Concentration polarization in translocation of DNA through nanopores and nanochannels

In this Letter we provide a theory to show that high-field electrokinetic translocation of DNA through nanopores or nanochannels causes large transient variations of the ionic concentrations in front and at the back of the DNA due to concentration polarization (CP). The CP causes strong local conductivity variations, which can successfully explain the nontrivial current transients and ionic distributions observed in molecular dynamics simulations of nanopore DNA translocations as well as the transient current dips and spikes measured for translocating hairpin DNA. Most importantly, as the future of sequencing of DNA by nanopore translocation will be based on time-varying electrical conductance, CP, must be considered in experimental design and interpretation--currently these studies are mostly based on the incomplete pore conductance models that ignore CP and transients in the electrical conductance.     

Ionic effects on overstretching transition of B-DNA

A three-dimensional model is proposed herein to study the ionic effects of a NaCl solution on the overstretching transition of long B-DNA molecules. In this model, the bending deformations of DNA backbones, cooperativity of base-stacking interactions, electrostatic interactions, and spatial effects of the DNA double-helix structure are taken into account. The energy of electrostatic interactions is given as a function of the ionic strength and of the folding angle based on the Poisson-Boltzmann equation. An expression is derived, which shows that the overstretching force is linear with the natural logarithm of the ionic strength. The analytical results of this model are in good agreement with recently reported experimental results.     

Chiral electrostatics breaks the mirror symmetry of DNA supercoiling

DNA supercoiling plays a fundamental role in regulating cellular activity and in the packaging of genetic material. In this communication, we analyse the effect of attractive chiral forces on the conformation of a closed circular DNA molecule, arising due to the helical patterns of charges on the DNA. We propose a model for closed loop DNA which uses the results of the recent theory of electrostatic interactions of a braid of two free-ended DNA molecules. Our model reproduces the known features of DNA supercoiling in an environment of low ionic strength. In high salt conditions, and in the presence of counterions that have high affinity to the DNA grooves, helix-specific forces significantly affect the conformation of the molecule by favouring a state characterized by a central left-handed braided section where there is close contact between distant portions of the loop. In such an environment we predict a previously unexplored possibility that nicked or topologically relaxed DNA molecules adopt a writhed state. This prediction suggests an alternative explanation for experiments in which it was assumed that the most stable topoisomer is always an open circle. Our results also give the first plausible explanation for the occurrence of tightly interwound molecules observed in cryo-electron microscopy and atomic force microscopy in a high ionic strength environment. We suggest several new experiments to test the predictions of this theory.     

Melting of columnar hexagonal DNA liquid crystals

The persistence length DNA hexagonal-cholesteric phase transition upon dilution and/or increase in solvent ionic strength is investigated with polarized light microscopy. The ionic strength dependence of the transition follows Lindemann criterion , i.e., the hexagonal lattice melts when the root-mean-square fluctuations in transverse order exceed 10% of the interaxial spacing. The spacings are derived from density and the fluctuations are estimated with a theory of undulation enhanced electrostatic interactions. Additional support for this theory is given by the DNA equation of state and anisotropic neutron radiation scattering from magnetically aligned cholesteric samples just below the phase transition. Received: 17 November 1997 / Revised: 21 January 1998 / Accepted: 25 February 1998     

SYBR Green I: Fluorescence Properties and Interaction with DNA

In this study, we have investigated the fluorescence properties of SYBR Green I (SG) dye and its interaction with double-stranded DNA (dsDNA). SG/dsDNA complexes were studied using various spectroscopic techniques, including fluorescence resonance energy transfer and time-resolved fluorescence techniques. It is shown that SG quenching in the free state has an intrinsic intramolecular origin; thus, the observed >1,000-fold SG fluorescence enhancement in complex with DNA can be explained by a dampening of its intra-molecular motions. Analysis of the obtained SG/DNA binding isotherms in solutions of different ionic strength and of SG/DNA association in the presence of a DNA minor groove binder, Hoechst 33258, revealed multiple modes of interaction of SG inner groups with DNA. In addition to interaction within the DNA minor groove, both intercalation between base pairs and stabilization of the electrostatic SG/DNA complex contributed to increased SG affinity to double-stranded DNA. We show that both fluorescence and the excited state lifetime of SG dramatically increase in viscous solvents, demonstrating an approximate 200-fold enhancement in 100?% glycerol, compared to water, which also makes SG a prospective fluorescent viscosity probe. A proposed structural model of the SG/DNA complex is compared and discussed with results recently reported for the closely related PicoGreen chromophore.     

