应用分子梳技术对DNA与组蛋白相互作用的研究

利用分子梳技术对λ DNA和组蛋白的相互作用进行了研究. 通过这种简单有效的方法，我们将λ DNA分子拉伸到26—28 μm，相当于其原长（约162 μm）的16—17倍. 当组蛋白与DNA结合后，DNA分子发生凝聚现象，复合体的拉伸长度明显变短，其峰值分布在10—14 μm之间. DNA 组蛋白复合体的拉伸长度与组蛋白的浓度、与碱基对和荧光染料的比例有显著的关系. 关键词： 分子梳 组蛋白 DNA 荧光显微     

钾离子通道布朗动力学研究

结合钾离子通道的三维精细结构,从第一性原理出发,在充分考虑电子相互作用的基础上,采用密度泛函方法计算得到了钾通道的位能曲线;以此作为钾通道布朗动力学模型的力场参数,应用布朗动力学方法研究了钾离子通道的动力学特征,得到了一些有益的结果。In the paper, based on the first principle and the X-ray structure of the potassium ion channel, the potential curve is calculated by the density functional theory. And forced by the potential, the dynamical properties of K channels are also studied.     

利用纳米孔研究DNA

脱氧核糖核酸 (DNA)和蛋白质是构成生命体最为重要的两类生物大分子 .随着科学技术的快速发展 ,越来越多的纳米技术被用来研究这些生物大分子 .文章详细介绍了近来利用纳米孔技术研究DNA的一些进展 .结合作者近期利用聚焦离子束 (FIB)制作纳米孔的工作 ,提出了利用纳米孔解离核小体的设想 .如果能够利用纳米孔将双螺旋DNA从组蛋白八聚体上剥离下来 ,并探测这一过程 ,将揭示核小体中包含的许多生物化学、物理信息 .文章对此进行了较为详细的分析 :处于电场中的核小体在电场的作用下 ,DNA分子穿越纳米孔 ,同时由于纳米孔的阻挡力 ,使组蛋白不能穿越 ,从而诱使DNA从组蛋白八聚体上分离下来 .通过准确检测DNA分子穿孔过程中引起的电流阻塞效应 ,可将DNA与组蛋白的相互作用的一些性质反映出来     

利用原子力显微镜研究在单分子水平上DNA与组蛋白的相互作用

核小体是DNA被压缩成染色质的第一级压缩结构. 为了更深刻描述DNA与组蛋白的相互作用,利用透析方法将DNA和组蛋白构建成核小体,并且应用原子力显微镜进行单分子水平上的观察. 实验结果表明利用透析方法得到了核小体的“串珠型排列”,并且对在两种不同的结合条件下DNA与组蛋白的相互作用进行了观察和比较.     

光阱中布朗粒子动力学分析

通过对光阱中的布朗粒子进行动力学方程求解,由解的结果分析得到观测系统的性能要求．结果表明：光阱中布朗颗粒服从Boltzmann分布;对其运动的观测需要纳米量级的空间分辨率和毫秒量级的时间分辨率．     

离子与通道相互作用对NaK 通道通透特性影响的研究

以NaK 通道的三维精细结构为基础,从理论上阐述了NaK 通道对钠离子、钾离子、铷离子以及钙离子的通透机理,钡离子可以作为NaK 通道阻断剂的微观机理,我们的研究结果表明,通道与离子的相互作用是决定通道对不同离子选择性的基础, 反映通道与离子相互作用的位能曲线是通道对不同离子通透性的外在表现. 关键词： NaK 通道 密度泛函 布朗动力学 通透性     

荧光光谱法研究抗癌药物与DNA的相互作用

荧光探针技术可以用来测定药物-核酸相互作用的强度。通过药物与核酸相互作用,使DNA与探针键合的程度减小,反映在探针荧光光谱的改变,从而可以了解药物和核酸的作用机理。相互作用常数D为DNA 探针中加入药物后探针的荧光强度相对于DNA 探针荧光强度减去纯探针荧光强度的下降百分数。文章利用盐酸小檗碱(Berberine)作为探针,测定几种抗癌药物加入DNA与荧光探针(盐酸小檗碱)混合溶液的荧光谱,探讨它们与DNA的相互作用。并根据相同浓度的不同药物与核酸相互作用的常数D确定作用强弱。     

顺铂与DNA间的相互作用

用荧光探针法研究化疗药物顺铂与ＤＮＡ（脱氧核糖核酸）的相互作用。还用吸收光谱法研究了它们间的相互作用。     

Brownian dynamics simulation of the cross-talking effect among modified histones on conformations of nucleosomes

Using Brownian dynamics simulation,we studied the effect of histone modifications on conformations of an array of nucleosomes in a segment of chromatin.The simulation demonstrated that the segment of chromatin shows the dynamic behaviour that its conformation can switch between a state with nearly all of the histones being wrapped by DNA and a state with nearly all of the histones being unwrapped by DNA,thus involving the "cross-talking" interactions among the histones.Each state can stay for a sufficiently long time.These conformational states are essential for gene expression or gene silence.The simulation also shows that these conformational states can be inherited by the daughter DNAs during DNA replication,giving a theoretical explanation of the epigenetic phenomenon.     

