Protamine loops DNA in multiple steps
Protamine loops DNA in multiple steps
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DOI：
10.1093/nar/gkaa365
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发表时间：
2020-05
影响因子：
14.9
通讯作者：
Obinna Ukogu;A. Smith;L. Devenica;Hilary Bediako;Ryan B. McMillan;Yuxing E. Ma;Ashwin Balaji;R. D. Schwab;Shahzad Anwar;M. Dasgupta;Ashley R. Carter
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文献类型：
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作者：
Obinna Ukogu;A. Smith;L. Devenica;Hilary Bediako;Ryan B. McMillan;Yuxing E. Ma;Ashwin Balaji;R. D. Schwab;Shahzad Anwar;M. Dasgupta;Ashley R. Carter
摘要精蛋白质在精子中显著地将DNA浓缩到几乎结晶的包装水平。在这里，我们测量了体外途径的第一步，DNA折叠成一个单环。目前的DNA环形成模型是一步，全有或全无的模型，具有成环状态和非成环状态。然而，当我们使用系留粒子运动（TPM）测定来测量鱼精蛋白对DNA的动态实时成环时，我们观察到存在多个折叠状态，这些折叠状态是长寿命的（约100 s）和可逆的。此外，我们还测量了太短而不能形成环的DNA分子的折叠。这表明鱼精蛋白使用多步骤过程来循环DNA，而不是一步过程。为了使DNA结构可视化，我们使用原子力显微镜（AFM）测定。我们看到，一些折叠的DNA分子是半径为10 nm的环，一些折叠的分子是部分环-c形或s形-曲率半径为10 nm。对这些结构的进一步分析表明，鱼精蛋白是弯曲DNA以实现这种曲率，而不是增加DNA的柔性。因此，我们得出结论，鱼精蛋白环DNA在多个步骤，弯曲成一个环。
Abstract Protamine proteins dramatically condense DNA in sperm to almost crystalline packing levels. Here, we measure the first step in the in vitro pathway, the folding of DNA into a single loop. Current models for DNA loop formation are one-step, all-or-nothing models with a looped state and an unlooped state. However, when we use a Tethered Particle Motion (TPM) assay to measure the dynamic, real-time looping of DNA by protamine, we observe the presence of multiple folded states that are long-lived (∼100 s) and reversible. In addition, we measure folding on DNA molecules that are too short to form loops. This suggests that protamine is using a multi-step process to loop the DNA rather than a one-step process. To visualize the DNA structures, we used an Atomic Force Microscopy (AFM) assay. We see that some folded DNA molecules are loops with a ∼10-nm radius and some of the folded molecules are partial loops—c-shapes or s-shapes—that have a radius of curvature of ∼10 nm. Further analysis of these structures suggest that protamine is bending the DNA to achieve this curvature rather than increasing the flexibility of the DNA. We therefore conclude that protamine loops DNA in multiple steps, bending it into a loop.