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

DNA是由一串连续交替的DNA碱基组成的，这些碱基定义了遗传密码（T, a，G，C），通过重复的糖和磷酸盐亚结构连接在一起。x射线、伽马射线和其他类型的电离辐射会破坏化学键，从而产生自由基。许多物理和化学试剂也会产生自由基，包括阳光、氧化剂（如过氧化氢）以及好氧生物中由生化反应产生的天然氧化剂。反过来，这些自由基可以与DNA亚基（核碱基、糖和磷酸基）反应，诱导DNA初级结构的变化。这些化学变化统称为DNA损伤，可产生严重的长期后果，如基因突变，或直接后果，如细胞死亡，如果这种损伤不能在合理的时间内被容忍或修复。我们已经很好地理解了在DNA亚基的小分子尺度上与DNA损伤形成有关的途径。然而，由于DNA碱基的特殊排列（即序列）和三维聚合物结构，从初始自由基到不可逆损伤的途径在DNA中要复杂得多。事实上，与在溶液中自由扩散的自由基相比，与DNA物理结合的自由基具有不同的反应性。从小分子尺度研究收集的知识中，我的研究项目致力于更全面地了解更复杂系统中DNA损伤的化学性质，包括长链DNA核碱基和具有独特3D构象的DNA。我们将把注意力集中在DNA自由基介导化学的特定领域，这些领域对未来的进展至关重要：低能电子与DNA的反应，金纳米粒子在辐射下放大DNA损伤的能力，以及DNA中可诱导两个连续损伤位点的过氧自由基的命运。此外，我们将在本研究和以前的研究中检查各种类型损伤的酶修复。我们将开发精确和独特的科学方法来推进这一领域的研究，利用先进的仪器库（如辐射源、质谱仪、核磁共振）。提出的研究将有助于阐明DNA损伤的化学结构和这种损伤的形成机制，这对于理解自然生物环境（如细胞和生物体）中DNA损伤的性质和后果是必要的。我们的研究将为未来DNA损伤和修复领域的科学家提供一个全面的培训环境。

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.