Dataset to manuscript "Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells" accepted for publication in Nucleic Acids Research

<strong>This folder contains all raw data underlying the results presented in a manuscript, accepted for publication in Nucleic Acids Research, and entitled:</strong> <strong><em>Trans</em></strong><strong>-<em>cis</em> isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells </strong> <strong>Authored by:</strong> Akira Kitamura^2,*, Johan Tornmalm^1,*, Baris Demirbay¹, Joachim Piguet¹, Masataka Kinjo², Jerker Widengren¹⁺ ¹ Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden ² Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan ^*Contributed equally ⁺ To whom correspondence should be addressed. Email: [e-mail]. Tel: [phone] <strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong> <strong>ABSTRACT</strong> Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to <em>in vitro</em> conditions. Evidence of how GGGGCC repeats form into G-quadruplexes <em>in vivo</em> is sparse. We devised a readout strategy, exploiting the sensitivity of <em>trans</em>-<em>cis</em> isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent <em>trans</em> isomer and a non-fluorescent <em>cis</em> isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.本文件夹包含了一篇已被《核酸研究》（Nucleic Acids Research）接收待发表的论文中所有结果对应的原始实验数据，该论文标题为： **反式-顺式（trans-cis）异构化动力学可反映活细胞中外源RNA G-四链体（G-quadruplexes）的折叠状态** 作者为：北村明（Akira Kitamura）^2,*、约翰·托恩马尔姆（Johan Tornmalm）^1,*、巴里斯·德米尔巴伊（Baris Demirbay）¹、约阿希姆·皮盖（Joachim Piguet）¹、金城正孝（Masataka Kinjo）²、耶克尔·维登格伦（Jerker Widengren）¹⁺ ¹ 瑞典皇家理工学院（KTH）应用物理系实验生物分子物理研究组 ² 日本北海道大学先进生命科学学院分子细胞动力学实验室 ^* 共同第一作者 ⁺ 通讯作者。电子邮箱：[e-mail]；电话：[phone] 本数据集文件按照产生数据所用的不同实验技术进行分组，且与论文中展示提取结果的对应图表相关联。 ## 摘要 富含鸟嘌呤（G）的核酸易组装形成四链结构，即G-四链体（G-quadruplexes）。异常的GGGGCC重复序列扩增，尤其是其折叠状态，与肌萎缩侧索硬化症和额颞叶痴呆密切相关。然而受限于实验方法学，目前绝大多数关于G-四链体结构的研究仅能在体外（in vitro）环境中开展，关于GGGGCC重复序列在体内（in vivo）形成G-四链体的相关证据仍十分匮乏。本研究设计了一种检测策略，利用花菁染料的反式-顺式异构化对局部黏度与空间位阻的敏感性，借此可高灵敏地识别经花菁染料标记的RNA，尤其是G-四链体的折叠状态。研究首先通过荧光相关光谱与瞬态态（transient state, TRAST）监测技术，在水溶液中对携带GGGGCC重复序列的RNA进行了异构化动力学表征：该动力学通过荧光反式异构体与非荧光顺式异构体之间的转变所产生的荧光闪烁现象进行监测。借助TRAST技术，通过平均荧光强度随激光激发调制参数的变化来监测异构化动力学，我们最终成功检测了导入活细胞内的荧光标记RNA的折叠状态。