,Real-time label-free analysis of the thermostability of DNA structures using GelRed

• 作 者: Ya-Ya Hao Lei Liu Lu-Hao Zhang Qiu-Ling Huang Fei Wang Jiang Li Jia-Qiang Xu Li-Hua Wang
• 机 构: NEST Lab, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China“,
• 出 处: 核技术（英文版）
• 发表日期: 2004年期
• 关键词: GelRed Secondary structure GC content Conformational transformation

In biological systems, conformational transfor-mations of nucleic acids play critical roles in genetic reg-ulation. However, it remains a tricky task to design and optimize specific labeling strategies to track these changes. In this study, we exploited an intercalating fluorescent dye, GelRed, to characterize different DNA structures. We studied the correlation between fluorescence intensity and DNA structural properties. We showed that single-stranded DNAs with predicted self-folded secondary structures show much stronger fluorescence than those without such structures. For double-stranded DNAs, we observed that fluorescence intensity is positively correlated to their GCcontent. We also demonstrated that GelRed can be used to monitor DNA conformational changes upon temperature variations in real time. Based on these findings, we con-cluded that the fluorescence intensity of a GelRed-stained DNA structure has a good correlation with its thermosta-bility in the form of a change in Gibbs free energy.