Lu Ping, Pegg Ian L, Sarkar Abhijit
Department of Physics and Vitreous State Laboratory, The Catholic University of America, 620 Michigan Ave NE, 20064, Washington, DC, USA.
Eur Phys J E Soft Matter. 2013 Feb;36(2):12. doi: 10.1140/epje/i2013-13012-5. Epub 2013 Feb 12.
We theoretically analyze the force signal expected during unzipping through a single double-stranded DNA (dsDNA) molecule with designed subsequences or inhomogeneities with large stability differentials compared to the rest of the molecule. Our calculations describe experiments where the extension between the unzipped ends is fixed--the so-called fixed-extension ensemble--and the equilibrium force is measured. Two different types of force traces are obtained depending on the inhomogeneity length and strength. For short inhomogeneities, a "sawtooth" force trace is obtained, with a force jump corresponding to release of the entire inhomogeneity at once, as observed in unzipping of natural-sequence DNA (Bockelmann et al., Biophy. J. 82, 1537 (2002)). For longer inhomogeneities, traces with force plateaus are obtained, corresponding to a gradual unpeeling of the strongly bound region. We find that inhomogeneities are disrupted in sequence giving rise to a succession of force spikes superposed on the baseline unzipping force of 15pN. The height of the force pulses diminishes as regions further down the molecule are unzipped, and asymptotically the force response approaches that of DNA without large stability-enhanced islands. Our model also allows us to describe the transition between intact and disrupted binding zones by thermally activated kinetics. We then analyze the related situation where multiple proteins are bound at specific points on the DNA with or without cooperative interactions between proteins, and where the removal of each protein is required for unzipping to proceed further along the DNA. The proteins bind stably to dsDNA and also to single-stranded DNA (ssDNA) but with a lower binding enthalpy. The force jumps correspond to the extra mechanical work that has to be done to overcome the large protein binding enthalpy to either dsDNA or ssDNA. Each force jump leads to the dissociation of a corresponding protein, but we do not find simultaneous release of cooperatively stabilized proteins under the range of interactions strengths considered here. Our model is then used to describe recent experiments where the stability of nucleosome and nucleosome-analogues was assayed by mechanically unzipping the DNA template. Using physiological values of model parameters we find good agreement with the data.
我们从理论上分析了在通过具有特定设计子序列或与分子其余部分相比具有大稳定性差异的不均匀性的单个双链DNA（dsDNA）分子进行解链过程中预期的力信号。我们的计算描述了这样的实验：解链末端之间的延伸是固定的——即所谓的固定延伸系综——并测量平衡力。根据不均匀性的长度和强度可获得两种不同类型的力迹线。对于短的不均匀性，会得到一种“锯齿状”力迹线，其力跃变对应于整个不均匀性的一次性释放，就像在天然序列DNA解链过程中所观察到的那样（博克尔曼等人，《生物物理学杂志》82卷，第1537页（2002年））。对于较长的不均匀性，会得到带有力平台的迹线，这对应于强结合区域的逐渐解链。我们发现不均匀性在序列中被破坏，导致一系列力尖峰叠加在15皮牛的基线解链力上。随着分子中更靠下的区域被解链，力脉冲的高度会减小，并且渐近地，力响应趋近于没有大稳定性增强岛的DNA的力响应。我们的模型还使我们能够通过热激活动力学来描述完整结合区和破坏结合区之间的转变。然后我们分析了相关情况，即多个蛋白质结合在DNA上的特定点，蛋白质之间有或没有协同相互作用，并且解链要沿着DNA进一步进行需要去除每个蛋白质。这些蛋白质与dsDNA以及单链DNA（ssDNA）都稳定结合，但与ssDNA结合时的结合焓较低。力跃变对应于为克服与dsDNA或ssDNA的大蛋白质结合焓而必须做的额外机械功。每次力跃变都会导致相应蛋白质的解离，但在此处考虑的相互作用强度范围内，我们没有发现协同稳定的蛋白质同时释放的情况。然后我们的模型被用于描述最近的实验，在这些实验中通过机械解链DNA模板来测定核小体和核小体类似物的稳定性。使用模型参数的生理值，我们发现与数据吻合良好。
