Radical-mediated DNA damage: Product analysis, mechanistic studies and biochemical processing

DNA 由一串连续的交替 DNA 碱基组成，这些碱基定义了通过重复糖和磷酸盐亚结构连接在一起的遗传密码 (T、A、G、C)。 X 射线、伽马射线和其他类型的电离辐射会破坏化学键，导致自由基物质的产生。许多物理和化学试剂也会产生自由基物质，包括阳光、氧化剂（例如过氧化氢）以及需氧生物中生化反应产生的天然氧化剂。反过来，这些自由基物质可以与 DNA 亚基（核碱基、糖和磷酸基团）发生反应，从而诱导 DNA 一级结构的变化。化学变化的集合，统称为 DNA 损伤，可能会产生严重的长期后果，例如基因突变，或直接后果，例如如果损伤无法在合理的时间内耐受或修复，则会导致细胞死亡。我们对 DNA 亚基小分子规模 DNA 损伤形成所涉及的途径有很好的了解。然而，由于 DNA 碱基（即序列）的特定排列和 3 维聚合结构，从最初的自由基物种到不可逆损伤的途径在 DNA 中要复杂得多。事实上，与 DNA 物理结合的自由基与在溶液中自由扩散的自由基相比具有不同的反应性。根据小分子规模研究收集的知识，我的研究项目致力于更全面地了解更复杂系统中 DNA 损伤的化学过程，包括长串 DNA 核碱基和呈现独特 3D 构象的核碱基。我们将把注意力集中在对未来进步至关重要的 DNA 自由基介导的化学的特定领域：低能电子与 DNA 的反应、金纳米粒子在辐射时放大 DNA 损伤的能力，以及 DNA 中过氧自由基的命运，它可以诱导两个连续的损伤位点。此外，我们将在本研究和之前的研究中检查各种类型损伤的酶修复。我们将开发精确而独特的科学方法，利用一系列先进的仪器（例如辐射源、质谱仪、核磁共振）来推进这一研究领域。拟议的研究将有助于阐明 DNA 损伤的化学结构以及这种损伤形成的机制，这对于了解自然生物环境（例如细胞和生物体）中 DNA 损伤的性质和后果是必要的。我们的研究将为不断发展的 DNA 损伤和修复领域的未来科学家提供全面的培训环境。

DNA is composed of a continuous string of alternating DNA bases that define the genetic code (T,A,G,C) connected together by repeating sugar and phosphate substructures. X-rays, gamma-rays, and other types of ionizing radiation break chemical bonds resulting in the generation of radical species. Numerous physical and chemical agents also create radical species, including sunlight, oxidizing agents such as hydrogen peroxide, as well as natural oxidants that are generated by biochemical reactions in aerobic organisms. In turn, these radical species can react with DNA subunits (nucleobase, sugar and phosphate groups) to induce changes in the primary structure of DNA. The ensemble of chemical changes, referred collectively as DNA damage, can have serious long-term consequences, such as genetic mutations, or immediate consequences, such as cell death if the damage cannot be tolerated or repaired within a reasonable time. We have a good understanding of the pathways that are implicated in the formation of DNA damage on a small molecule scale with DNA subunits. However, the pathways going from initial radical species to irreversible damage is much more complicated in DNA due to its specific arrangement of DNA bases (i.e., sequence) and the 3-dimensional polymeric structure. Indeed, radicals physically bound to DNA have a different reactivity compared to radicals that are free to diffuse in solution. From knowledge gleaned by small molecule scale studies, my research program strives toward a more complete understanding of the chemistry of DNA damage in more complicated systems, including long strings of DNA nucleobases and ones that assume unique 3D conformations. We will focus our attention on specific areas of DNA radical-mediated chemistry that are crucial to future advancements: the reaction of low energy electrons with DNA, the ability of gold nanoparticles to amplify DNA damage upon irradiation, and the fate of peroxyl radicals within DNA that can induce two contiguous damaged sites. In addition, we will examine the enzymatic repair of various types of damage in this and previous studies. We will develop precise and unique scientific approaches to advance this area of research tapping into an arsenal of sophisticated instruments (e.g., radiation sources, mass spectrometers, nuclear magnetic resonance). The proposed studies will help clarify the chemical structures of DNA damage and the mechanism of formation of this damage, which is necessary to understand the nature and consequences of DNA damage in natural biological contexts (e.g., cells and organisms). Our studies will nurture a well-rounded training environment for future scientists in the growing field of DNA damage and repair.