Direct observation of λ-DNA molecule reversal movement within microfluidic channels under electric field with single molecule imaging technique

The electrodynamic characteristics of single DNA molecules moving within micro-/nano-fluidic channels are important in the design of biomedical chips and bimolecular sensors. In this study, the dynamic properties of λ-DNA molecules transferring along the microchannels driven by the external electrickinetic force were systemically investigated with the single molecule fluorescence imaging technique. The experimental results indicated that the velocity of DNA molecules was strictly dependent on the value of the applied electric field and the diameter of the channel. The larger the external electric field, the larger the velocity, and the more significant deformation of DNA molecules. More meaningfully, it was found that the moving directions of DNA molecules had two completely different directions:(i) along the direction of the external electric field, when the electric field intensity was smaller than a certain threshold value;(ii) opposite to the direction of the external electric field, when the electric field intensity was greater than the threshold electric field intensity.The reversal movement of DNA molecules was mainly determined by the competition between the electrophoresis force and the influence of electro-osmosis flow. These new findings will theoretically guide the practical application of fluidic channel sensors and lab-on-chips for precisely manipulating single DNA molecules.     

Three-wave interaction between interstrand modes of the DNA

We consider the regime in which the bands of the torsional acoustic (TA) and hydrogen-bond-stretch (HBS) modes of DNA interpenetrate each other. We propose a simple model accommodating the helix structure of DNA and, within its framework, find a three-wave interaction between the TA and HBS modes. The phenomenon could be useful for studying the action of microwave radiation on a DNA molecule. Thus, using Zhang’s mechanism of the interaction between the system of electric dipoles of a DNA molecule and microwave radiation, we show that the latter could bring about torsional vibrations that maintaining HBS vibrations. We show an estimate of the microwave power density necessary for generating the HBS mode, which significantly depends on the viscous properties of the ambient medium.     

Itinerant electron model and conductance of DNA

DNA (Deoxyribonucleic acid) has recently caught the attention of chemists and physicists. A major reason for this interest is DNA’s potential use in nanoelectronic devices, both as a template for assembling nanocircuits and as an element of such circuits. However, the electronic properties of the DNA molecule remain very controversial. Charge-transfer reactions and conductivity measurements show a large variety of possible electronic behavior, ranging from Anderson and band-gap insulators to effective molecular wires and induced superconductors. In this review article, we summarize the wide-ranging experimental and theoretical results of charge transport in DNA. An itinerant electron model is suggested and the effect of the density of itinerant electrons on the conductivity of DNA is studied. Calculations show that a DNA molecule may show conductivity from insulating to metallic, which explains the controversial and profuse electric characteristics of DNA to some extent.      

Electronic and thermoelectric properties of a single pyrene molecule

We propose a system containing a single pyrene molecule sandwiched between two metallic electrodes. The transport properties of the single pyrene molecule with four configurations are investigated using a steady-state theoretical model. We calculate the transmission probability and the electric current for the structure (1, 8), the structure (1, 7), the structure (1, 5) and the structure (1, 4). By applying a gate voltage on the pyrene molecule, we calculate the thermoelectric properties. The thermoelectric and electron transport properties can be controlled by quantum interference, the contact geometry and the gate voltage. The asymmetric behavior and the splitting of resonances in the transmission spectrum occur due to applying a gate voltage on the pyrene molecule. As a result, the structures (1, 5) and (1, 7) have a maximum value of the figure of merit reaching to 0.8 at the Fermi level. According to the results, the structures (1, 5) and (1, 7) can be act as promising thermoelectric applications in molecular electronics.     

Electrophoretic collision of a DNA molecule with an insulating post

We study the dynamics of single DNA molecules driven by an electric field into a stationary obstacle. These collisions are broadly classified as "hook" and "roll-off" events. We show that obstacle-induced electric field gradients stretch impacting DNA and thus greatly influence the hooking probability. Consequently, in addition to collision geometry, determination of the hooking probability depends on the Deborah number (De) for 0.5相似文献   

Quantification of Low Concentrations of DNA Using Single Molecule Detection and Velocity Measurement in a Microchannel

We present a novel method for quantifying low concentrations of DNA based on single molecule detection (SMD) for molecular counting and flow measurements inside a microchannel. A custom confocal fluorescence spectroscopic system is implemented to detect fluorescent bursts emitted from stained DNA molecules. Measurements are made one molecule at a time as they flow through a femtoliter-sized laser focal probe. Durations of single molecule fluorescent bursts, which are found to be strongly related to the molecular transit times through the detection region, are statistically analyzed to determine the in situ flow speed and subsequently the sample volume flowing through the focal probe. Therefore, the absolute concentration of a DNA sample can be quantified based on the single molecule fluorescent counts from the DNA molecules and the associated probe volume for a measured time course. To validate this method for quantifying low concentrations of biomolecules, we tested samples of pBR322 DNA ranging from 1 pM to 10 fM (∼3 ng/ml to 30 pg/ml). Besides molecular quantification, we also demonstrate this method to be a precise and non-invasive way for flow profiling within a microchannel.     

