Sequence dependent rigidity of single stranded DNA

Single stranded DNA (ssDNA) equilibrium dynamics are investigated using a fluorophore/quencher-labeled hairpin structure which thermally fluctuates between open and closed states. Temporal correlations of the fluorescence fluctuations are used to determine the energy barrier to conformational change. We find that ssDNA distortion is purely entropic for poly(T) but requires an additional enthalpy of +0.5 kcal x mol(-1) x base(-1) for poly(A), consistent with the disruption of base stacking. Such sequence dependent dynamics challenge the classical model of ssDNA as a completely flexible coil.     

Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups, hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact, we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.     

Modeling DNA beacons at the mesoscopic scale

We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; alternative calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported. Stem formation is modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of opening and closing is described in terms of a diffusion-controlled motion in an effective free-energy landscape. Melting profiles, dependence of melting temperature on loop length, and kinetic time scales are in semiquantitative agreement with experimental data obtained from fluorescent DNA beacons forming poly(T) loops. Variation in strand rigidity is not sufficient to account for the large activation enthalpy of closing and the strong loop length dependence observed in hairpins forming poly(A) loops. Implications for modeling single strands of DNA or RNA are discussed.     

高聚物减阻溶液对壁湍流输运过程的影响

基于相同雷诺数下清水和高分子聚合物溶液壁湍流的高时间分辨率粒子图像测速技术(time-resolved particle image velocimetry, TRPIV)的对比实验, 从高聚物溶液对湍流边界层动量能量输运影响的角度分析其减阻的机理. 对比两者的雷诺应力发现高聚物的存在抑制了湍流输运过程. 这一影响与高聚物对壁湍流中占主导地位的涡旋运动和低速条带等相干结构的作用密切相关. 运用条件相位平均、相关函数和线性随机估计(linear stochastic estimation, LSE)等方法, 分析提取了高聚物溶液流场中的发卡涡和发卡涡包等典型相干结构的空间拓扑形态. 相比于清水, 高聚物溶液中相干结构的流向尺度增大, 涡旋运动的发展及低速流体喷射的强度受到削弱, 表明了添加的高聚物阻碍了湍流原有的能量传递和自维持的机理. 正是通过影响相干结构, 高聚物抑制了湍流边界层中近壁区与外区之间的动量和能量输运, 使得湍流的无序性降低, 从而减小了湍流流动的阻力.     

湍流边界层中下扫流与“反发卡涡”

用氢气泡法观测湍流边界层的下扫流和有关的流动结构.实验中发现一种新型涡结构，它的特征与典型的发卡涡正好相反.发卡涡的头部指向下游，而它的头部指向上游； 发卡涡的两腿之间，由于涡的诱导产生上升流，而它则在其两腿之间，由于涡的诱导产生下扫流. 关键词： 湍流边界层 流动显示 流动结构 发卡涡     

Convection and correlation of coherent structure in turbulent boundary layer using tomographic particle image velocimetry

The present experimental work focuses on a new model for space–time correlation and the scale-dependencies of convection velocity and sweep velocity in turbulent boundary layer over a flat wall. A turbulent boundary layer flow at Reθ= 2460 is measured by tomographic particle image velocimetry(tomographic PIV). It is demonstrated that arch, cane,and hairpin vortices are dominant in the logarithmic layer. Hairpins and hairpin packets are responsible for the elongated low-momentum zones observed in the instantaneous flow field. The conditionally-averaged coherent structures systemically illustrate the key roles of hairpin vortice in the turbulence dynamic events, such as ejection and sweep events and energy transport. The space–time correlations of instantaneous streamwise fluctuation velocity are calculated and confirm the new elliptic model for the space–time correlation instead of Taylor hypothesis. The convection velocities derived from the space–time correlation and conditionally-averaged method both suggest the scaling with the local mean velocity in the logarithmic layer. Convection velocity result based on Fourier decomposition(FD) shows stronger scale- dependency in the spanwise direction than in streamwise direction. Compared with FD, the proper orthogonal decomposition(POD) has a distinct distribution of convection velocity for the large- and small-scales which are separated in light of their contributions of turbulent kinetic energy.     

Forward-facing steps induced transition in a subsonic boundary layer

A forward-facing step (FFS) immersed in a subsonic boundary layer is studied through a high-order flux reconstruction (FR) method to highlight the flow transition induced by the step. The step height is a third of the local boundary-layer thickness. The Reynolds number based on the step height is 720. Inlet disturbances are introduced giving rise to streamwise vortices upstream of the step. It is observed that these small-scale streamwise structures interact with the step and hairpin vortices are quickly developed after the step leading to flow transition in the boundary layer.     