Brownian dynamics simulation of two confined colloidal particles

The dynamics of two confined colloidal particles is studied by means of Brownian dynamics simulation. The autocorrelation function and cross-correlation function of the two colloidal spheres are computed by utilizing the formulae of hydrodynamic diffusion matrix expanded to different orders, as well as the accurate tensor through numerical algorithm. Furthermore, the numerical results are compared with the experimental results and the theoretical approximation. It is found that the relatively simple theoretical approximation gives good predictions when two spheres are far away from each other, but fails when the two spheres are very close.     

Rotational Brownian dynamics of semiflexible broken rods

Using the Brownian dynamics simulation technique, we study the rotational dynamics of a semiflexible broken rod. We employ a suitable bead model with stiff springs between beads and strong forces opposing to bending, except at the joint where flexibility is variable. We consider mostly broken rods with equal arms. From the simulated Brownian trajectories we obtain the correlation function for the second order Legendre polynomial of the reorientational angle of the end-to-end vector and of the arm vector. These correlation functions are closely related to fluorescence anisotropy decay and electric birefringence decay, respectively. In the first case, the relaxation time for a completely flexible rod agrees with the Harvey-Wegener theory, and in the second, the longest relaxation time agrees well with that obtained from the rigid-body treatment over the whole range of flexibility. Furthermore, we discuss the relative importance of flexibility in both types of decay. Finally, we present results for a case with unequal arms, confirming the validity of the Harvey-Wegener theory and the rigid-body treatment.     

Field-induced dynamics in the quantum Brownian oscillator: An exact treatment

We consider a quantum linear oscillator coupled to a bath in equilibrium at an arbitrary temperature and then exposed to an external field arbitrary in form and strength. We then derive the reduced density operator in closed form of the coupled oscillator in a non-equilibrium state at an arbitrary time.     

Nonequilibrium Brownian dynamics simulations of shear thinning in concentrated colloidal suspensions

The effect of interparticle forces on shear thinning in concentrated aqueous and nonaqueous colloidal suspensions was studied using nonequilibrium Brownian dynamics. Hydrodynamic interactions among particles were neglected. Systems of 108 particles were studied at volume fractions of 0.2 and 0.4. For the nonaqueous systems, shear thinning could be correlated with the gradual breakup of small flocs present because of the weak, attractive secondary minimum in the interparticle potential. At the highest shear rate for=0.4, the particles were organized into a hexagonally packed array of strings. For the strongly repulsive aqueous systems, the viscosity appeared to be a discontinuous function of the shear rate. For=0.4, this discontinuity coincided with a transition from a disordered state to a lamellar structure for the suspension.     

Adsorption of a spherical nanoparticle in polymer brushes: Brownian dynamics investigation

We use Brownian dynamics simulations to study the adsorption behavior of a nanosized particle in polymer brushes. The adsorption process, the dynamic behavior of the nanoparticle in the brush, the penetration depth, the diffusion coefficient of the nanoparticle in different depths of the brush, and the forces exerted on the nanoparticle by the surrounding brush are all investigated for different grafting densities.     

谐振势阱中的布朗运动——磁镊实验与模拟

从磁镊实验和模拟角度研究了处于谐振势阱中的布朗运动. 利用实验和模拟的结果验证了理论.然后通过理论与实验的对照, 对磁镊实验中DNA分子的持久长度大小对小球位移分布的影响, 以及磁镊实验中的测力误差作了相关分析.分析指出:持久长度的变化对沿 DNA链方向上的布朗运动影响更大;小的外力作用下力的测量会出现较大误差.     

Coupling effect of Brownian motion and laminar shear flow on colloid coagulation:a Brownian dynamics simulation study

Simultaneous orthokinetic and perikinetic coagulations(SOPCs) are studied for small and large Peclet numbers(P e) using Brownian dynamics simulation.The results demonstrate that the contributions of the Brownian motion and the shear flow to the overall coagulation rate are basically not additive.At the early stages of coagulation with small Peclet numbers,the ratio of overall coagulation rate to the rate of pure perikinetic coagulation is proportional to P 1/2 e,while with high Peclet numbers,the ratio of overall coagulation rate to the rate of pure orthokinetic coagulation is proportional to P 1/2 e.Moreover,our results show that the aggregation rate generally changes with time for the SOPC,which is different from that for pure perikinetic and pure orthokinetic coagulations.By comparing the SOPC with pure perikinetic and pure orthokinetic coagulations,we show that the redistribution of particles due to Brownian motion can play a very important role in the SOPC.In addition,the effects of redistribution in the directions perpendicular and parallel to the shear flow direction are different.This perspective explains the behavior of coagulation due to the joint effects of the Brownian motion(perikinetic) and the fluid motion(orthokinetic).