DNA-based tunable THz oscillator

The intrinsic helix conformation of the DNA strands is known to be the key ingredient of control of the electric current through the molecule by the perpendicular (gate) electric field. We show theoretically that Bloch oscillations in periodic systems with helical conformation are also strongly affected by such lateral field; the oscillation frequency splits into a manifold of several generally non-commensurate frequencies leading to a complicated pattern of the charge motion. For model parameters typical for the DNA the frequency of such oscillations falls in the THz domain, suggesting a possibility to design a DNA-based nano-scale source of THz radiation.     

DNA在熵受限管道中穿越过程的计算机模拟

利用Metropolis Monte-Carlo动力学方法结合键长涨落算法，模拟了单链DNA分子在电场作用下穿越熵受限管道的动力学过程.结果表明，DNA分子穿越管道时将经历无规迁移、受限迁移及快速迁移等几个显著不同的阶段.平均迁移率随外场增加而增大并最终达到饱和值μ0，受限时间的对数与所加场强的倒数之间基本满足线性关系.模拟结果不仅与文献所给的实验结果基本一致，而且还可以提供实验不能直接观察到的DNA分子较为详细的穿越过程.     

Single Molecule Genotyping by TIRF Microscopy

As part of a programme to develop a metrological framework for single molecule measurements in biology, we have investigated the applications of single molecule imaging to genomics. Specifically, we have developed a technique for measuring the frequencies of single nucleotide polymorphisms (SNPs) in complex or pooled samples of DNA. We believe that this technique has applications to statistical genotyping—the identification of correlations between SNP frequencies and particular phenotypes—and other areas where it is desirable to track the frequencies of SNPs in complex DNA populations.     

Electrostatic surface guiding of cold polar molecules with a single charged wire

This paper proposes a scheme to guide cold polar molecules by using a single charged wire half embanked in an insulating substrate and a homogeneous bias electric field, which is generated by a plate capacitor composed of two infinite parallel metal plates. The spatial distributions of the electrostatic field produced by the combination of the charged wire and the plate capacitor and the corresponding Stark potentials (including dipole forces) for metastable CO molecules are calculated, the relationships between the electric field and the parameters of our charged-wire layout are analysed. It also studies the influences of the insulator on the electric field distribution and the discharge effect. This study shows that the proposed scheme can be used to guide cold polar molecules in the weak-field -- seeking states, and to form various molecule-optical elements, such as molecular funnel, molecular beam-splitters and molecule interferometer, even to construct a variety of integrated molecule-optical elements and their molecule chips.     

电场中MgO分子吸附H2的理论研究

研究电场中MgO分子与H2的相互作用是探索MgO材料储氢性能的基础。在B3LYP/6-31G**水平上研究了电场中H2在MgO分子上的吸附行为。结果给出电场中单个H2在Mg/O上的吸附能由无电场时-0.021/-0.099eV提高到场强为0.005a.u.时的-0.037/-0.139 eV。H2吸附在O离子上时,电场效应更显著。电场中MgO分子最多能吸附10个H2,相应的质量密度达33wt%。表明电场诱导MgO材料吸附H2是一种具有潜力的储氢方法。通过电子结构分析讨论了电场中MgO分子储氢的机理。     

电场中MgO分子吸附H_2的理论研究

研究电场中MgO分子与H_2的相互作用是探索MgO材料储氢性能的基础.在B3LYP/6-31G**水平上研究了电场中H2在MgO分子上的吸附行为.结果给出电场中单个H_2在Mg/O上的吸附能由无电场时-0.021/-0.099eV提高到场强为0.005a.u.时的-0.037/-0.139eV.H2吸附在O离子上时,电场效应更显著.电场中MgO分子最多能吸附10个H_2,相应的质量密度达33wt%.表明电场诱导MgO材料吸附H_2是一种具有潜力的储氢方法.通过电子结构分析讨论了电场中MgO分子储氢的机理.     

外电场作用下乙炔分子的激发态研究P

本文采用密度泛函方法(B3LYP)和组态相互作用原理(CIS)在6-311++G**水平上研究了外电场对乙炔分子的激发态的影响规律,结果表明,外电场的大小和方向对乙炔分子的激发态都有明显的影响,沿分子方向的外加电场对分子偶极矩的影响比垂直于分子方向的外加电场更大.     