Model for DNA hairpin denaturation

We investigate the thermal denaturation of DNA hairpins using molecular dynamics simulations of a simple model describing the molecule at a scale of a nucleotide. The model allows us to analyze the different interacting features that determine how an hairpin opens, such as the role of the loop and the properties intrinsic to the stem.     

Electrophoresis Poly(Dimethylsiloxane)/Glass Chips with Integrated Active Cooling for Quantification of Amino Acids

Abstract

The objective of this work was to develop and characterize a poly(dimethylsiloxane) device with an integrated active cooling function able to carry out capillary electrophoresis separations. Polymer-based microdevices are indispensable to recent advances in biomedical analysis. In particular, they have been applied to many microfluidic platforms owing to their low cost, ease of fabrication, and versatility in preparing complex microstructures. However, when applied to capillary electrophoresis separations, polymer microfluidic structures present an inherent disadvantage compared to glass and Si structures; they have a lower thermal conductivity than glass and Si. Although miniaturized devices allow operation at high electric fields, they face separation efficiency limitations due to Joule heating. There is, therefore, a strong need of developing capillary electrophoresis microfluidic structures with active cooling in order to operate at a higher electric field and potentially increase separation efficiency in these microdevices. A poly(dimethylsiloxane)/glass hybrid microfluidic capillary electrophoresis system is presented, where Joule heating was minimized by using an integrated active cooling function. Two poly(dimethylsiloxane) slabs with embedded microfluidic structures were irreversibly sealed on both sides of a thin glass slide. The top poly(dimethylsiloxane) slab was used to carry out capillary electrophoresis separations, whereas the bottom poly(dimethylsiloxane) slab was employed to cool down the buffer solution used during the capillary electrophoresis separation. As demonstrated on current versus voltage plots and on capillary electrophoresis electropherograms, capillary electrophoresis separation was able to be operated at a higher electric field when using the cooling function. The cooling rate was adjustable by varying the flow rate and the initial temperature of the liquid flowing in the cooling microfluidic structure.     

聚有机硅结构和规整性对链柔性和极性的影响

基于旋转异构态模型的构象构型统计方法,考虑侧基的结构,导出有机硅聚合物基础量统一计算公式,得到Poly(silastyrene)(PSS)、Polysilapropylene(PSP)、Poly(methylphenylsiloxane)(PMPS)、Poly(dimethylsilmethylene)(PDMSM)和Poly(dimethylsilylene)(PDMS)无规链的均方回转半径特征比分别为1.45、0.63、0.97、0.69和1.99,均方二极矩特征比为2.49、0.99、0.61、0.48和0.27.发现PSS和PMPS的特征比随链长、链规整程度、构象能和温度等均呈现较大的变化,而侧基、构象能和温度对PSP、PDMSM基础量影响则不大,分析极性大侧基对有机硅聚合物链柔性和极性的影响十分重要.     

Scalar dispersion by coherent structures in uniformly sheared flow generated in a water tunnel

In order to investigate the role of coherent structures as mechanisms of scalar dispersion, we studied measurements of a passive scalar plume released in a uniformly sheared turbulent flow generated in a water tunnel. The flow had homogeneous turbulence properties in the measurement domain and contained hairpin vortices similar to those in boundary layers, and so was an ideal test bed to study the effects of coherent structures on turbulent dispersion, free from the effects of inhomogeneities or boundaries. Measurements of the velocity and concentration fields were acquired simultaneously using stereo particle image velocimetry and planar laser-induced fluorescence. We found that dye was preferentially located far away from vortices and was less likely to appear in close proximity to vortices, which is attributed to the high dissipation at the periphery of the vortices. However, we also found that dye was not directly correlated with the uniform momentum zones in the flow, suggesting a more complex relationship exists between these zones, the locations of vortices, and dye transport. Considering scalar flux events rather than simply the presence of dye as our condition of interest, a conditional eddy analysis demonstrated that hairpin vortices are responsible for the large scalar flux events as well as the large Reynolds stress events in the flow. The fact that the Reynolds stress was correlated with the scalar flux further confirmed that coherent structures are dominant mechanisms for scalar transport. Furthermore, we found that the scalar flux vector was preferentially inclined by 155° and ?25° with respect to the streamwise direction, and was thus approximately orthogonal to the planes of the legs of the most common upright and inverted hairpin structures in the flow. These findings demonstrate that coherent structures play an important and intricate role in turbulent diffusion.     

