DNA damage and repair

The aesthetic appeal of the DNA double helix initially hindered notions of DNA mutation and repair, which would necessarily interfere with its pristine state. But it has since been recognized that DNA is subject to continuous damage and the cell has an arsenal of ways of responding to such injury. Although mutations or deficiencies in repair can have catastrophic consequences, causing a range of human diseases, mutations are nonetheless fundamental to life and evolution.     

Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions

DNA damage checkpoint genes, such as p53, are frequently mutated in human cancer, but the selective pressure for their inactivation remains elusive. We analysed a panel of human lung hyperplasias, all of which retained wild-type p53 genes and had no signs of gross chromosomal instability, and found signs of a DNA damage response, including histone H2AX and Chk2 phosphorylation, p53 accumulation, focal staining of p53 binding protein 1 (53BP1) and apoptosis. Progression to carcinoma was associated with p53 or 53BP1 inactivation and decreased apoptosis. A DNA damage response was also observed in dysplastic nevi and in human skin xenografts, in which hyperplasia was induced by overexpression of growth factors. Both lung and experimentally-induced skin hyperplasias showed allelic imbalance at loci that are prone to DNA double-strand break formation when DNA replication is compromised (common fragile sites). We propose that, from its earliest stages, cancer development is associated with DNA replication stress, which leads to DNA double-strand breaks, genomic instability and selective pressure for p53 mutations.     

Base-excision repair of oxidative DNA damage

Maintaining the chemical integrity of DNA in the face of assault by oxidizing agents is a constant challenge for living organisms. Base-excision repair has an important role in preventing mutations associated with a common product of oxidative damage to DNA, 8-oxoguanine. Recent structural studies have shown that 8-oxoguanine DNA glycosylases use an intricate series of steps to locate and excise 8-oxoguanine lesions efficiently against a high background of undamaged bases. The importance of preventing mutations associated with 8-oxoguanine is shown by a direct association between defects in the DNA glycosylase MUTYH and colorectal cancer. The properties of other guanine oxidation products and the associated DNA glycosylases that remove them are now also being revealed.     

Inducible repair of oxidative DNA damage in Escherichia coli

Hydrogen peroxide is lethal to many cell types, including the bacterium Escherichia coli. Peroxides yield transient radical species that can damage DNA and cause mutations. Such partially reduced oxygen species are occasionally released during cellular respiration and are generated by lethal and mutagenic ionizing radiation. Because cells live in an environment where the threat of oxidative DNA damage is continual, cellular mechanisms may have evolved to avoid and repair this damage. Enzymes are known which evidently perform these functions. We report here that resistance to hydrogen peroxide toxicity can be induced in E. coli, that this novel induction is specific and occurs, in part, at the level of DNA repair.     

Recognition of DNA damage by the Rad4 nucleotide excision repair protein

Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognizing the lesion and recruiting downstream factors. Here we present the crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer (CPD) lesion. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognized by Rad4, whereas the two CPD-linked nucleotides become disordered. These findings indicate that the lesions recognized by Rad4/XPC thermodynamically destabilize the Watson-Crick double helix in a manner that facilitates the flipping-out of two base pairs.     

一种低危害的基因组DNA和总RNA的提取方法

从生物组织里提取基因组DNA和总RNA是多数专业研究人员都需要操作的实验内容,但该实验的常规操作流程中却存在致病性微生物的感染风险和有毒有害试剂的危害.本文从选择安全的实验材料和改进低危的实验方法两个方面入手,提出了以盐藻为实验材料的基因组DNA和总RNA的新的实验提取方法,该方法有效避免了致病性微生物的感染风险,也避免了有毒、挥发性试剂苯酚、氯仿和Trizol的使用,对核酸提取实验操作的安全性提供了一定的保障,可供研究者选取实验方案时参考.     

Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA

Repair of DNA damage is essential for maintaining genome integrity, and repair deficiencies in mammals are associated with cancer, neurological disease and developmental defects. Alkylation damage in DNA is repaired by at least three different mechanisms, including damage reversal by oxidative demethylation of 1-methyladenine and 3-methylcytosine by Escherichia coli AlkB. By contrast, little is known about consequences and cellular handling of alkylation damage to RNA. Here we show that two human AlkB homologues, hABH2 and hABH3, also are oxidative DNA demethylases and that AlkB and hABH3, but not hABH2, also repair RNA. Whereas AlkB and hABH3 prefer single-stranded nucleic acids, hABH2 acts more efficiently on double-stranded DNA. In addition, AlkB and hABH3 expressed in E. coli reactivate methylated RNA bacteriophage MS2 in vivo, illustrating the biological relevance of this repair activity and establishing RNA repair as a potentially important defence mechanism in living cells. The different catalytic properties and the different subnuclear localization patterns shown by the human homologues indicate that hABH2 and hABH3 have distinct roles in the cellular response to alkylation damage.     

