the good agreement with experiment suggests that pause point locations are primarily determined by the DNA sequence. The model is also used to predict pause point spectra for the bacteriophage ϕX174 genome. The algorithm for extracting the pause point spectrum might also be useful for studying related systems which exhibit pausing behavior such as molecular motors.

Fullerene C 60 as stabiliser for acrylic polymers

The influence of fullerene C 60 additives on thermal behaviour and thermodegradation of poly- n-alkyl acrylates, from butyl to heptyl, and of corresponding polymethacrylates was investigated by thermogravimetry in dynamical conditions and pyrolysis/gas chromatography in isothermal conditions at 400–650 °C. The fullerene is a well-known efficient acceptor of radicals and its presence influences the thermal degradation of acrylic polymers, shifting the decomposition process from a radical pathway to a non-radical mechanism. For poly- n-alkyl acrylates the addition of fullerene leads to increase in the yields of olefin and alcohol, degradation products coming from non-radical pathways. On the other hand, the yields of the pyrolysis products deriving from the random main-chain scission, i.e. monomer, dimer, saturated diester, trimer, corresponding acetate and methacrylate, decrease. The recorded temperatures of maximum weight loss (obtained by thermogravimetric experiments) are slightly increased by the presence of fullerene. The effect of fullerene is more noticeable in the thermal behaviour of poly- n-alkyl methacrylates, in fact the enhancements of the temperature of maximum weight loss are 19–25 °C. The mixtures containing fullerene give rise to a marked decrease of the monomer yield and, at the same time, an increase of olefin and methacrylic acid amounts. The fullerene acts as radical acceptor suppressing the unzipping process and favouring the non-radical side-chain reactions.

Nonlinear excitations in DNA: Aperiodic models versus actual genome sequences

We study the effects of the genetic sequence on the propagation of nonlinear excitations in simple models of DNA in which we incorporate actual data from the human genome. We show that kink propagation requires forces over a certain threshold, a phenomenon already found for aperiodic sequences [F. Domínguez-Adame et al., Phys. Rev. E 52, 2183 (1995)]. For forces below threshold, the final stop positions are highly dependent on the specific sequence. Contrary to the conjecture advanced by Domínguez-Adame and co-workers, we find no evidence supporting the dependence of the kink dynamics on the information content of the genetic sequences considered. We discuss possible reasons for that result as well as its practical consequences. Physically, the results of our model are consistent with the stick-slip dynamics of the unzipping process observed in experiments. We also show that the effective potential, a collective coordinate formalism introduced by Salerno and Kivshar [Phys. Lett. A 193, 263 (1994)], is a useful tool to identify key regions in DNA that control the dynamical behavior of large segments. As a side result, we extend the previous studies on aperiodic sequences by analyzing the effect of the initial position of the kink, leading to further insight on the phenomenology observed in such systems.

Pyrolysis kinetics of poly( l-lactide) with carboxyl and calcium salt end structures

To clarify the pyrolysis mechanism of poly( l-lactide), which has been reported as complex, the thermal decomposition of carboxyl type and calcium ion end capped PLLA (PLLA-H and PLLA-Ca, respectively) was investigated by means of thermogravimetric analysis (TG), and pyrolysis–gas chromatography–mass spectrometry (Py–GC–MS). The TG data revealed that PLLA-Ca has a lower pyrolysis temperature (220–360 °C) than that of carboxyl type PLLA-H (280–370 °C). The apparent activation energy of the decomposition reaction was estimated from TG curves at different heating rates by plural methods to be 176 and 98 kJ mol −1 for PLLA-H and PLLA-Ca, respectively. Further kinetic studies indicated that PLLA-H degraded mainly through a random reaction with a pre-exponential factor A=2.0×10 12 s −1, whereas PLLA-Ca degraded by way of a 1st-order reaction with A=8.4×10 5 s −1. Pyrolysis products of PLLA-H were composed of lactides and other cyclic oligomers, while the degradation products of PLLA-Ca were principally lactides. The main reaction pathway for PLLA-H pyrolysis was regarded as the random transesterification, whereas for PLLA-Ca pyrolysis the unzipping depolymerization process was dominant.

Racemization on thermal degradation of poly( l-lactide) with calcium salt end structure

Poly( l-lactide) with calcium salt end structure (PLLA-Ca) is a promising material for PLLA recycling because of the ease of lactide recovery through the unzipping depolymerization process. However, the pyrolysis of PLLA-Ca also causes meso-lactide to form. In this article, the racemization in PLLA-Ca pyrolysis was analyzed in detail with Py-MS, Py-GC/MS, and a glass tube oven. The results suggested that at a temperature lower than 250 °C, nucleophilic attack by a carboxylate anion end on an asymmetrical methyne carbon in a penultimate lactate unit occurred, resulting in the predominant formation of meso-lactide. On the other hand, also at temperatures over 320 °C, by-reactions, such as enolization reactions, caused the meso-lactide to form, but not dominantly. In the temperature range of 250–320 °C, l,l-lactide was produced exclusively, because unzipping depolymerization proceeded as the main reaction. This is a very significant result for PLLA recycling, because PLLA-Ca is an easily recyclable material, which depolymerizes based on the 1st-order weight loss process.

Mechanisms and kinetics of thermal degradation of poly(epsilon-caprolactone).

Thermogravimetric analysis (TGA) simultaneously coupled with mass spectrometry (MS) and Fourier transform infrared spectrometry (FTIR) was developed as an original technique to study the thermal modification/degradation of poly(epsilon-caprolactone) (PCL) through in depth analysis of the evolved gas. Perfectly well-defined PCL samples with controlled end groups, predictable molecular weight, and narrow molecular weight distribution were synthesized by living "coordination-insertion" ring-opening polymerization of epsilon-caprolactone initiated by aluminum triisopropoxide. TGA analyses carried out on purified PCL samples, deprived from any residual catalyst or monomer, highlighted a two-step thermal degradation. Evolved gas analysis by both MS and FTIR showed that the first process implies a statistical rupture of the polyester chains via ester pyrolysis reaction. The produced gases were identified as H(2)O, CO(2), and 5-hexenoic acid. The second step leads to the formation of epsilon-caprolactone (cyclic monomer) as result of an unzipping depolymerization process. The influence of parameters such as polyester molecular weight, nature of the PCL end groups, and presence of catalytic residues as well as the type of purge gas were investigated. The activation energy of the thermal degradation was also studied.