All-valence-electron band structures of infinite TCNQ and TTF stacks

MINDO/3 crystal orbital (CO) calculations have been performed for infinite neutral TCNQ and TTF stacks. The width of the conduction band of poly(TCNQ) (0.556 eV) and of the valence band of poly(TTF) (0.524 eV) agrees well with the previous MINDO/2 value of poly(TCNQ) and with the estimated value of poly(TTF). The band structures show a strong dependence on the stacking distance in the case of poly(TCNQ) and a much less strong dependence in the case of poly(TTF).     

Raman spectra and structure of a 25mer HCV RNA

We have employed Raman spectroscopy to investigate the conformation of an (Hepatitis C virus) HCV RNA 25mer (1–25 nucleotides) in solution. The principal findings of this study are (1) the A‐form secondary structure involving C3′‐ endo/anti ribofuranose pucker is predominant; (2) some uridine and guanosine nucleoside residues adopt the C2′‐ endo/anti and C3′‐ endo/syn conformations, respectively, which appear in looped nucleotide sequences; and (3) six out of nine guanine residues are base‐paired probably forming a stem. These results are interpreted as formation of a hairpin whose secondary structure is consistent with that proposed on the basis of phylogenetic comparisons with other viral RNAs. Copyright © 2009 John Wiley & Sons, Ltd.     

Polyphosphate-dependent nicotinamide adenine dinucleotide (NAD) kinase: A novel missing link in human mitochondria

Polyphosphate [poly(P)] is described as a homopolymer of inorganic phosphates. Nicotinamide adenine dinucleotide kinase (NAD kinase) catalyzes the phosphorylation of NAD⁺ to NADP⁺ in the presence of ATP (ATP-NAD kinase). Novel NAD kinase that explicitly phosphorylates NAD⁺ to NADP⁺ using poly(P), besides ATP [ATP/poly(P)-NAD kinase], was found in bacteria, in particular, Gram-positive bacteria, and the gene encoding ATP/poly(P)-NAD kinase was also newly identified in Mycobacterium tuberculosis H37Rv. Both NAD kinases required multi-homopolymeric structures for activity expression. The enzymatic and genetic results, combined with their primary and tertiary structures, have led to the discovery of a long-awaited human mitochondrial NAD kinase. This discovery showed that the NAD kinase is a bacterial type of ATP/poly(P)-NAD kinase. These pioneering findings, i.e., ATP/poly(P)-NAD kinase, NAD kinase gene, and human mitochondrial NAD kinase, have significantly enhanced research on the biochemistry, molecular biology, and evolutionary biology of NAD kinase, mitochondria, and poly(P), including some biotechnological knowledge applicable to NADP⁺ production.     

Synthesis and Investigation of Double Stimuli-Responsive Behavior of N-Isopropylacrylamide and Maleic Acid Copolymer in Solutions

Poly(N-isopropylacrylamide-co-maleic acid) [poly(NIPAAm-co-MA)] linear copolymer with comonomer molar ratio NIPAAm:MA = 94:6 was synthesized by free-radical copolymerization. The molar mass, M_sD = 28,000 Da, of poly(NIPAAm-co-MA) was determined using hydrodynamic methods. The self-assembly of poly(NIPAAm-co-MA) in aqueous solution at a concentration of 0.015 g cm^?3 within the pH interval from 1.8 to 10.6 and the temperature interval from 22 to 60°C was investigated by static and dynamic light scattering. The copolymer showed a double temperature and pH responsiveness. Three types of particles, namely, macromolecules (or unimers), micellar-like structures, and loose aggregates existed in the poly(NIPAAm-co-MA) aqueous solutions. The fraction of dissolved entities and the hydrodynamic radii of the micellar-like structures and loose aggregates depended considerably on temperature and pH. The temperature of the phase separation and the width of the phase separation interval increased with pH. An influence of pH on kinetic processes in poly(NIPAAm-co-MA) solutions was observed.     

