Distribution functions, loop formation probabilities, and force-extension relations in a model for short double-stranded DNA molecules

We obtain, using transfer-matrix methods, the distribution function P(R) of the end-to-end distance, the loop formation probability, and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the appearance of "bubbles," localized regions of enhanced flexibility associated with the opening of a few base pairs of double-stranded DNA in thermal equilibrium, leads to dramatic changes in P(R) and unusual force-extension curves. An analytic formula for the loop formation probability in the presence of bubbles is proposed. For short heterogeneous chains, we demonstrate a strong dependence of loop formation probabilities on sequence.     

Force-extension curves of dimerized polyglutamic acid

Measurement of the force-extension curve for the mechanical unfolding process of a single protein molecule is expected to provide a value for the force necessary to deform the molecule. Integration of the observed curves can then yield an accurate estimate of the intra-molecular cohesive energy of the protein. To understand the details of such force-extension curves, it is necessary to begin by understanding the mechanical properties of simple structural elements such as the !-helix and #-sheet. In a series of experiments designed to obtain force-extension curves of helical and randomly coiled polyglutamic acid, we found an interesting phenomenon in linearly cross-linked dimer samples of the polymer. The remarkable observation indicated the possibility of a lateral interaction of helical rods within molecules. Mechanical distinction of such interactions will be useful for application of atomic force microscopy in studying the nanomechanics of tertiary interactions among peptide segments in protein molecules.     

Bubble nucleation and cooperativity in DNA melting

The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Dauxois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with previously published experimental results finding excellent agreement. Melting curves, critical DNA segment length for stability of bubbles, and the possibility of a two-state transition are studied.     

Simulations of stretching a flexible polyelectrolyte with varying charge separation

We calculated the force-extension curves for a flexible polyelectrolyte chain with varying charge separations by performing Monte Carlo simulations of a 5000 bead chain using a screened Coulomb interaction. At all charge separations, the force-extension curves exhibit a Pincus-like scaling regime at intermediate forces and a logarithmic regime at large forces. As the charge separation increases, the Pincus regime shifts to a larger range of forces and the logarithmic regime starts are larger forces. We also found that force-extension curve for the corresponding neutral chain has a logarithmic regime. Decreasing the diameter of bead in the neutral chain simulations removed the logarithmic regime, and the force-extension curve tends to the freely jointed chain limit. This result shows that only excluded volume is required for the high force logarithmic regime to occur.     

Constrained thermal denaturation of DNA under fixed linking number

A DNA molecule with freely fluctuating ends undergoes a sharp thermal denaturation transition upon heating. However, in circular DNA chains and some experimental setups that manipulate single DNA molecules, the total number of turns (linking number) is constant at all times. The consequences of this additional topological invariant on the melting behaviour are nontrivial. Below, we investigate the melting characteristics of a homogeneous DNA where the linking number along the melting curve is preserved by supercoil formation in duplex portions. We obtain the mass fraction and the number of loops and supercoils below and above the melting temperature. We also argue that a macroscopic loop appears at T _c and calculate its size as a function of temperature.     

Supercoiling induces denaturation bubbles in circular DNA

We present a theoretical framework for the thermodynamic properties of supercoiling-induced denaturation bubbles in circular double-stranded DNA molecules. We explore how DNA supercoiling, ambient salt concentration, and sequence heterogeneity impact on the bubble occurrence. An analytical derivation of the probability distribution to find multiple bubbles is derived and the relevance for supercoiled DNA discussed. We show that in?vivo sustained DNA bubbles are likely to occur due to partial twist release in regions rich in weaker AT base pairs. Single DNA plasmid imaging experiments clearly demonstrate the existence of bubbles in free solution.     

Thermal denaturation of fluctuating DNA driven by bending entropy

A statistical model of homopolymer DNA, coupling internal base-pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the fraction of denaturation bubbles and their correlation length is deduced. The thermal denaturation transition emerges naturally when the chain fluctuations are integrated out and is driven by the difference in bending (entropy dominated) free energy between broken and unbroken segments. Conformational properties of DNA, such as persistence length and mean-square-radius, are also explicitly calculated, leading, e.g., to a coherent explanation for the experimentally observed thermal viscosity transition.     

Melting and unzipping of DNA

Existing experimental studies of the thermal denaturation of DNA yield sharp steps in the melting curve suggesting that the melting transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic configurations of a DNA molecule consist of an alternating sequence of non-interacting bound segments and denaturated loops. Studies of these models neglect the repulsive, self-avoiding, interaction between different loops and segments and have invariably yielded continuous denaturation transitions. In the present study we take into account in an approximate way the excluded-volume interaction between denaturated loops and the rest of the chain. This is done by exploiting recent results on scaling properties of polymer networks of arbitrary topology. We also ignore the heterogeneity of the polymer. We obtain a first-order melting transition in d = 2 dimensions and above, consistent with the experimental results. We also consider within our approach the unzipping transition, which takes place when the two DNA strands are pulled apart by an external force acting on one end. We find that the under equilibrium condition the unzipping transition is also first order. Although the denaturation and unzipping transitions are thermodynamically first order, they do exhibit critical fluctuations in some of their properties. For instance, the loop size distribution decays algebraically at the transition and the length of the denaturated end segment diverges as the transition is approached. We evaluate these critical properties within our approach. Received 21 August 2001 and Received in final form 26 January 2002     

盐离子对DNA延伸力的影响

在Ahsan等给出的描述DNA分子弹性的两状态虫链模型的基础上,考虑到盐离子浓度对静电自由能的影响,得到了延伸力随盐浓度的变化规律,结果表明:在低力和高力范围延伸力受盐浓度的影响较小,相变延伸范围随盐浓度的增加非线性增加,与实验测量一致.     