拉直的单个DNA分子的全内反射荧光实时成像研究

全内反射荧光(TIRF)成像技术利用穿透深度仅200 nm左右的隐失波来激发诱导荧光,探测灵敏度和图像信噪比大大提高,成为单分子研究的有力工具。分子梳技术利用DNA末端与固体表面的结合力和周围流体流动产生的侧向力将DNA分子拉伸并平铺在表面上。结合这两种技术,对分子梳拉直的单个DNA分子进行了清晰的实时荧光成像,发现TIRF成像条件下DNA分子与荧光探针YOYO-1组成的复合体可自然避免发生光敏断裂现象;实时监测了单个DNA-YOYO-1复合体的光漂白过程,通过对激发光照射时间与探测器曝光时间进行同步控制,可大幅降低光漂白程度,为拉直的单个DNA分子的长时间实时观察和成像研究优化了实验条件,为实时、可视化地研究其与蛋白质相互作用的动力学过程奠定了基础。     

Proposition of Single Molecular Orientation Determination Using polarization Controlled Beam by Liquid Crystal Spatial Light Modulators

We have proposed a method to control the three-dimensional electric field in the focus of an optical microscope using two non-twisted liquid crystal spatial light modulators, and to detect the molecular orientation of a single molecule. The three-dimensional electric field is generated by focusing the beam with two dimensional spatial distribution of polarization. The possibility of detection of three-dimensional single molecular orientation was shown by numerical calculations. © 2005 The Optical Society of Japan     

Entanglement in a three spin system controlled by electric and magnetic fields

We study the effect of electric field and magnetic flux on spin entanglement in an artificial triangular molecule built of coherently coupled quantum dots. In a subspace of doublet states an explicit relation of concurrence with spin correlation functions and chirality is presented. The electric field modifies superexchange correlations and shifts many-electron levels (the Stark effect), as well as changing spin correlations. For some specific orientation of the electric field one can observe monogamy, for which one of the spins is separated from two others. Moreover, the Stark effect manifests itself in a different spin entanglement for small and strong electric fields. The role of magnetic flux is opposite: it leads to circulation of spin supercurrents and spin delocalization.     

电场作用下C60富勒烯二聚体分子的几何构型与失效

采用分子力学与量子力学相结合的方法,模拟了电场作用下C60富勒烯二聚体(2C60)分子的几何构型与失效行为,讨论了三种不同方向外加电场对2C60分子几何变形、构型失效、电荷分布与极化偶极矩的影响,并与电场作用下C60富勒烯分子的几何变形与失效行为进行了对比.研究结果表明,2C60分子的几何变形与失效行为与外加电场的方向密切相关.当外加电场与2C60分子的桥接C-C键平行时,2C60分子很容易发生失效,且失效形式也十分独特.     

Optical detection of DNA translocation through silicon nanopore by ultraviolet light

In this paper, we propose a new optical detection scheme for nanopore-based DNA sequencing with high resolution towards eventual base identification. We use ultraviolet light for excitation of a fluorescent probe attached to DNA and a nanopore in the silicon membrane that has a significantly large refractive index and an extinction coefficient at ultraviolet wavelengths. In this study, numerical electromagnetic simulation revealed that the z-polarization component (perpendicular to the membrane plane) of the electric field was dominant near the nanopore and generated a large electric field gradient at the nanopore exit, typically with a decay length of 2 nm for a nanopore with diameter of 7 nm. The large extinction coefficient contributed to reduction in background noise coming from fluorophore-labeled DNA strands that remain behind the membrane (the cis side of the membrane). We observed a high signal-to-noise ratio of single DNA translocation events under the application of an electric field.     

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MARTINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell surrounding the DNA molecule, whereas the solvent in the outer shell is modeled by the coarse-grained model. The solvent entities can exchange between the two domains and adapt their resolution accordingly. We critically asses the performance of our multiscale model in adaptive resolution simulations of an infinitely long DNA molecule, focusing on the structural characteristics of the solvent around DNA. Our analysis shows that the adaptive resolution scheme does not produce any noticeable artifacts in comparison to a reference system simulated in full detail. The effect of using a bundled-SPC model, required for multiscaling, compared to the standard free SPC model is also evaluated. Our multiscale approach opens the way for large scale applications of DNA and other biomolecules which require a large solvent reservoir to avoid boundary effects.     

Electronic Transport in Single-Stranded DNA Molecule Related to Huntington’s Disease

We report a numerical analysis of the electronic transport in single chain DNA molecule consisting of 182 nucleotides. The DNA chains studied were extracted from a segment of the human chromosome 4p16.3, which were modified by expansion of CAG (cytosine-adenine-guanine) triplet repeats to mimics Huntington’s disease. The mutated DNA chains were connected between two platinum electrodes to analyze the relationship between charge propagation in the molecule and Huntington’s disease. The computations were performed within a tight-binding model, together with a transfer matrix technique, to investigate the current-voltage (I–V) of 23 types of DNA sequence and compare them with the distributions of the related CAG repeat numbers with the disease. All DNA sequences studied have a characteristic behavior of a semiconductor. In addition, the results showed a direct correlation between the current-voltage curves and the distributions of the CAG repeat numbers, suggesting possible applications in the development of DNA-based biosensors for molecular diagnostics.