Nuclear Science and Techniques

《核技术》(英文版) ISSN 1001-8042 CN 31-1559/TL     2019 Impact factor 1.556

Nuclear Science and Techniques ›› 2018, Vol. 29 ›› Issue (10): 138 doi: 10.1007/s41365-018-0486-x


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

Ya-Ya Hao 1,2 • Lei Liu 2,3 • Lu-Hao Zhang 2 • Qiu-Ling Huang 2,3 • Fei Wang 2,3 • Jiang Li 2 • Jia-Qiang Xu 1 • Li-Hua Wang 2   

  1. 1 NEST Lab, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
    2 Division of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
    3 University of Chinese Academy of Sciences, Beijing 10049, China
  • Contact: Jiang Li
  • Supported by:

    This work was supported by the National Natural Science Foundation of China (Nos. U1532119, 21775157, 21675167, and 31571014), and the Instrument Developing Project of the Chinese Academy of Sciences (Develop the Microsystems for Single Particle Tracking).

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Ya-Ya Hao, Lei Liu, Lu-Hao Zhang, Qiu-Ling Huang, Fei Wang, Jiang Li, Jia-Qiang Xu, Li-Hua Wang. Real-time label-free analysis of the thermostability of DNA structures using GelRed.Nuclear Science and Techniques, 2018, 29(10): 138     doi: 10.1007/s41365-018-0486-x


In biological systems, conformational transformations of nucleic acids play critical roles in genetic regulation. 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 GC content. We also demonstrated that GelRed can be used to monitor DNA conformational changes upon temperature variations in real time. Based on these findings, we concluded that the fluorescence intensity of a GelRed-stained DNA structure has a good correlation with its thermostability in the form of a change in Gibbs free energy.

Key words: GelRed, Secondary structure, GC content, Conformational transformation