Physics of multiple level hairpin vortex structures in turbulence

Previous experimental and numerical studies have revealed that the hairpin vortex is a basic flow element of transitional boundary layer. The hairpin vortex is believed to have legs, necks and a ring head. Based on our DNS study, the legs and the ring head are generated separately by different mechanisms. The legs function like an engine to generate low speed zones by rotation, create shear layers with surrounding high speed neighbor fluids, and further cause vortex ring formation through shear layer instability. In addition, the ring head is ?-shaped and separated from quasi-streamwise legs from the beginning. Contrary to the classical concept of "vortex breakdown", we believe transition from laminar flow to turbulence is a "buildup" process of multiple level vortical structures. The vortex rings of first level hairpins are mostly responsible for positive spikes, which cause new vorticity rollup, second level vortex leg formation and finally smaller second level vortex ring generation. The third and lower level vortices are generated following the same mechanism. In this paper, the physical process from ?-vortex to multi-level hairpin vortices is described in detail.     

Localization properties of electronic states in a polaron model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers

We numerically investigate localization properties of electronic states in a static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with realistic parameters obtained by quantum-chemical calculation. The randomness in the on-site energies caused by the electron-phonon coupling is completely correlated to the off-diagonal parts. In the single electron model, the effect of the hydrogen-bond stretchings, the twist angles between the base pairs and the finite system size effects on the energy dependence of the localization length and on the Lyapunov exponent are given. The localization length is reduced by the influence of the fluctuations in the hydrogen bond stretchings. It is also shown that the helical twist angle affects the localization length in the poly(dG)-poly(dC) DNA polymer more strongly than in the poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy dependence of the localization length when the system size is relatively small.     

Fluorescence Properties of Intercalating Neutral Chromophores in Complexes with Polynucleotides of Various Base Compositions and Secondary Structures

Changes in the relative quantum yield and polarization degree of steady-state fluorescence of daunomycin (DM) on its binding to six synthetic single- and double-stranded polynucleotides of various nucleotide compositions were measured over a wide range of molar polymer-to-dye ratios, in solutions of low ionic strength. Guanine base was found to be an effective quencher of DM fluorescence [in the DM–poly(G) complex the intensity of residual emission was ~0.5% of the free dye intensity]. The quenching of DM fluorescence by another purine base, i.e., adenine, was also revealed. But, unlike guanine, adenine exhibits quenching activity when it is in close contact with the DM chromophore, as realized in the complex with single-stranded poly(A). In intercalative complexes with double-stranded nucleic acids, where such contact is lacking, the quenching ability of adenine does not manifest itself, which has been demonstrated with the DM–poly(A) · poly(U) complex. It was found that the interaction with pyrimidine bases does not substantially change the DM quantum yield. The quenching feature of DM fluorescence is identical to that observed earlier by us for a glycoside phenazine dye containing, like DM, a neutral chromophore.     

Poly（dA）h·poly（dT）结构的喇曼光谱和晶格动力学研究

我们成功地获得了溶液中 poly(d A)·poly(d T)的喇曼光谱 ,并利用晶格动力学方法对于异规模型进行了简正分析。根据势能分布矩阵 (PED)对每一个模式进行了指定。结果表明异规模型的简振频率和 poly(d A)·poly(d T)的喇曼光谱符合得相当好 ,这说明溶液中的 poly(d A)· poly(d T)完全有可能保留了固体纤维中的异规模型结构。     

Angle dependent laser nanopatterning of poly(ethylene terephthalate) surfaces

Interference effects can lead to the formation of ripple structures at laser-irradiated poly(ethylene terephthalate) surfaces. Poly(ethylene terephthalate) surface was irradiated with linearly polarized light of a pulsed 157 nm laser. In a certain range of irradiation parameters, the irradiation resulted in the formation of coherent ripples patterns. The dimension of the pattern depends on the angle of the laser beam incidence. The surface morphology of the nano-patterned poly(ethylene terephthalate) was analyzed by atomic force microscopy and focused ion beam-scanning electron microscopy. Oxygen concentration in the modified polymer surface was studied by angular resolved X-ray induced photo-electron spectroscopy. Gold nano-layers were consecutively sputtered onto the laser irradiated poly(ethylene terephthalate) surfaces. The morphology of the sputtered gold nano-layers was investigated with atomic force microscopy too. We found that the morphology of the gold nano-layers changes and depends on the surface pattern of the laser irradiated poly(ethylene terephthalate). Formation of gold “nano-hills” is observed at the ridges of the ripple structures. The amount of oxygen together with the morphology of prepared polymer pattern may be the dominant factors controlling the gold layer growth. The present results are compared with those obtained earlier on PET irradiated with krypton fluoride laser.