急剧弯曲DNA柔韧性的研究进展

基因调控,核小体和病毒的包装行为都会涉及DNA的急剧弯曲成环。DNA分子的环化是研究其本身柔韧性的主要方法。目前已经发展出很多研究DNA环化的模型,其中WLC(worm-likechain)模型较为成熟。近年来,在DNA环化的重要参数、影响因素以及DNA急剧弯曲成环的理论研究等诸多方面都有了新进展。     

基于一种紧束缚模型的DNA电性质分析

DNA的电学性质关系到生命信息静态的存储和动态的释放,因此一直备受关注。在一种紧束缚模型的基础上,研究了DNA的电传输性质,并分析了DNA的导电性的生物意义。在特定的传导距离下,可以利用导电性来分辨基因所在的编码区。     

冷活性酶的结构柔韧性

冷活性酶是一类在低温条件下具有很高催化活性的酶。冷活性酶结构的柔韧性是其低温催化活性的结构基础。该论述了冷活性酶结构的柔韧性与低温催化活性的关系,从蛋白质结构的不同层次分析了冷活性酶柔韧性的结构特征,分析了冷活性酶结构的柔韧性、稳定性和酶活性之间的相互关系。     

DNA甲基化与病毒感染的研究进展

DNA甲基化是基因表达的表观遗传调控机制之一,在细胞分化和疾病发生过程中发挥着重要的作用。病毒感染可导致DNA甲基化水平变化,从而影响疾病的发生与发展。随着全基因组甲基化测序等生物学新技术的飞速发展,对DNA甲基化也有了更深的认识。现就DNA甲基化和去甲基化的主要影响因素以及病毒感染过程中导致甲基化水平改变的机制做一概述,为从表观遗传角度研究病毒致病机制提供一定的理论依据。     

哺乳动物卵母细胞的DNA损伤与修复研究进展

DNA损伤是影响配子发生和胚胎发育的关键因素之一。卵母细胞容易被各种内外源因素(如活性氧、辐射、化疗药物等)诱发DNA损伤。目前研究发现,对于各类DNA损伤,各发育阶段的卵母细胞能够做出相应的DNA损伤反应,通过复杂的机制对DNA进行修复或者启动细胞凋亡。相比于进入生长阶段的卵母细胞,原始卵泡卵母细胞更容易被DNA损伤诱导凋亡。DNA损伤不易诱导卵母细胞减数分裂成熟进程停滞,然而携带DNA损伤的卵母细胞的发育能力明显下降。在临床上,衰老、放疗和化疗是导致女性卵母细胞DNA损伤、卵巢储备降低和不孕的常见原因。为此,人们尝试了能够减轻卵母细胞DNA损伤和增强DNA修复能力的多种方法,试图保护卵母细胞。本文对哺乳动物的各发育阶段卵母细胞的DNA损伤与修复的相关研究进行了梳理和总结,并讨论了其潜在的临床价值,以期为生育力保护提供新的策略。     

DNA纳米舱可逆开关的性质与应用

由于生物大分子的一些特殊物理、化学属性,蛋白质、核酸等一类生物分子被广泛应用于制备各种纳米结构与器件,但是基于生物分子集体动力学性质的纳米器件还没有真正开发出来。本文讨论一种在表面上自组装形成的具有可逆开关性质的DNA纳米舱结构。由于DNA杂交动力学集体行为的一些特性,此纳米舱可以对小分子进行有效的禁闭和释放,从而可能被应用于开发DNA序列检测芯片的基本元件。我们的研究表明,根据此纳米舱的工作原理制造的DNA检测器件可以探测到一个碱基对的错配,其选择性远高于传统的DNA芯片,同时检测灵敏度也有一定的提高。这个研究结果开创了发展不需要荧光标记的DNA芯片的新思路。     

DNA依赖蛋白激酶研究进展

DNA依赖蛋白激酶由Ku异二聚体和DNA-PKcs组成,结合Ku蛋白后,DNA-PK激酶活性激活,DNA依赖蛋白激酶具有多功能性,参与DNA修复、基因重组以及复制、转录等多种细胞学过程.     