The effect of physiological conditions on the surface structure of proteins: Setting the scene for human digestion of emulsions

Understanding and manipulating the interfacial mechanisms that control human digestion of food emulsions is a crucial step towards improved control of dietary intake. This article reports initial studies on the effects of the physiological conditions within the stomach on the properties of the film formed by the milk protein (b \beta -lactoglobulin) at the air-water interface. Atomic force microscopy (AFM), surface tension and surface rheology techniques were used to visualize and examine the effect of gastric conditions on the network structure. The effects of changes in temperature, pH and ionic strength on a pre-formed interfacial structure were characterized in order to simulate the actual digestion process. Changes in ionic strength had little effect on the surface properties. In isolation, acidification reduced both the dilatational and the surface shear modulus, mainly due to strong repulsive electrostatic interactions within the surface layer and raising the temperature to body temperature accelerated the rearrangements within the surface layer, resulting in a decrease of the dilatational response and an increase of surface pressure. Together pH and temperature display an unexpected synergism, independent of the ionic strength. Thus, exposure of a pre-formed interfacial b \beta -lactoglobulin film to simulated gastric conditions reduced the surface dilatational modulus and surface shear moduli. This is attributed to a weakening of the surface network in which the surface rearrangements of the protein prior to exposure to gastric conditions might play a crucial role.     

光谱法研究硫酸酯化壳聚糖与DNA的作用机理

以荧光光谱法、吸收光谱法、碱变性曲线、离子强度和荧光猝灭等方法研究了两种硫酸酯化壳聚糖与DNA的相互作用机理。结果表明, 硫酸酯化壳聚糖与荧光探针DNA/EB的作用存在嵌插和静电作用两种模式。 高取代度硫酸酯化壳聚糖(CT-H)与低取代度硫酸酯化壳聚糖(CT-L)存在下,DNA的紫外吸收光谱产生不同的增色效应和减色效应;碱变性pH增大、发光体系稳定性增加;金属阳离子Mg2+可与DNA的磷酸基团产生弱静电相互作用。极微量硫酸酯化壳聚糖存在下,荧光被有效地猝灭,证明在EB、CT-H或CT-L和DNA之间产生了强的竞争键合作用,表明不同硫酸酯化壳聚糖是一种有希望的基因治疗靶向分子。     

Liquid-liquid interfacial tension of electrolyte solutions

It is theoretically shown that the excess liquid-liquid interfacial tension between two electrolyte solutions as a function of the ionic strength I behaves asymptotically as O(-sqrt[I]) for small I and as O(+/-I) for large I. The former regime is dominated by the electrostatic potential due to an unequal partitioning of ions between the two liquids whereas the latter regime is related to a finite interfacial thickness. The crossover between the two asymptotic regimes depends sensitively on material parameters suggesting that the experimentally accessible range of ionic strengths can correspond to either the small or the large ionic strength regime. In the limiting case of a liquid-gas surface where ion partitioning is absent, the image charge interaction can dominate the surface tension for small ionic strength I such that an Onsager-Samaras limiting law O(-Iln(I)) is expected.     

Persistence length for a model semirigid polyelectrolyte as seen by small angle neutron scattering: a relevant variation of the lower bound with ionic strength

In a SANS experiment, we have directly determined for the first time the conformation of hyaluronan, a model semirigid polyelectrolyte. At high ionic strength, this is completely possible, where the scattered intensity crosses over (when decreasing q) from a q(-1) rod variation to a q(-2) and, where fitting to the "wormlike" chain model gives the backbone, intrinsic, persistence length: L0 = 86.5 A. At low ionic strength, we can safely check that the measured persistence length appears increased by at least the amount predicted by Odijk for the electrostatic contribution, L(e) (approximately kappa(-2), square of the Debye screening length). However, the intensity at the lowest q is not only due to the single chain, since it crosses over from a q(-1) to a q(-4) variation, characteristic of polymer associations.     

