Predicting the onset of DNA supercoiling using a non-linear hemitropic elastic rod

Elastic rod models provide a means to interpret single molecule DNA experiments as well as predict DNA behavior under physiological conditions. Here we use an elastic rod model to predict the stability boundary (critical torque vs. applied tension) for single molecule DNA experiments in which the molecule is subjected to applied tension and twist. We discuss the shortcomings of the usual isotropic rod model. We then derive a consistent non-linear material law from the general representation for a hemitropic (chiral) rod. Finally, we present results of a standard bifurcation analysis predicting the stability boundary. We find results from the non-linear hemitropic rod to match the data closely.     

Synthesis of a hairpin pyrrole-imidazole polyamide conjugate containing a quinone methide precursor and vinyl linking group

Standard procedures for elaborating a quinone methide precursor for conjugation to a DNA ligand was not compatible with the presence of a vinyl group. Instead, an acrylate linker was attached by Heck coupling subsequent to o-substitution of the phenolic precursor. This transformation required protection of the phenolic group and use of ethyl acrylate rather than acrylic acid. The presence of the vinyl group also rendered the quinone methide precursor more labile to alkaline conditions than its equivalent saturated derivative and required mild conditions for coupling to the pyrrole-imidazole polyamide.     

Reversible 5′-end biotinylation and affinity purification of synthetic RNA

A reversible biotinylation phosphoramidite was synthesized and incorporated onto the 5′-end of an oligoribonucleotide on a solid phase synthesizer. After cleavage and deprotection, the crude synthetic oligomer mixture was incubated with NeutrAvidin^® coated microspheres, and the failure sequences removed by washing with a buffer followed by treating the microspheres with tetrabutylammonium fluoride to give a high quality unmodified full-length oligoribonucleotide.     

Breakage of λ-DNA by inorganic tin and organotin compounds as environmental pollutants

In proportion to the environmental pollution problems caused by organotin compounds, the genotoxicities of tin compounds in the environments have become of interest so as to estimate their safety in recent years. In this work, isolated λ-DNA (double-strand DNA) was incubated with inorganic tin(II) and tin(IV) and five organotin compounds [n-butyltin trichloride, di(n-butyltin) dichloride, methyltin trichloride, dimethyltin dichloride and trimethyltin chloride] in reaction systems both with and without hydrogen peroxide (H₂O₂) content. The tin compounds tested in this study did not induce DNA breakage in the absence of hydrogen peroxide. Divalent inorganic tin (SnCl₂) and tetravalent inorganic tin (SnCl₄) caused DNA breakage in the presence of hydrogen peroxide (10 mM), and the DNA damage activity of inorganic tin was much more potent in divalent inorganic tin (SnCl₂) than in tetravalent inorganic tin (SnCl₄). Divalent inorganic tin (SnCl₂) induced DNA breakage in a concentration-dependent fashion at concentrations greater than 0.1 mM of SnCl₂ in the presence of hydrogen peroxide (10 mM). DNA breakage was not caused by n-butyltin compounds and methyltin compounds either in the presence or in the absence of hydrogen peroxide.     

Cu(phen)22+与6-巯基嘌呤及DNA间的相互作用

在Tris-NaCl（pH=7.2）缓冲溶液中,应用伏安法、电子吸收光谱分析、溴化乙锭荧光分析、粘度测量和琼脂糖凝胶电泳等技术研究了Cu（phen）2^2＋（phen=1,10-邻菲咯啉）与6-巯基嘌呤（6-MP）及DNA间的相互作用。结果表明,Cu（phen）2^2＋与6-MP发生了明显的相互作用,其作用产物不仅与小牛胸腺DNA具有更强的相互作用,并且在H2O2和抗坏血酸存在下对质粒pBR322 DNA具有更强的断裂能力,与DNA的作用模式可能为部分插入模式。     

稀土-香兰素缩赖氨酸希夫碱配合物的合成、表征及其与DNA作用的研究

合成了香兰素缩赖氨酸希夫碱配体(HL)和15种香兰素缩赖氨酸希夫碱的稀土配合物REL(NO3)2.3H2O(RE=Y,La,Ce,Pr,Nd,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu),并通过元素分析、摩尔电导、热重分析、红外光谱、紫外光谱、核磁共振方法对配合物的组成和结构进行了表征。采用紫外光谱和荧光光谱方法初步研究了Nd,Tb,Yb,Lu这4种希夫碱配合物与DNA的相互作用,实验结果显示,随着DNA的加入,配合物在280 nm处的紫外吸收峰不断增强,同时配合物在418 nm左右的荧光发射峰随DNA浓度的增大均逐渐减小,说明配合物和DNA是以静电模式结合。