Statistical mechanics of thermal denaturation of DNA oligomers

Double stranded DNA chain is known to have non-trivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or intact) state. The effect of this constraint on the denaturation profile of the oligomer has been calculated using the Peyrard-Bishop Hamiltonian. The denaturation profile is found to be very different from the free (i.e. without the constraint) oligomer. We have also examined how this constraint affects the denaturation profile of the oligomer having a segment of defect sites located at different parts of the chain.     

Force-extension curve of a polymer in a high-frequency electric field

We study theoretically the conformation and force-extension curve of a semiflexible polymer in a spatially uniform ac electric field. The polymer backbone minimizes its energy by aligning along one of two orientations parallel to the field. In a strong ac field, hairpin kinks develop between regions of opposite alignment. These kinks are mathematically described as sine-Gordon solitons. We calculate the equation of state of the one-dimensional kink gas, which yields the force-extension curve of the polymer. A sufficiently strong ac field causes the polymer to extend spontaneously to almost its full contour length. The theory is applied to recent experiments on dielectrophoretic stretching of DNA.     

Existence and uniqueness of stabilized propagating wave segments in wave front interaction model

Recent experimental studies of photosensitive Belousov–Zhabotinskii reaction have revealed the existence of propagating wave segments. The propagating wave segments are unstable, but can be stabilized by using a feedback control to continually adjust the excitability of the medium. Experimental studies also indicate that the locus of the size of a stabilized wave segment as a function of the excitability of the medium gives the excitability boundary for the existence of 2D wave patterns with free ends in excitable media. To study the properties of this boundary curve, we use the wave front interaction model proposed by Zykov and Showalter. This is equivalent to study a first order system of three ordinary differential equations which includes a singular nonlinearity. Using two different reduced first order systems of two ordinary differential equations, we first show the existence of wave segments for any given propagating velocity. Then the wave profiles can be classified into two types, namely, convex and non-convex types. More precisely, when the normalized propagating velocity is small, we show that the wave profile is of convex type, while the wave profile is of non-convex type when the normalized velocity is close to 1.     

Stretching of semiflexible polymers with elastic bonds

A semiflexible harmonic chain model with extensible bonds is introduced and applied to the stretching of semiflexible polymers or filaments. The semiflexible harmonic chain model allows to study effects from bending rigidity, bond extension, discrete chain structure, and finite length of a semiflexible polymer in a unified manner. The interplay between bond extension and external force can be described by an effective inextensible chain with increased stretching force, which leads to apparently reduced persistence lengths in force-extension relations. We obtain force-extension relations for strong- and weak-stretching regimes which include the effects of extensible bonds, discrete chain structure, and finite polymer length. We discuss the associated characteristic force scales and calculate the crossover behaviour of the force-extension curves. Strong stretching is governed by the discrete chain structure and the bond extensibility. The linear response for weak stretching depends on the relative size of the contour length and the persistence length which affects the behaviour of very rigid filaments such as F-actin. The results for the force-extension relations are corroborated by transfer matrix and variational calculations.PACS: 87.15.-v Biomolecules: structure and physical properties - 87.15.Aa Theory and modeling; computer simulation - 87.15.La Mechanical properties     

An Efficient NMR Experiment for Analyzing Sugar-Puckering in Unlabeled DNA: Application to the 26-kDa Dead Ringer–DNA Complex

We present a new NMR experiment for estimating the type and degree of sugar-puckering in high-molecular-weight unlabeled DNA molecules. The experiment consists of a NOESY sequence preceded by a constant-time scalar coupling period. Two subexperiments are compared, each differing in the amount of time the (3)J(H3'H2') and (3)J(H3'H2") couplings are active on the H3' magnetization. The resultant data are easy to analyze, since a comparison of the signal intensities of any resolved NOE cross peak originating from H3' atoms of the duplex can be used to estimate the sum of the (3)J(H3'H2') and (3)J(H3'H2") couplings and thus the puckering type of the deoxyribose ring. Isotope filters to eliminate signals of the (13)C-labeled component in the F1-dimension are implemented, facilitating analyses of high-molecular-weight protein-DNA complexes containing (13)C-labeled protein and unlabeled DNA. The utility of the experiment is demonstrated on the 26-kDa Dead Ringer protein-DNA complex and reveals that the DNA uniformly adopts the S-type configuration when bound to protein.     

