Probing DNA and RNA single molecules with a double optical tweezer

A double-tweezer setup is used to induce mechanical stress in systems of molecular biology. A double strand of DNA is first stretched and the data is compared to precedent experiments to check the experimental setup. Then a short foldable fragment of RNA is probed; the typical unfolding/refolding hysteresis behaviour of this kind of construction is shown and followed by a study of its elasticity and a comparison to a worm-like chain model. Eventually, we describe the unfolding of a larger RNA structure, which unfolds by multiple steps. We show that this unfolding is not reversible and that it presents numerous unfolding pathways.     

Formation and positioning of nucleosomes: Effect of sequence-dependent long-range correlated structural disorder

The understanding of the long-range correlations (LRC) observed in DNA sequences is still an open and very challenging problem. In this paper, we start reviewing recent results obtained when exploring the scaling properties of eucaryotic, eubacterial and archaeal genomic sequences using the space-scale decomposition provided by the wavelet transform (WT). These results suggest that the existence of LRC up to distances ∼ 20-30kbp is the signature of the nucleosomal structure and dynamics of the chromatin fiber. Actually the LRC are mainly observed in the DNA bending profiles obtained when using some structural coding of the DNA sequences that accounts for the fluctuations of the local double-helix curvature within the nucleosome complex. Because of the approximate planarity of nucleosomal DNA loops, we then study the influence of the LRC structural disorder on the thermodynamical properties of 2D elastic chains submitted locally to mechanical/topological constraint as loops. The equilibrium properties of the one-loop system are derived numerically and analytically in the quite realistic weak-disorder limit. The LRC are shown to favor the spontaneous formation of small loops, the larger the LRC, the smaller the size of the loop. We further investigate the dynamical behavior of such a loop using the mean first passage time (MFPT) formalism. We show that the typical short-time loop dynamics is superdiffusive in the presence of LRC. For displacements larger than the loop size, we use large-deviation theory to derive a LRC-dependent anomalous-diffusion rule that accounts for the lack of disorder self-averaging. Potential biological implications on DNA loops involved in nucleosome positioning and dynamics in eucaryotic chromatin are discussed.     

Magnetic solids in analytical chemistry: A review

Magnetic solids are widely used in detection and analytical systems because of the performance advantages they offer compared to similar solids that lack magnetic properties. These solids can be used to pre-concentrate analytes and for the magnetic separation and molecular identification of biomolecules, and organic and inorganic species. Magnetic solid separation techniques also offer benefits over centrifugation, filtration, and solid-phase extraction. In this review, we describe the synthesis, characterization and applications of a series of solids including silica supports, carbon nanotubes, alumina, organic polymers and other materials, mostly containing magnetite or paramagnetic metals. Also addressed are the future perspectives of magnetic solid applications.     

Comparison of surfactants for dynamic surface modification of poly(dimethylsiloxane) microchips

In the present report, the use of negatively charged surfactants as modifiers of the background electrolyte is reported using poly(dimethylsiloxane) (PDMS) microchips. In particular, the use of anionic surfactants, such as sodium dodecyl sulfate, phosphatidic acid, and deoxycholate, was studied. When surfactants were present in the run buffer, an increase in the electroosmotic flow (EOF) was observed. Two additional effects were also observed: (i) stabilization of the run-to-run EOF, (ii) an improvement in the electrochemical response for several biomolecules. In order to characterize the analysis conditions, the effects of different surfactant, electrolyte, and pH were studied. EOF measurements were performed using either the current monitoring method or by detection of a neutral molecule. The first adsorption/desorption kinetics studies are also reported for different surfactants onto PDMS. The separation of biologically important analytes (glucose, penicillin, phenol, and homovanillic acid) was improved decreasing the analysis time from 200 to 125 s. However, no significant changes in the number of theoretical plates were observed.     

高效液相色谱-紫外检测法测定水产品中氨苯砜及其代谢物残留量EI北大核心CSCD

建立了水产品中氨苯砜及其代谢产物N-乙酰氨苯砜残留量同时测定的高效液相色谱-紫外检测法(HPLC-UV)。样品经1%氨化乙腈提取,正己烷去脂,MCX阳离子固相萃取柱富集净化,氮吹浓缩,定容过膜后测定。以甲醇和水为流动相,ZORBAX SB-C_(18)色谱柱梯度洗脱分离,采用保留时间定性,外标法定量。在最佳检测条件下,目标化合物质量浓度在5~200 ng/mL范围内线性关系良好(R^(2)> 0.999),检出限(LOD)为10.0μg/kg,定量限(LOQ)为20.0μg/kg。以不同类型的水产品为空白基质,在20,50,100μg/kg加标水平下,氨苯砜的回收率为70.1%~81.7%,N-乙酰氨苯砜的回收率为84.2%~109.5%,相对标准偏差(RSD)均小于10%。该方法能够实现大批量水产品中氨苯砜及其代谢物残留量的检测。     

Unfolding designable structures

Among an infinite number of possible folds, nature has chosen only about 1000 distinct folds to form protein structures. Theoretical studies suggest that selected folds are intrinsically more designable than others; these selected folds are unusually stable, a property called the designability principle. In this paper we use the 2D hydrophobic-polar lattice model to classify structures according to their designability, and Langevin dynamics to account for their time evolution in the presence of shear flow. We demonstrate that, among all possible folds, the more designable ones are easier to unfold due to their large number of surface-core bonds.     

Elasticity and plasticity of two-dimensional amorphous solid layers of β-lactoglobulin

We investigate the mechanical properties of a two-dimensional amorphous solid. It is formed spontaneously by the adsorption of a protein (the β-lactoglobulin) at the surface of water. We measure its mechanical response in both elastic and plastic regimes by applying a point-like force (using a glass fiber). We compare our results with previous measurements of shear moduli using a floating torsion device. Received: 10 February 2003 / Accepted: 23 April 2003 / Published online: 27 May 2003 RID="a" ID="a"Present address: Cavendish Laboratory, Madingley Road, Cambridge, CB3 0HE, UK; e-mail: sc374@phy.cam.ac.uk RID="b" ID="b"e-mail: graner@ujf-grenoble.fr     

Effects of NH3, O2, and N2 co-implantation on Cu out-diffusion and antimicrobial properties of copper plasma-implanted polyethylene

Metal antibacterial reagents are effective in the enhancement of the antimicrobial properties of medical polymers. However, incorporation of metal antibacterial reagents into polymers using conventional methods usually results in unstable antimicrobial effects. Our previous research demonstrates that plasma immersion ion implantation (PIII) can be used to effectively incorporate metal antibacterial reagents such as Cu into polyethylene (PE) in the near surface region up to several hundred nanometers without causing noticeable damage to the polymer matrix. In this work, various gases including NH₃, O₂, and N₂ were plasma-implanted in concert with Cu plasma immersion ion implantation to study the effects of these gas species on the release rate of Cu from the substrate. Our experimental results reveal that the copper depth profiles are not affected significantly by NH₃, O₂, or N₂ co-implantation and these gas elements have similar depth profiles as Cu. Chemical analyses demonstrate that polar functional CO, CO, CN, CN, and CN bonds formed in the substrate play an important role in regulating Cu out-diffusion. Among the three gas species, N₂ shows the best effects in regulating Cu out-diffusion and produces the best long term antibacterial properties. The Cu retention and out-diffusion mechanism in the ion-implanted polyethylene is described.