Kinetics of DNA looping by Anabaena sensory rhodopsin transducer (ASRT) by using DNA cyclization assay

• Published in: Scientific reports Vol. 11; no. 1; p. 23721
• Main Authors: Lee, Jae Jin, Kim, Sung Hyun, Lee, Keon Ah, Chuon, Kimleng, Jung, Kwang-Hwan, Kim, Doseok
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 09-12-2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/45/612/1229; 631/57/2265; Anabaena; Anabaena - physiology; Crystallography; Cyclization; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - genetics; DNA - metabolism; DNA-Binding Proteins - metabolism; Dyes; Fluorescence resonance energy transfer; Gene expression; Gene Expression Regulation, Bacterial; Gene regulation; Humanities and Social Sciences; Magnesium; Models, Biological; multidisciplinary; Nucleic Acid Conformation - drug effects; Physiology; Proteins; Rhodopsin; RNA polymerase; Science; Science (multidisciplinary); Sensory Rhodopsins - metabolism; Sodium Chloride - pharmacology; Spectrum Analysis
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-03148-4

DNA cyclization assay together with single-molecule FRET was employed to monitor protein-mediated bending of a short dsDNA (~ 100 bp). This method provides a simple and easy way to monitor the structural change of DNA in real-time without necessitating prior knowledge of the molecular structures for the optimal dye-labeling. This assay was applied to study how
Anabaena
sensory rhodopsin transducer (ASRT) facilitates loop formation of DNA as a possible mechanism for gene regulation. The ASRT-induced DNA looping was maximized at 50 mM of Na
+
, while Mg
2+
also played an essential role in the loop formation.