Reductive electron transfer in phenothiazine-modified DNA is dependent on the base sequence

A new DNA assay has been designed, prepared and applied for the chemical investigation of reductive electron transfer through the DNA. It consists of 5-(10-methyl-phenothiazin-3-yl)-2'-deoxyuridine (Ptz-dU, 1) as the photoexcitable electron injector and 5-bromo-2'-deoxyuridine (Br-dU) as the electron trap. The Ptz-dU-modified oligonucleotides were synthesised by means of a Suzuki-Miyaura cross-coupling protocol and subsequent automated phosphoramidite chemistry. Br-dU represents a kinetic electron trap, since it undergoes a chemical modification after its one-electron reduction that can be analysed by piperidine-induced strand cleavage. The quantification of the strand cleavage yields from irradiation experiments reveals important information about the electron-transfer efficiency. The performed DNA studies focused on the base sequence dependence of the electron-transfer efficiency with respect to the proposal that C*- and T*- act as intermediate electron carriers during electron hopping. From our observations it became evident that excess-electron transfer is highly sequence dependent and occurs more efficiently over T-A base pairs than over C-G base pairs.     

光谱法和电化学法研究中性红与小牛胸腺DNA的相互作用

利用紫外 可见和圆二色光谱(CD)法和伏安方法,研究了小分子染料中性红(NR)与小牛胸腺DNA(CTDNA)的相互作用。实验表明在NR低浓度下,NR能嵌入至核酸双螺旋的碱基内部在G C处与核酸结合,而在较高浓度情况下,嵌入的NR分子与后来的在核酸双螺旋外部的NR分子相互作用发生聚集,从而堆积在DNA双螺旋的表面,同时使核酸的构象由B型转变为Z型。用光谱滴定的方法获得NR与CTDNA作用内部结合常数,分别为:Ka1=2 4×104mol·L-1·cm-1和Ka2=2 1×10-2mol·L-1·cm-1。     

DNA光复活作用机理研究中的模型化合物

用模型化合物模拟光解酶诱导的DNA光复活作用，能深入认识其作用机理。介 绍了用于DNA光复活机理研究的各种模型化合物的合成，并综述了由模型化合物研 究得到的光复活机理，以及底物嘧啶二聚体的修复效率受外界因素的影响。     

The binding of single-stranded DNA and PNA to single-walled carbon nanotubes probed by flow linear dichroism

The binding of single-stranded DNAs and a neutral DNA analogue (peptide nucleic acid, PNA) to single-walled carbon nanotubes in solution phase has been probed by absorbance spectroscopy and linear dichroism. The nanotubes are solubilised by aqueous sodium dodecyl sulfate, in which the nucleic acids also dissolve. The linear dichroism (LD) of the nanotubes, when subtracted from that due to the nanotubes/nucleic acid samples, gives the LD of the bound nucleic acid. The binding of the single-stranded DNA to the single-walled nanotubes is quite different from that previously observed for double-stranded DNA. It is likely that the nucleic acid bases lie flat on the nanotube surface with the backbone wrapping round the nanotube at an oblique angle in the region of 45 degrees . The net effect is like beads on a string. The base orientation with the single-stranded PNA is inverted with respect to that of the single-stranded DNA, as shown by their oppositely signed LD signals.     

Synthesis of oligonucleotides containing an O-G-alkyl-O-G interstrand cross-link

A methodology to synthesize oligonucleotides containing an alkyl interstrand cross-link between the two O6 atoms of deoxyguanosine has been developed. This cross-link is designed to serve as a stable structural mimic of the lesion formed in duplex DNA with the bifunctional alkylating agent hepsulfam. The O6-alkyl coupling is performed via a Mitsunobu reaction between a nucleoside and mono-protected 1,7-heptanediol. Solid-phase oligonucleotide synthesis using a nucleoside bis-phosphoramidite allows for the assembly of the cross-linked duplex. Sufficient quantities of this cross-linked duplex were obtained for various structural and biological investigations.     

Coupling of an indicator-free electrochemical DNA biosensor with polymerase chain reaction for the detection of DNA sequences related to the apolipoprotein E

This paper describes a disposable indicator-free electrochemical DNA biosensor applied to the detection of apolipoprotein E (apoE) sequences in PCR samples. In the indicator-free assays, the duplex formation was detected by measuring the electrochemical signal of the guanine base of nucleic acids. The biosensor format involved the immobilisation of an inosine-modified (guanine-free) probe onto a screen-printed electrode (SPE) transducer and the detection of the duplex formation in connection with the square-wave voltammetric measurement of the oxidation peak of the guanine of the target sequence.The indicator-free scheme has been characterised using 23-mer oligonucleotides as model: parameters affecting the hybridisation assay such as probe immobilisation conditions, hybridisation time, use of hybridisation accelerators were examined and optimised.The analysis of PCR samples (244 bp DNA fragments, obtained by amplification of DNA extracted from human blood) required a further optimisation of the experimental procedure. In particular, a lower steric hyndrance of the probe modified surface was essential to allow an efficient hybridisation of the target DNA fragment. Negative controls have been performed using the PCR blank and amplicons unrelated to the immobilised probe. A 10 min hybridisation time allowed a full characterisation of each sample.     

Effect of glutaraldehyde on the activity of some DNA restriction endonucleases

The effect of the bifunctional crosslinking reagent glutaraldehyde on the activity of the restriction enzymes Bam HI,Hind III, EcoRI, and Tthlll I was investigated. The four enzymes exhibited differential sensitivity to inactivation. Tthlll I was the most sensitive, with activity losses occurring at levels of 0.0025% and above.Hind III was the most stable of the four and remained fully active at concentrations as high as 0.075%. Addition of BSA to incubation mixtures generally had a stabilizing effect. Implications of these results for the design of glutaraldehyde-based methods for the immobilization of restriction endonucleases are discussed.     

咪唑-金属配合物的合成、性质及其与DNA的作用机理

Three hexakis（imidazole）metallo complexes of Co, Cd and Ni were synthesized and spectroscopically characterized. The crystal and molecular structures have been determined by X-ray crystallography analysis. The metal ions have an octahedral geometry with the MN6 chromophore. The electrochemical experimental results indicate that both [Co（Im）6]C12·2HCl·2H2O （1） and [Ni（Im）6]C12·4H2O （3） [Im=imidazole] could interact with DNA mainly by intercalation.     

喜树碱类抗肿瘤药物作用模式的柔性分子对接研究

研究采用柔性分子对接技术，将15个喜树碱类化合物对接到拓扑异构酶I (Topo I)-DNA切割复合物中，从原子水平和分子力场角度阐明了喜树碱类抗肿瘤药 物与DNA，Topo I的相互作用机制。研究发现，喜树碱分子插入Topp I-DNA复合物 的切割位点，并与Asn722，Asp533，Lys532和Lys720形成氢键作用网络。定量构效 关系研究进一步表明喜树碱分子可以与Topo I-DNA切割复合物形成电荷迁移作用。 该对接模型系统解释了喜树碱类化合物的构效关系、定点突变等诸多实验事实，为 下一步设计、合成新型高效的喜树碱类衍生物打下了坚实基础。