Identification of Areas of Oxidative Damage in Human Genomic DNA

人类基因组 DNA 氧化损伤区域的鉴定

• 批准号: 7440180
• 负责人: David G. Kaufman
• 金额: $ 16.43万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-06-08 至 2011-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7440180
• 关键词: Area; Attention; Biological; Biotin; Carcinogens; Cells; Chromosome Fragile Sites; Comb animal structure; CpG Islands; DNA; DNA Damage; DNA Replication Induction; DNA Sequence; DNA biosynthesis; Detection; Feasibility Studies; Fiber; Fibroblasts; Fluorescence; Fluorescent Probes; Fluorescent in Situ Hybridization; Future; Generations; Genes; Genome; Genomics; Goals; Human; In Situ Hybridization; Induced Mutation; Intercistronic Region; Learning; Lesion; Localized; Location; Malignant Neoplasms; Maps; Methods; Molecular; Numbers; O-(biotinylcarbazoylmethyl)hydroxylamine; Oxidative Stress; Promoter Regions; Property; Relative (related person); Research; Research Personnel; Sampling; Signal Transduction; Site; Structure; Study Section; Techniques; Testing; Visual; cancer cell; chemical carcinogen; density; novel; programs; research study

DESCRIPTION (provided by applicant): While considerable attention has been given to mapping sites of carcinogen-induced mutations in a number of cancer related genes, less is known about the distribution of the original DMA damage that might have given rise to mutagenic lesions. The goal of this R21 project is to develop and validate methods that would detect sites of DNA damage and allow us to determine the distribution of such lesions both globally and at specific locations in genomic DNA. It is our hypothesis that the distribution of DNA damage is not random, but is influenced by the structure and functional properties of genomic DNA. To test this hypothesis, we need to demonstrate that the methods that we are developing will enable us to visualize the distribution of DNA damage sites and relate the damage sites to specific genomic locations. Once we have demonstrated the general feasibility of this approach, we will perform experiments to evaluate the distribution of DNA damage in specific functional targets. We have demonstrated the ability to perform each of the following research steps necessary for the proposed analysis: (1) We have been able to prepare DNA for fiber analysis using molecular combing; (2) We localized a specific DNA sequence among an excess of genomic DNA using fluorescence in situ hybridization (FISH) on combed DNA fibers; (3) We visualized the distribution of apurinic/apyrimidinic (AP) sites in DNA using either an aldehyde reactive probe tagged with biotin or a fluorescent probe; (4) We were able to visually identify AP sites within regions undergoing replication; and (5) We identified specific regions undergoing replication (all described in the Preliminary Studies section). In this study, we propose to show that it is feasible to combine these techniques in a novel way to establish whether certain areas of the genome, for example sites that are being replicated, are more sensitive to DNA damage than other genomic regions (or, the same sites in the absence of DNA replication). To accomplish this goal, we will determine the sensitivity of detection of AP sites in combed DNA using DNA fibers with a known number of AP sites. We will then determine the background distribution of AP sites in untreated and treated DNA. Finally, we will determine whether it is possible to detect visual signals from all three techniques (AP sites, FISH, DNA counterstain) in the same experimental samples. ASSESSMENT:

描述（由申请人提供）：虽然大量关注了许多癌症相关基因中致癌物诱导突变的定位，但对可能引起诱变性病变的原始DMA损伤的分布知之甚少。这个R21项目的目标是开发和验证检测DNA损伤位点的方法，并使我们能够确定这种损伤在全球和基因组DNA中特定位置的分布。我们假设DNA损伤的分布不是随机的，而是受基因组DNA的结构和功能特性的影响。为了验证这一假设，我们需要证明我们正在开发的方法将使我们能够可视化DNA损伤位点的分布，并将损伤位点与特定的基因组位置联系起来。一旦我们证明了这种方法的一般可行性，我们将进行实验，以评估特定功能靶点中DNA损伤的分布。我们已经证明了进行所提出的分析所必需的以下每个研究步骤的能力：（1）我们已经能够使用分子梳理来制备用于纤维分析的DNA;（2）我们在梳理的DNA纤维上使用荧光原位杂交（FISH）在过量的基因组DNA中定位特定的DNA序列;（3）我们用生物素标记的醛反应探针或荧光探针显示了DNA中脱嘌呤/脱嘧啶（AP）位点的分布：（4）我们能够直观地识别复制区域内的AP位点;（5）我们确定了进行复制的特定区域（均在初步研究部分中描述）。在这项研究中，我们建议表明，它是可行的联合收割机，这些技术在一个新的方式来确定是否基因组的某些区域，例如正在复制的网站，是更敏感的DNA损伤比其他基因组区域（或相同的网站，在没有DNA复制）。为了实现这一目标，我们将使用具有已知数量的AP位点的DNA纤维来确定在梳理的DNA中检测AP位点的灵敏度。然后，我们将确定未处理和处理过的DNA中AP位点的背景分布。最后，我们将确定是否有可能在相同的实验样本中检测来自所有三种技术（AP位点，FISH，DNA复染）的视觉信号。 评估：