DNA免疫的基础研究进展

ＤＮＡ免疫或ＤＮＡ疫苗是近年发展的新型疫苗。ＤＮＡ免疫除可诱生保护性体液免疫应答,更重要的是能诱生以特异性ＣＴＬ为代表的保护性细胞免疫应答,因而从１９９０年发现至今,对其研究的进展迅速。本文介绍了近年ＤＮＡ免疫的基础性研究进展,讨论了ＤＮＡ免疫作为嵌合型及多重抗原型疫苗的可能性,诱生的免疫尖答特征及与保护性的关系,ＤＮＡ免疫的某些影响因素,最后对ＤＮＡ免疫的可能机制亦作了一些讨论。     

DNA传感器研究进展

本文概述了当前生物传感器的研究特点以及发展ＤＮＡ生物传感器的迫切性;从不同角度阐述了ＤＮＡ生物传感器的概念和研究内容;着重讨论了ＤＮＡ生物传感器的研究现状和发展趋势。文中分别对ＤＮＡ光生物传感器和ＤＮＡ压电晶体生物传感器的基本原理、特点、研究进展及存在的问题进行了分析与说明。进而,对我国ＤＮＡ生物传感器研究存在的差距和发展前景进行了简要论述。     

三链DNA与反基因技术的研究进展

三链ＤＮＡ与反基因技术的研究进展方晔,白春礼（中国科学院化学研究所北京１０００８０）寡聚核苷酸及其衍生物能通过几个战略来实现选择性地调节基因表达［１］,在反义技术中,寡聚核苷酸以信使ＲＮＡ的专一性序列作为靶物,并由此阻止信使ＲＮＡ将信息翻译成蛋白质;...     

Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA

DNA methylation occurs on CpG sites and is important to form pericentric heterochromatin domains. The satellite 2 sequence, containing seven CpG sites, is located in the pericentric region of human chromosome 1 and is highly methylated in normal cells. In contrast, the satellite 2 region is reportedly hypomethylated in cancer cells, suggesting that the methylation status may affect the chromatin structure around the pericentric regions in tumours. In this study, we mapped the nucleosome positioning on the satellite 2 sequence in vitro and found that DNA methylation modestly affects the distribution of the nucleosome positioning. The micrococcal nuclease assay revealed that the DNA end flexibility of the nucleosomes changes, depending on the DNA methylation status. However, the structures and thermal stabilities of the nucleosomes are unaffected by DNA methylation. These findings provide new information to understand how DNA methylation functions in regulating pericentric heterochromatin formation and maintenance in normal and malignant cells.     

Bending and flexibility of methylated and unmethylated EcoRI DNA

We used cyclization kinetics experiments and Monte Carlo simulations to determine a structural model for a DNA decamer containing the EcoRI restriction site. Our findings agree well with recent crystal and NMR structures of the EcoRI dodecamer, where an overall bend of seven degrees is distributed symmetrically over the molecule. Monte Carlo simulations indicate that the sequence has a higher flexibility, assumed to be isotropic, compared to that of a "generic" DNA sequence. This model was used as a starting point for the investigation of the effect of cytosine methylation on DNA bending and flexibility. While methylation did not affect bend magnitude or direction, it resulted in a reduction in bending flexibility and under-winding of the methylated nucleotides. We demonstrate that our approach can augment the understanding of DNA structure and dynamics by adding information about the global structure and flexibility of the sequence. We also show that cyclization kinetics can be used to study the properties of modified nucleotides.     

