Protein-DNA Dynamics in Base Excision DNA Repair

描述（由申请人提供）：DNA碱基的自发损伤是致癌突变的主要来源。考虑到每个基因组每天产生数千个病变，值得注意的是，癌症仍然是一个相对罕见的事件，大多数病例发生在生命的相对晚期。随着预期寿命的增加和外源性DNA损伤剂的暴露，社会承担了越来越多的诊断和治疗癌症的费用。在细胞水平上，防止这些自发病变的能力主要依赖于碱基切除修复（BER）途径，即DNA糖基酶扫描基因组以定位和切除碱基病变。无嘌呤（AP）特异性核酸内切酶、AP裂解酶/DNA聚合酶和DNA连接酶的作用是完成DNA修复所必需的。我们的长期目标是了解BER蛋白如何定位和选择性地作用于基因组DNA中的广泛DNA损伤，以及蛋白质-蛋白质和蛋白质-DNA相互作用的动力学如何使多步骤，多酶修复途径的协调成为可能。最近的证据表明，核苷酸翻转，即从DNA双链中提取核苷酸并结合在活性位点口袋中的过程，为区分受损和未受损的碱基提供了很大的选择性。我们建议通过直接观察DNA糖基酶对受损和未受损核苷酸的翻转来验证这一假设（目的1）。通过对每个DNA结合事件的许多核苷酸进行检查，可以促进罕见病变的基因组搜索，因此我们将描述BER酶沿着DNA移动的能力，并测量扫描过程中损伤位点的有效参与效率（目标2）。由于DNA修复中间体具有潜在的细胞毒性或致突变性，因此完成启动的BER事件至关重要。我们建议研究BER中蛋白质-蛋白质相互作用的动力学，并确定它们在多种酶活性协调中的功能意义（目标3）。通过结合预稳态酶动力学，荧光光谱和结构-活性关系的结果，我们有一个独特的机会来剖析蛋白质- dna动力学对损伤识别和修复的重要作用。由于BER是细胞防御癌症的关键组成部分，并且由于这些途径对用于治疗癌症的一些DNA损伤剂具有拮抗作用，因此这些研究有可能有助于我们对突变的理解和癌症治疗的进展。

DESCRIPTION (provided by applicant): Spontaneous damage of DNA bases is a major source of cancer-causing mutations. Given the thousands of lesions generated per genome every day, it is remarkable that cancer remains a relatively infrequent event with the majority of cases arising relatively late in life. With increasing life expectancy and exposure to exogenous DNA damaging agents, society bears the ever increasing cost of diagnosing and treating cancer. At the cellular level the ability to safeguard against these spontaneous lesions relies largely on the base excision repair (BER) pathway whereby DNA glycosylases scan the genome to locate and excise base lesions. The action of an apurinic (AP)-specific endonuclease, AP-lyase/DNA polymerase, and DNA ligase are required to complete repair of the DNA. Our long-term goals are to understand how BER proteins locate and selectively act on a wide range of DNA lesions within genomic DNA and how the dynamics of protein-protein and protein-DNA interactions enable coordination of multi-step, multi-enzyme repair pathways. Recent evidence suggests that nucleotide flipping, the process by which a nucleotide is extracted from the DNA duplex and bound in an active site pocket, provides much of the selectivity in distinguishing damaged and undamaged bases. We propose to test this hypothesis by directly observing flipping of damaged and undamaged nucleotides by DNA glycosylases (Aim 1). The genomic search for rare lesions is facilitated by the examination of many nucleotides with each DNA binding event, therefore we will characterize the ability of BER enzymes to move along DNA and measure the efficiency with which sites of damage are productively engaged during a scanning encounter (Aim 2). As DNA repair intermediates are potentially cytotoxic or mutagenic, it is critical that initiated BER events be completed. We propose to investigate the dynamics of protein-protein interactions in BER and determine their functional significance in the coordination of multiple enzymatic activities (Aim 3). By combining the results from pre-steady state enzyme kinetics, fluorescence spectroscopy, and structure-activity relationships we have a unique opportunity to dissect the protein-DNA dynamics important for damage recognition and repair. As BER is a critical component of the cellular defense against cancer, and because these pathways are antagonistic toward some DNA damaging agents used in the treatment of cancer, these studies have the potential to contribute both to our understanding of mutagenesis and to advances in cancer therapy.