Knotting probability of DNA molecules confined in restricted volumes:: DNA knotting in phage capsids
Knotting probability of DNA molecules confined in restricted volumes:: DNA knotting in phage capsids
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DOI：
10.1073/pnas.032095099
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发表时间：
2002-04-16
影响因子：
11.1
通讯作者：
Roca, J
中科院分区：
文献类型：
--
作者：
Arsuaga, J;Vázquez, M;Roca, J
当线性双链DNA被包装在噬菌体衣壳内时，它变得高度紧凑。然而，噬菌体被认为只有在DNA不纠缠的情况下才完全有效。然而，当从P4噬菌体的无尾突变体中提取DNA时，发现DNA是环状和打结的（概率为0.95）。纽结谱非常复杂，大多数纽结都有大量的交叉点。我们量化了这些结的频率和交叉数，并得出结论，对于P4无尾突变体，至少一半的打结分子是在DNA仍在病毒衣壳内而不是在提取过程中形成的。为了分析衣壳内部形成的结的起源，我们将我们的实验结果与封闭体积中等边多边形随机打结的Monte Carlo模拟进行了比较。这些模拟结果表明，封闭链的限制，严格限制的体积结果在高打结概率和形成大交叉数的结。我们的结论是，病毒衣壳内的结的形成主要是由禁闭的影响。
When linear double-stranded DNA is packed inside bacteriophage capsids, it becomes highly compacted. However, the phage is believed to be fully effective only if the DNA is not entangled. Nevertheless, when DNA is extracted from a tailless mutant of the P4 phage, DNA is found to be cyclic and knotted (probability of 0.95). The knot spectrum is very complex, and most of the knots have a large number of crossings. We quantified the frequency and crossing numbers of these knots and concluded that, for the P4 tailless mutant, at least half the knotted molecules are formed while the DNA is still inside the viral capsid rather than during extraction. To analyze the origin of the knots formed inside the capsid, we compared our experimental results to Monte Carlo simulations of random knotting of equilateral polygons in confined volumes. These simulations showed that confinement of closed chains to tightly restricted volumes results in high knotting probabilities and the formation of knots with large crossing numbers. We conclude that the formation of the knots inside the viral capsid is driven mainly by the effects of confinement.