Vemulapalli Sridhar, Hashemi Mohtadin, Kolomeisky Anatoly B, Lyubchenko Yuri L
Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States.
Department of Chemistry-MS60, Rice University, 6100 Main Street, Houston, Texas 77005-1892, United States.
J Phys Chem B. 2021 May 13;125(18):4645-4653. doi: 10.1021/acs.jpcb.1c00763. Epub 2021 Apr 29.
Interactions between distant DNA segments play important roles in various biological processes, such as DNA recombination. Certain restriction enzymes create DNA loops when two sites are held together and then cleave the DNA. DNA looping is important during DNA synapsis. Here we investigated the mechanisms of DNA looping by restriction enzyme SfiI by measuring the properties of the system at various temperatures. Different sized loop complexes, mediated by SfiI-DNA interactions, were visualized with AFM. The experimental results revealed that small loops are more favorable compared to other loop sizes at all temperatures. Our theoretical model found that entropic cost dominates at all conditions, which explains the preference for short loops. Furthermore, specific loop sizes were predicted as favorable from an energetic point of view. These predictions were tested by experiments with transiently assembled SfiI loops on a substrate with a single SfiI site.
远距离DNA片段之间的相互作用在各种生物过程中发挥着重要作用，如DNA重组。当两个位点结合在一起时，某些限制酶会形成DNA环，然后切割DNA。DNA环化在DNA联会过程中很重要。在这里，我们通过测量系统在不同温度下的特性，研究了限制酶SfiI介导的DNA环化机制。由SfiI-DNA相互作用介导的不同大小的环复合物，通过原子力显微镜（AFM）进行了可视化观察。实验结果表明，在所有温度下，小环比其他环大小更有利。我们的理论模型发现，在所有条件下熵成本占主导地位，这解释了对短环的偏好。此外，从能量角度预测了特定的环大小是有利的。这些预测通过在具有单个SfiI位点的底物上瞬时组装SfiI环的实验进行了验证。