Ultra-fast spreading on superhydrophilic fibrous mesh with nanochannels

In this paper, we fabricated a TiO₂ mesh with ultra-fast spreading superhydrophilic property without UV irradiation. Through electrospinning process followed by calcinations, we obtained meshes with special micropores and nanochannels composite hierarchical structures. Each fiber exhibits a bundle structure of aligned elementary filaments with nanochannels, which should be resulted from phase separation and stretch of electrostatic force during electrospinning process. The mesh shows ultra-fast spreading property within only tens of milliseconds (ms). It is concluded that the special topography offered a multi-scale 3D capillary effect that play crucial role in ultra-fast spreading superhydrophilic property of the mesh. This study provides interesting insights to design novel materials concerning liquid transport and dissipation, which may find its way in various applications.     

Parabolic oxidation of metals in homogeneous electric fields

A previously proposed thin film parabolic growth law (Fromhold, 1963) is extended to include film growth due to any number of diffusing defect species of arbitrary valence, and an analysis is made of the effects of applying external electrostatic potentials during oxidation. The total electrical conductivity and the partial conductivities are markedly position-dependent in the protective film, varying by orders of magnitude from one interface to the other. The built in electrostatic potential across the film is independent of thickness of the film and is a function of the partial conductivities of the diffusing ionic and electronic defect species. Effects of electrical shorting of the oxide film by external circuitry are analyzed. Depending on polarity, a constant applied potential can increase or decrease the rate constant but does not alter the kinetics from the parabolic form, in accordance with published experimental data. The net electrostatic potential required to stop metal oxidation is derived for the model in question. For growth by a single ionic species, the stopping potential is that electrostatic potential which gives an equal electrochemical potential at the metal-oxide and the oxideoxygen interfaces. For growth by multiple ionic species, the stopping potential is a function of the ionic partial conductivities.     

Theoretical resistance of an ionic crystal to destruction by an electric field

We describe an electrostriction mechanism for destruction of an ionic crystal by an electric field. We present a simple theory that transforms into the well-known Rogowskii theory when there is no electrostatic breakdown. We show that electrostatic breakdown of the crystal lattice is due to separation of nearestneighbor ions with different charges to the point where the electric field exceeds the interionic attractive forces. The theoretical tensile strength of a crystal lattice undergoing electrostriction by an electric field is 15 MV/cm.Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 3, pp. 47–50, March, 1989.     

Salt-induced swelling-to-shrinking transition in polyelectrolyte multilayer capsules

We study the size of polyelectrolyte multilayer capsules as a function of ionic strength, temperature, and time. A dynamic micromechanical model is developed which successfully describes the experiments. The model includes the polymer-solvent surface tension, an electrostatic force which is strongly ionic strength dependent, and a temperature-dependent mobility parameter. The activation of >50 kT suggests that multiple ion pairs must be broken simultaneously in the process of chain rearrangement. In support of our physical model capsules can repeatedly swell and shrink by varying ionic strength.     

Aggregation and Deposition Characteristics of Fullerene Nanoparticles in Aqueous Systems

The propensity of n-C₆₀ to aggregate and deposit will play a key role in determining its longevity in aquatic systems, and therefore the potential exposure and risk presented by these colloids. We consider the origin of n-C₆₀ stability and compare the aggregation and deposition characteristics of n-C₆₀ under conditions of variable ionic strength using an indifferent electrolyte. Relatively weak electrolyte solutions (0.001 M) were observed to destabilize suspensions of n-C₆₀ resulting in the formation of settleable aggregates. This behavior supports the hypothesis that the stabilizing mechanism for n-C₆₀ clusters is electrostatic in origin. Similarly, the deposition of n-C₆₀ in porous media increased as ionic strength increased. These observations suggest that under some conditions present in natural aquatic systems, these materials may have limited mobility as they form large aggregates that may settle out of suspension or deposit on surfaces. These phenomena may, at least partially, offset any risk presented by n-C₆₀ toxicity due to a reduced potential for exposure.     

