Itaya Ryota, Idei Wakana, Nakamura Takashi, Nishihara Tatsuya, Kurihara Ryohsuke, Okamoto Akimitsu, Tanabe Kazuhito
Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Japan.
Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan.
ACS Omega. 2021 Nov 17;6(47):31595-31604. doi: 10.1021/acsomega.1c04074. eCollection 2021 Nov 30.
Non-canonical protonation at cytosine (C) in DNA is related to a formation of second order DNA structures such as i-motif, which has a role in gene regulation. Although the detailed structural information is indispensable for comprehension of their functions in cells, the protonation status of C in complicated environments is still elusive. To provide a reporter system of non-canonical protonation, we focused on the molecular vibration that could be monitored using the Raman spectroscopy. We prepared a cytosine derivative (C) with an acetylene unit as a Raman tag, and found that the Raman signal of acetylene in C in oligodeoxynucleotides (ODNs) changed due to protonation at the cytosine ring which shortened an acetylene bond. The signal change in i-motif-forming ODNs was also observed in crowded environments with polyethylene glycol, evidencing protonation in i-motif DNA in complicated environments. This system would be one of tracking tools for protonation in DNA structures.
DNA中胞嘧啶（C）的非经典质子化与二级DNA结构如i-基序的形成有关，i-基序在基因调控中发挥作用。尽管详细的结构信息对于理解它们在细胞中的功能必不可少，但复杂环境中C的质子化状态仍然难以捉摸。为了提供一种非经典质子化的报告系统，我们专注于可通过拉曼光谱监测的分子振动。我们制备了一种带有乙炔单元作为拉曼标签的胞嘧啶衍生物（C），并发现寡脱氧核苷酸（ODN）中C的乙炔拉曼信号因胞嘧啶环上的质子化而发生变化，这缩短了乙炔键。在含有聚乙二醇的拥挤环境中也观察到了形成i-基序的ODN的信号变化，证明了复杂环境中i-基序DNA的质子化。该系统将成为追踪DNA结构中质子化的工具之一。