Visualization of coalescence behavior of two bubbles with smoothness constraint

A new method based on 2D contour curve fitting and 3D rotation surface generation to visualize the coalescence phenomenon of two bubbles in static water is presented. First, some contour points are extracted from key frame images in different coalescence stages of two bubbles. Second, those points are fitted using a new approach combining piecewise curve fitting with a smoothing constraint. Third, a family of transition functions is proposed to deal with continuous changes of contour curves in the process of coalescence. Finally, we use those contours to generate dynamical 3D rotation surfaces and achieve the continuous deformation visualization of two-bubble coalescence.     

Large-deviation properties of resilience of transportation networks

In this study, we consider a propagating wave segment in two dimensions. A reaction diffusion system with global feedback is proposed, and spiral waves and propagating wave segments are shown. Propagating wave segments with large arc lengths can exist due to the absence of strong lateral inhibition. In order to study the properties of propagating wave segments, we propose a kinematic model with global feedback. When the elongating and shortening effects on the curve are balanced, stable propagating wave segments exist. For other cases, the initial wave segment evolves into a spiral wave or expanding wave or shrinking wave. The conditions for the propagating wave segment and the dependences of the solutions on the various relevant parameters are discussed.     

Application of high-resolution ESI and MALDI mass spectrometry to metabolite profiling of small interfering RNA duplex

We investigated the application of a high-resolution Orbitrap mass spectrometer equipped with an electrospray ionization (ESI) source and a matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometer to the metabolite profiling of a model small interfering RNA (siRNA) duplex TSR#34 and compared their functions and capabilities. TSR#34 duplex was incubated in human serum in vitro, and the duplex and its metabolites were then purified by ion exchange chromatography in order to remove the biological matrices. The fraction containing the siRNA duplex and its metabolites was collected and desalted and then subjected to high-performance liquid chromatography (HPLC) equipped with a reversed phase column. The siRNA and its metabolites were separated into single strands by elevated chromatographic temperature and analyzed using the ESI-Orbitrap or the MALDI-TOF mass spectrometer. Using this method, the 5' and/or 3' truncated metabolites of each strand were detected in the human serum samples. The ESI-Orbitrap mass spectrometer enabled differentiation between two possible RNA-based sequences, a monoisotopic molecular mass difference which was less than 2 Da, with an intrinsic mass resolving power. In-source decay (ISD) analysis using a MALDI-TOF mass spectrometer allowed the sequencing of the RNA metabolite with characteristic fragment ions, using 2,4-dihydroxyacetophenone (2,4-DHAP) as a matrix. The ESI-Orbitrap mass spectrometer provided the highest mass accuracy and the benefit of on-line coupling with HPLC for metabolite profiling. Meanwhile, the MALDI-TOF mass spectrometer, in combination with 2,4-DHAP, has the potential for the sequencing of RNA by ISD analysis. The combined use of these methods will be beneficial to characterize the metabolites of therapeutic siRNA compounds. Copyright ? 2012 John Wiley & Sons, Ltd.     

Symplectic analysis for periodical electro-magnetic waveguides

Symplectic analysis is introduced into electro-magnetic waveguide theory, by using Hamiltonian system theory in which the transverse electric and magnetic field vectors are the dual vectors. The method can accommodate arbitrary anisotropic material and includes the interface conditions between adjacent segments of the waveguide. An electro-magnetic stiffness matrix is introduced which relates to the two ends of each segment of the waveguide. Both the pass- and stop-band stiffness matrices for plane waveguides with constant cross-section are given analytically and also a transformation matrix is given to permit abrupt changes of cross-section to occur. The variational principle is applied to obtain the segment combination algorithm needed to generate the electro-magnetic stiffness matrix related to the two ends of the fundamental periodical segment. Then the Wittrick-Williams algorithm is used to extract the eigenvalues. Thereafter, an energy band analysis is performed for a periodical waveguide, e.g., a grating, by using the symplectic eigensolutions.     

新型光谱曲线特征参数与水稻叶绿素含量间的关系研究

利用高光谱信息检测作物叶绿素含量信息是田间作物长势诊断的重要研究内容。利用水稻光谱和叶绿素含量田间实测数据,从作物叶绿素含量不同,光谱曲线峰谷波形有高矮胖瘦形态变化的观点出发,提出光谱曲线峰谷波形中特征边的上升、下降速率以及组成峰谷波形两边的夹角等新型特征量,利用归一化光谱信息,分析了这些变量与水稻叶绿素含量间的相关关系。研究结果显示:(1)可见光波段范围520～740nm之间的归一化光谱反射率与叶绿素含量间呈良好的负相关关系;(2)绿峰反射光谱曲线特征边的变化速率及绿峰两边的夹角等变量与水稻叶绿素含量具有较好的相关性,表明利用这些新型变量开展叶绿素含量高光谱无损监测成为可能,这将为利用高光谱信息开展作物长势与营养诊断提供新的思路和方法。     

Diffraction efficiency of holographic blazed diffraction gratings

Holographic blazed diffraction grating is analysed as a periodic relief of an inclined sinusoidal curve in the shallow profile approximation. Under the condition that the rate of the development is a linear function of the development dose the evolution of the relief during the development is discussed. Theoretical curves of diffraction efficiency are compared with measurements on gratings made by direct holographic method for uv spectral region.