Probing Transient DNA Conformation Changes with an Intercalative Fluorescent Excimer
Dr. Bin Chen
Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
These authors contributed equally to this work.
Search for more papers by this authorQiuling Huang
Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
University of Chinese Academy of Sciences, Beijing, 100049 China
These authors contributed equally to this work.
Search for more papers by this authorDr. Zhibei Qu
School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
Search for more papers by this authorCong Li
School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
Search for more papers by this authorProf. Qian Li
School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
Search for more papers by this authorProf. Jiye Shi
Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
University of Chinese Academy of Sciences, Beijing, 100049 China
Search for more papers by this authorProf. Chunhai Fan
School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
Search for more papers by this authorProf. Lihua Wang
Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
University of Chinese Academy of Sciences, Beijing, 100049 China
Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
Search for more papers by this authorProf. Xiaolei Zuo
Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
Search for more papers by this authorCorresponding Author
Prof. Jianlei Shen
School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
Search for more papers by this authorCorresponding Author
Prof. Jiang Li
Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
University of Chinese Academy of Sciences, Beijing, 100049 China
Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
Search for more papers by this authorDr. Bin Chen
Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
These authors contributed equally to this work.
Search for more papers by this authorQiuling Huang
Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
University of Chinese Academy of Sciences, Beijing, 100049 China
These authors contributed equally to this work.
Search for more papers by this authorDr. Zhibei Qu
School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
Search for more papers by this authorCong Li
School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
Search for more papers by this authorProf. Qian Li
School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
Search for more papers by this authorProf. Jiye Shi
Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
University of Chinese Academy of Sciences, Beijing, 100049 China
Search for more papers by this authorProf. Chunhai Fan
School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
Search for more papers by this authorProf. Lihua Wang
Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
University of Chinese Academy of Sciences, Beijing, 100049 China
Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
Search for more papers by this authorProf. Xiaolei Zuo
Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
Search for more papers by this authorCorresponding Author
Prof. Jianlei Shen
School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
Search for more papers by this authorCorresponding Author
Prof. Jiang Li
Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
University of Chinese Academy of Sciences, Beijing, 100049 China
Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
Search for more papers by this authorAbstract
Variation of DNA conformation is important in regulating gene expression and mediating drug-DNA interactions. However, directly probing transient DNA conformation changes is challenging owing to the dynamic nature of this process. We show a label-free fluorescence method to monitor transient DNA conformation changes in DNA structures with various lengths and shapes using a DNA intercalator, K21. K21 can form transient excimers on the surface of DNA; the ratiometric emission of monomer and excimer correlate to DNA transient conformation stability in numerous DNA structures, including i-motifs, G-quadruplex structures, and single nucleotide mutation at random position. We analyzed the conformation dynamics of a single plasmid before and after enzyme digestion with confocal fluorescence microscopy. This method provides a label-free fluorescence strategy to probe transient conformation changes of DNA structures and has potential in uncovering transient genomic processes in living cells.
Conflict of interest
The authors declare no conflict of interest.
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