核黄素与鲱鱼精DNA相互作用的荧光光谱

荧光光谱法研究了核黄素(RF)与鲱鱼精DNA的相互作用.考查了离子强度、温度及磷酸盐对RF-DNA体系的影响.结果表明,DNA的存在使得RF的荧光光谱发生了规律性猝灭,其猝灭机制为静态猝灭;运用Stern-Volmer方程对实验数据进行了分析,得到了猝灭常数为2.82×103L·mol-1、结合位点数为1.17.核黄素...     

Self-energy-limited ion transport in subnanometer channels

The current-voltage characteristics of the alpha-Hemolysin protein pore during the passage of single-stranded DNA under varying ionic strength C are studied experimentally. We observe strong blockage of the current, weak superlinear growth of the current as a function of voltage, and a minimum of the current as a function of C. These observations are interpreted as the result of the ion electrostatic self-energy barrier originating from the large difference in the dielectric constants of water and the lipid bilayer. The dependence of DNA capture rate on C also agrees with our model.     

低维限域结构中水与物质的输运

低维限域结构中水与物质的输运研究,对于解决界面化学和流体力学中的遗留问题十分关键.近年来,研究人员采用分子动力学模拟和实验手段研究低维限域结构中水与物质的输运,并将其应用于物质输运、纳米限域化学反应、纳米材料制备等领域.本文从理论和实验的角度总结一维和二维纳米通道的水与物质输运,介绍了本研究组提出的"量子限域超流体"概念,并用于解释纳米通道中超快物质的输运现象;在此基础上概述了一维纳米通道中的分子动力学模拟和水浸润性,以及外部环境(如温度和电压)对限域结构中水浸润性的调控,同时阐述了低维限域结构中的液体输运;对二维纳米通道中的分子动力学模拟、液体浸润性以及液体输运进行了综述;讨论了纳米通道限域结构在物质输运、纳米限域化学反应和纳米材料制备等领域的应用;对低维限域结构中水与物质输运面临的挑战和前景进行了展望.     

氯铝酸离子液体的酸性及其催化烷基化反应研究

分别采用吡啶探针和乙腈探针红外光谱法研究了氯铝酸离子液体的酸性,结合固体酸表征方法,研究了离子液体的酸性对吡啶探针各振动模式的影响。发现当氯铝酸离子液体AlCl₃的摩尔分数x为0.4～0.5时,离子液体显弱Lewis酸性,强碱性吡啶探针分子能很好地表征离子液体的酸性,而弱碱性乙腈探针分子只适用于表征酸性较强的离子液体。考察了氯铝酸离子液体酸强度对苯与长链烯烃烷基化反应的影响,结果发现,AlCl₃的摩尔分数x≤ 0.5时,离子液体没有催化活性;x>0.55时,随着离子液体酸性的增强,烯烃转化率升高,但2位烷基苯选择性下降。结合离子液体的酸强度对烷基化反应机理进行初步分析认为具有催化活性的物质是强Lewis酸Al₂Cl-₇。     

Electronic States and Schottky Barrier Height at Metal/MgO(100) Interfaces

Using an ab initio total energy approach, we study the electronic structure of metal/MgO(100) interfaces. By considering simple and transition metals, different adsorption sites and different interface separations, we analyze the influence of the character of metal and of the detailed interfacial atomic structure. We calculate the interface density of states, electron transfer, electric dipole, and the Schottky barrier height. We characterize three types of electronic states: states due to chemical bonding which appear at well defined energies, conventional metal-induced gap states associated to a smooth density of states in the MgO gap region, and metal band distortions due to polarization by the electrostatic field of the ionic substrate. We point out that, with respect to the extended Schottky limit, the interface formation yields an electric dipole mainly determined by the substrate characteristics. Indeed, the metal-dependent contributions (interfacial states and electron transfer) remain small with respect to the metal polarization induced by the substrate electrostatic field.     

Compression and free expansion of single DNA molecules in nanochannels

We investigated compression and ensuing expansion of long DNA molecules confined in nanochannels. Transverse confinement of DNA molecules in the nanofluidic channels leads to elongation of their unconstrained equilibrium configuration. The extended molecules were compressed by electrophoretically driving them into porelike constrictions inside the nanochannels. When the electric field was turned off, the DNA strands expanded. This expansion, the dynamics of which has not previously been observable in artificial systems, is explained by a model that is a variation of de Gennes's polymer model.