Bhandari Aditya Bikram, Dorfman Kevin D
Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA.
Biomicrofluidics. 2019 Aug 8;13(4):044110. doi: 10.1063/1.5109566. eCollection 2019 Jul.
Hairpins in the conformation of DNA confined in nanochannels close to their persistence length cause the distribution of their fractional extensions to be heavily left skewed. A recent theory rationalizes these skewed distributions using a correlated telegraph process, which can be solved exactly in the asymptotic limit of small but frequent hairpin formation. Pruned-enriched Rosenbluth method simulations of the fractional extension distribution for a channel-confined wormlike chain confirm the predictions of the telegraph model. Remarkably, the asymptotic result of the telegraph model remains robust well outside the asymptotic limit. As a result, the approximations in the theory required to map it to the polymer model and solve it in the asymptotic limit are not the source of discrepancies between the predictions of the telegraph model and experimental distributions of the extensions of DNA during genome mapping. The agreement between theory and simulations motivates future work to determine the source of the remaining discrepancies between the predictions of the telegraph model and experimental distributions of the extensions of DNA in nanochannels used for genome mapping.
限制在接近其持久长度的纳米通道中的DNA构象发夹会导致其分数延伸分布严重左偏。最近的一个理论使用相关电报过程对这些偏态分布进行了合理化解释，该过程在小但频繁的发夹形成的渐近极限中可以精确求解。对通道限制的蠕虫状链的分数延伸分布进行的剪枝富集罗森布鲁斯方法模拟证实了电报模型的预测。值得注意的是，电报模型的渐近结果在渐近极限之外仍然非常稳健。因此，将其映射到聚合物模型并在渐近极限中求解所需的理论近似不是电报模型预测与基因组图谱绘制过程中DNA延伸的实验分布之间差异的来源。理论与模拟之间的一致性促使未来开展工作，以确定电报模型预测与用于基因组图谱绘制的纳米通道中DNA延伸的实验分布之间剩余差异的来源。