RadA： A protein involved in DNA damage repair processes of Deinococcus radiodurans R1

RadA is highly conserved in bacteria and belongs to the RecA/RadA/Rad51 protein su-perfamily found in bacteria,archaea and eukarya. In Archaea,it plays a critical role in homologous re-combination process due to its RecA-like function. In Escherichia coli,it takes part in conjugational recom-bination and DNA repair but is not as important as that of archaea. Using PSI-BLAST searches,we found that Deinococcus radiodurans RadA had a higher similarity to that of bacteria than archaea and eukarya. Disruption of radA gene in D. radiodurans resulted in a modestly decreased resistance to gamma radiation and ultraviolet,but had no effect on the resistance to hydrogen peroxide. Complementa-tion of the radA disruptant by both E. coli radA and D. radiodurans radA could fully restore its resistance to gamma radiation and ultraviolet irradiation. Further domain function analyses of D. radiodurans RadA showed that the absence of the zinc finger domain resulted in a slightly more sensitive phenotype to gamma and UV radiation than that of the radA mutant,while the absence of the Lon protease domain exhib-ited a slightly increased resistance to gamma and UV radiation. These data suggest that D. radiodurans RadA does play an important role in the DNA damage repair processes and its three different domains have different functions.     

Deficiencies in DNA damage repair limit the function of haematopoietic stem cells with age

A diminished capacity to maintain tissue homeostasis is a central physiological characteristic of ageing. As stem cells regulate tissue homeostasis, depletion of stem cell reserves and/or diminished stem cell function have been postulated to contribute to ageing. It has further been suggested that accumulated DNA damage could be a principal mechanism underlying age-dependent stem cell decline. We have tested these hypotheses by examining haematopoietic stem cell reserves and function with age in mice deficient in several genomic maintenance pathways including nucleotide excision repair, telomere maintenance and non-homologous end-joining. Here we show that although deficiencies in these pathways did not deplete stem cell reserves with age, stem cell functional capacity was severely affected under conditions of stress, leading to loss of reconstitution and proliferative potential, diminished self-renewal, increased apoptosis and, ultimately, functional exhaustion. Moreover, we provide evidence that endogenous DNA damage accumulates with age in wild-type stem cells. These data are consistent with DNA damage accrual being a physiological mechanism of stem cell ageing that may contribute to the diminished capacity of aged tissues to return to homeostasis after exposure to acute stress or injury.     

DNA损伤修复蛋白在胆囊病变组织中的表达及其临床意义

目的 研究胆囊腺癌、癌旁组织、腺瘤性息肉和慢性胆囊炎组织中DNA损伤修复蛋白hMSH2和hMLH1表达及其临床意义.方法 选取胆囊腺癌108例、癌旁组织46例、腺瘤性息肉15例和慢性胆囊炎35例手术切除标本常规作石蜡包埋切片,采用EnVisionTM免疫组化法检测hMSH2和hMLH1.结果 hMSH2和hMLH1表达阳性率,胆囊腺癌分别为50.0%和49.1%、评分分别为2.2±1.9和2.2±1.8,均明显低于癌旁组织（阳性率分别为84.8%和87.0%;评分分别为3.9±1.3和4.2±1.2）、腺瘤性息肉（阳性率分别为80.0%和86.7%;评分分别为3.7±1.3和4.0±1.1）及慢性胆囊炎组织（阳性率分别为88.6%和88.6%;评分分别为4.1±1.1和3.9±1.1）（P＜0.05）;不同类型良性病变中2种DNA损伤修复蛋白表达阳性率及其评分均无明显差异（P＞0.05）.hMSH2和hMLH1表达阴性的良性病变胆囊上皮均呈中至重度不典型增生的病理形态学表现.腺瘤癌变或高分化腺癌、肿块最大径＜2 cm,无淋巴结转移及未侵犯周围组织的病例hMSH2和hMLH1表达阳性率及其评分均明显地高于低分化腺癌、肿块最大径≥2 cm、淋巴结转移及侵犯周围组织病例（P＜0.05）;2种DNA损伤修复蛋白表达与患者性别、年龄及有无胆囊结石均无明显关系（P＞0.05）.结论 DNA损伤修复蛋白表达水平均为反映胆囊腺癌发生、进展、临床生物学行为及预后的重要标记物,检测其表达水平对指导预防和早期发现、临床化疗胆囊癌可能有一定临床意义.     