The cyclization of linear DNA in Escherichia coli by site-specific recombination

The efficiency with which linearized plasmid DNA can transform competent Escherichia coli can be significantly increased by use of the Cre-lox site-specific recombination system of phage P1. Linear plasmid molecules containing directly repeated loxP sites (lox² plasmids) are cyclized in Cre⁺ E. coli strains after introduction either by transformation or by mini-Mu transduction, Exonuclease V activity of the RecBC enzyme inhibits efficient cyclization of linearized lox² plasmids after transformation. By use of E. coli mutants which lack exonuclease V activity, Cre-mediated cyclization results in transformation efficiencies for linearized lox² plasmids identical to those obtained with covalently closed circular plasmid DNA. Moreover, Cre⁺ E. coli recBC strains allow the efficient recovery of lox² plasmids integrated within large linear DNA molecules such as the 150-kb genome of pseudorabies virus.     

Relative flexibility of DNA and RNA: a molecular dynamics study

State of the art molecular dynamics simulations are used to study the structure, dynamics, molecular interaction properties and flexibility of DNA and RNA duplexes in aqueous solution. Special attention is paid to the deformability of both types of structures, revisiting concepts on the relative flexibility of DNA and RNA duplexes. Our simulations strongly suggest that the concepts of flexibility, rigidity and deformability are much more complex than usually believed, and that it is not always true that DNA is more flexible than RNA.     

Correlation between the flexibility and periodic dinucleotide patterns in yeast nucleosomal DNA sequences

Nucleosome formation and positioning, which play important roles in a number of biological processes, are thought to be related to the distinctive periodic dinucleotide patterns observed in the DNA sequence wrapped around the protein octamer. Previous research shows that flexibility is a key structural property of a nucleosomal DNA sequence. However, the relationship between the flexibility and the periodic dinucleotide patterns has received little attention in research in the past. In this study, we propose the use of three different models to measure the flexibility of yeast DNA sequences. Although the three models involve different parameters, they deliver consistent results showing that yeast nucleosomal DNA sequences are more flexible than non-nucleosomal ones. In contrast to random flexibility values along non-nucleosomal DNA sequences, the flexibility of nucleosomal DNA sequences shows a clear periodicity of 10.14 base pairs, which is consistent with the periodicity of dinucleotide distributions. We also demonstrate that there is a strong relationship between the peak positions of the flexibility and the dinucleotide frequencies. Correlation between the flexibility and the dinucleotide patterns of CA/TG, CG, GC, GG/CC, AG/CT, AC/GT and GA/TC are positive with an average value of 0.5946. The highest correlation is shown by CA/TG with a value of 0.7438 and the lowest correlation is shown by AA/TT with a value of −0.7424. The source codes and data sets are available for downloading on http://www.hy8.com/bioinformatics.htm.     

Immunocytochemical analysis of in vivo DNA modification

In the past decades a large number of DNA adducts induced in the intact animal by alkylating agents have been identified. The formation and repair of these adducts are important determinants, not only of mutagenesis, tumor initiation and DNA-mediated toxicity but probably also of tumor progression. Most studies on in vivo DNA modification have been performed on isolated bulk DNA.

More recently, methods have been developed to study the distribution of DNA adducts at the level of either the individual gene or the individual cell. This paper reviews immunocytochemical methods to study the formation and repair of DNA adducts and other DNA modifications at the level of the individual cell. DNA modifications induced by alkylating agents and a variety of other agents including ultraviolet radiation, aromatic amines, polycyclic aromatic hydrocarbons and platinum anti-cancer drugs will be discussed.

Up to now, immunocytochemical analysis of in vivo modified DNA has largely concentrated on experimental animals. These studies have revealed striking heterogeneities with regard to formation and/or repair of DNA adducts in tissues from rat, hamster and mouse. Immunocytochemical adduct analysis can be used to identify in a convenient, fast and detailed way cell types, cell stages and sites in which biological effects of the adducts might be expressed. More recently, immunocytochemical analysis of DNA adducts also proved to be feasible on in situ exposed human samples.

A number of existing and potential applications in the field of chemical carcinogenesis, experimental chemotherapy and molecular epidemiology are discussed.