Recent radiochemical studies of the fission process

This article summarizes the recent radiochemical investigations on mass, charge kinetic energy and fragment angular distributions in low energy fission of actinides.     

5-Aza-2′-deoxycytidine reactivates the CDH1 gene without influencing methylation of the entire CpG island or histone modification in a human cancer cell line

It is well-recognized that DNA methylation and histone modifications play critical roles in epigenetic regulation of gene activity through the alteration of chromatin structure. Recent studies have shown that in a subset of cancer cells, the silencing of the human E-cadherin (CDH1) gene is associated with hypermethylation of the CpG island. However, the associated molecular mechanism remains unclear. To understand the mechanism, we have investigated the alteration of CpG island methylation and histone modifications during the reactivation of the CDH1 gene by treatment with 5-aza-2′-deoxycytidine (5-aza-dC). Although the CDH1 gene expression was recovered by treatment with 5-aza-dC in a liver cancer cell line Li21, the methylation status of the entire CpG island and acetylation and methylation status of associated histones were not significantly altered. These results demonstrate that the silenced CDH1 gene can be reactivated without apparent alteration of histone modification or CpG island methylation.     

Random coil phosphorus chemical shift of deoxyribonucleic acids

Random coil phosphorus chemical shift has been studied using 16 17-nucleotide DNA sequences. Due to the presence of residual base stacking in these sequences, the temperature and sequence effects were investigated at 50 and 55 degrees C. The phosphorus chemical shifts of random coil DNA sequences have been found to be independent of temperature. Sequence effect analysis shows that the phosphorus chemical shift of a nucleotide in a random coil DNA sequence depends on both its 5'- and 3'-nearest neighbors. A trimer model has been used to establish the random coil 31P chemical shift prediction protocol which shows an accuracy of 0.02 ppm.     

Zn^2＋对DNA稳定性影响的喇曼光谱研究

利用喇曼光谱技术研究了不同摩尔浓度的Zn2+对DNA结构稳定性的影响.结果表明,当Zn2+/PO2- ≤2.0时,Zn2+与DNA磷酸基团上的氧原子结合,形成-PO2-…Zn2+…N7(G)螯合物,这种螯合作用增强了GC 碱基对之间的氢键能量,使得GC碱基对更加稳定;此外,在低浓度情况下,Zn2+还会与腺嘌呤A上的N3结合, 而与A上N3的结合只对AT碱基对有轻微的扰动.当Zn2+/PO2->2.0时,大量的Zn2+开始与胞嘧啶C上的 N3-O2螯合以及与DNA中A上的N1结合,Zn2+与C上的N3-O2的螯合,打断了GC碱基对之间的氢键;与A 上的N1结合时,AT碱基对之间的氢键也被打断.因此,低浓度的Zn2+对DNA的构像起着稳定性作用,但是高浓 度的Zn2+则破坏了DNA构象的稳定性.在高浓度的Zn2+ DNA溶液中,GC受损比AT更为严重,部分C甚至经 过脱氨基现象转化成了T,碱基配对被解开,DNA结构变得不稳定,其主链的几何形状和次级结构发生变化,不 再是一个典型的B型DNA,而是一个修饰过的B′型DNA.     

生物分子拉曼散射测定过程中荧光背景的抑制

拉曼共焦技术、表面拉曼增强技术以及降低入射激光强度的方法，被运用于SOD、DNA等生物分子拉曼散身实验中，以抑制其荧光背景，改善光谱质量。     

Bubbles in DNA by random force

We model single strand binding (SSB) proteins as agents exerting randomly oriented force on the bonds in DNA unzipping. The fluctuating force is found to unzip the double stranded DNA (dsDNA) via opening of bubbles along the chain.     

Kinetics of protein-release by an aptamer-based DNA nanodevice

A recently introduced DNA nanodevice can be used to selectively bind or release the protein thrombin triggered by DNA effector strands. The release process is not well described by simple first or second order reaction kinetics. Here, fluorescence resonance energy transfer and fluorescence correlation spectroscopy experiments are used to explore the kinetics of the release process in detail. To this end the influence of concentration variations and also of temperature is determined. The relevant kinetic parameters are extracted from these experiments and the kinetic behavior of the system is simulated numerically using a set of rate equations. The hydrodynamic radii of the aptamer device alone and bound to thrombin are determined as well as the dissociation constant for the aptamer device-thrombin complex. The results from the experiments and a numerical simulation support the view that the DNA effector strand first binds to the aptamer device followed by the displacement of the protein.     

钌(Ⅱ)配合物与DNA相互作用的瞬态发光特性

以三种新合成的钌配合物[Ru(bpy)₂(7-CH₃-dppz)]²⁺、[Ru(bpy)₂(7-F-dppz)]²⁺、[Ru(phen)₂(7-F-dppz)]²⁺为研究对象,采用时间分辨的荧光光谱技术分别测量了这三种钌配合物与小牛胸腺DNA相互作用时的瞬态荧光动力学过程。结果表明:[Ru(bpy)₂(7-CH₃-dppz)]²⁺的发光寿命最长(约382 ns),而[Ru(bpy)₂(7-F-dppz)]²⁺的发光寿命最短(约65 ns)。分析表明:钌配合物的发光来源于配合物分子中的电荷转移态到基态的辐射跃迁。通过钌配合物与DNA的相互作用,使得配合物激发态分子的无辐射弛豫几率减小,从而导致发光寿命的增加。配合物的分子与DNA相互作用越强,激发态分子的无辐射弛豫几率越小,发光寿命也越长,最终导致高的发光效率。配合物的分子结构对配合物的分子与DNA的相互作用具有重要的影响。     

十二羰基三铁与DNA相互作用的紫外和荧光光谱研究

采用紫外-可见吸收光谱、荧光光谱等法研究了十二羰基三铁簇合物与小牛胸腺DNA的相互作用.在簇合物存在下,DNA的紫外吸收光谱产生了明显的增色效应.荧光光谱表明簇合物的荧光强度随DNA的加入其荧光强度增加,说明簇合物与DNA之间发生了插入作用.     

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.