SCGE检测人单个核细胞细胞DNA损伤

用单细胞凝胶电泳法检测了人全血在4℃储存时单个核细胞DNA损伤的情况。结果发现，细胞随储存时间延长基础损伤逐渐增高，储存1，24，48，72h时细胞损伤率分别为8.84%，18.5%，45.2%和54.3%，而细胞对H2O2的敏感性却逐渐降低。以50цmol/L H2O2处理后，其细胞损伤率在0，24，48h分别为63%，61.8%和51.5%。     

DNA cross-linking and monoadduct repair in nitrosourea-treated human tumour cells

The 1-(2-chloroethyl)-1-nitrosoureas are potent anti-cancer drugs which produce DNA inter-strand cross-links in a two-step reaction sequence. The first step was proposed to be an addition of a chloroethyl group to a guanine-O6 position of DNA; the second step, which occurs over a period of several hours in the absence of free drug, could then form an interstrand cross-link by the slow reaction of the bound chloroethyl group with a nucleophilic site on the opposite DNA strand. The delay between the formation of chloroethyl monoadducts and the formation of inter-strand cross-links allows time for a DNA repair mechanism, capable of removing the monoadducts, to prevent the cross-linking. We recently proposed this mechanism to account for a difference in inter-strand cross-linking between a normal and a transformed human cell strain. Day and his coworkers (see refs 7, 8 and previous paper) found that some human tumour cell strains (designated Mer- phenotype) are deficient in the ability to repair O6-methylguanine lesions in DNA. We therefore hypothesized that the repair function that removes O6-methylguanine residues from DNA would also remove chloroethyl monoadducts and hence prevent chloroethylnitrosourea-induced inter-strand cross-linking. We now present evidence that supports this hypothesis and indicates also that the O6-methylguanine repair confers resistance to cell killing by chloroethylnitrosourea.     

Requirement for the replication protein SSB in human DNA excision repair

Replication and repair are essential processes that maintain the continuity of the genetic material. Dissection of simian virus 40 (SV40) DNA replication has resulted in the identification of many eukaryotic replication proteins, but the biochemistry of the multienzyme process of DNA excision repair is less well defined. One protein that is absolutely required for semiconservative replication of SV40 DNA in vitro is human single-stranded DNA-binding protein (SSB, also called RF-A and RP-A). SSB consists of three polypeptides of relative molecular mass 70,000, 34,000 and 13,000, and acts with T antigen and topoisomerases to unwind DNA, allowing the access of other replication proteins. Human SSB can also stimulate the activity of polymerases alpha and delta, suggesting a further role in elongation during DNA replication. We have now found a role for human SSB in DNA excision repair using a cell-free system that can carry out nucleotide excision repair in vitro. Monoclonal antibodies against human SSB caused extensive inhibition of DNA repair in plasmid molecules damaged by ultraviolet light or acetylaminofluorene. Addition of purified SSB reversed this inhibition and further stimulated repair synthesis by increasing the number of repair events. These results show that a mammalian DNA replication protein is also essential for repair.     

ATM damage response and XLF repair factor are functionally redundant in joining DNA breaks

Classical non-homologous DNA end-joining (NHEJ) is a major mammalian DNA double-strand-break (DSB) repair pathway. Deficiencies for classical NHEJ factors, such as XRCC4, abrogate lymphocyte development, owing to a strict requirement for classical NHEJ to join V(D)J recombination DSB intermediates. The XRCC4-like factor (XLF; also called NHEJ1) is mutated in certain immunodeficient human patients and has been implicated in classical NHEJ; however, XLF-deficient mice have relatively normal lymphocyte development and their lymphocytes support normal V(D)J recombination. The ataxia telangiectasia-mutated protein (ATM) detects DSBs and activates DSB responses by phosphorylating substrates including histone H2AX. However, ATM deficiency causes only modest V(D)J recombination and lymphocyte developmental defects, and H2AX deficiency does not have a measurable impact on these processes. Here we show that XLF, ATM and H2AX all have fundamental roles in processing and joining DNA ends during V(D)J recombination, but that these roles have been masked by unanticipated functional redundancies. Thus, combined deficiency of ATM and XLF nearly blocks mouse lymphocyte development due to an inability to process and join chromosomal V(D)J recombination DSB intermediates. Combined XLF and ATM deficiency also severely impairs classical NHEJ, but not alternative end-joining, during IgH class switch recombination. Redundant ATM and XLF functions in classical NHEJ are mediated by ATM kinase activity and are not required for extra-chromosomal V(D)J recombination, indicating a role for chromatin-associated ATM substrates. Correspondingly, conditional H2AX inactivation in XLF-deficient pro-B lines leads to V(D)J recombination defects associated with marked degradation of unjoined V(D)J ends, revealing that H2AX has a role in this process.     

DNA损伤及氧化应激在放射性心脏损伤中的作用

 放射性心脏损伤（RIHD）是放射诱导的一种进行性加重的疾病,它几乎影响心脏所有结构,从而产生一系列心脏并发症。从早期的无症状到慢性心力衰竭,常需几年至十几年时间。近年来文献报道心脏在正常组织耐受剂量控制下,常规胸部放疗所致的心脏损伤,特别是迟发型心肌损伤问题日益突出。本文综述了DNA损伤及氧化应激在RIHD的发生发展中的作用,现有研究认为RIHD可使心脏僵硬度增加、心肌收缩及舒张功能下降,引起心肌电生理紊乱、心律失常、心功能不全甚至猝死。但目前尚缺乏对RIHD的有效治疗,其根本原因在于对RIHD的原因及发病机制尚未完全阐明。