Progress in Physics ›› 2020, Vol. 40 ›› Issue (6): 188-193.doi: 10.13725/j.cnki.pip.2020.06.002

Special Issue: 2022年, 第42卷

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A Method for Calculating the Time Required for DNA Looping


  1. 1. School of Science, Jiangnan University, Wuxi 214122, China, 100124  2. Universal biology institute, Tokyo University, Tokyo, Japan, 153-8902

  • Online:2020-12-20 Published:2020-12-18


The formation of a DNA loop takes a crucial role in transcriptional regulation, where the enhancer is tethered to its promoter. This step is a time-limiting step for activating transcriptional initiation. Here, We review a formula that is appropriate for computing the time required for formatting such a loop, or other DNA loops at the similar length scale where the looping can be attributed to a spontaneous decrease in conformation entropy. The formula shows that topological structure due to the orientation of two big grooves where a protein binds primarily determines whether two sites could be looped, and that the intervening DNA length de nes the looping time. This method takes the advantages of bypassing the complexity of DNA structure and cellular circumstances, but requiring some parameters to be measured experimentally.

Key words: rigidity and , exibility, conformation entropy, topological structure

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