Lee N, Obukhov S, Rubinstein M
Department of Physics, University of Florida, Gainesville 32611, USA.
Electrophoresis. 1996 Jun;17(6):1011-7. doi: 10.1002/elps.1150170608.
We present a new model for the motion of a megabase-long DNA molecule undergoing gel electrophoresis. We assume that the dynamics of large segments of DNA is almost deterministic and can be described by a set of simple mechanical equations. This allows the numerical study of gel electrophoresis of ultra-high molecular weight DNA. A strong electric field forces DNA in a gel into a tree-like structure with branches-loops of different sizes. We determined the loop-size distribution function. This distribution has a power law form, confirming the hypothesis of the statistical self-similarity of a moving polymer. We find periodic configuration changes in the motion of a circular polymer, with the average period proportional to the molecular weight. During the period, a polymer goes through three distinct phases: a simple V-shape configuration, a growing tree, and a decaying tree. For a linear polymer this periodicity is much less pronounced because of additional perturbations to the dynamics caused by free ends. A circular polymer stays in a simple V-shaped configuration about 30% of the time, independent of molecular weight (10% for a linear polymer).
我们提出了一种用于兆碱基长的DNA分子进行凝胶电泳运动的新模型。我们假设DNA大片段的动力学几乎是确定性的，并且可以用一组简单的力学方程来描述。这使得对超高分子量DNA的凝胶电泳进行数值研究成为可能。强电场迫使凝胶中的DNA形成具有不同大小分支-环的树状结构。我们确定了环大小分布函数。这种分布具有幂律形式，证实了移动聚合物统计自相似性的假设。我们发现圆形聚合物运动中存在周期性构型变化，平均周期与分子量成正比。在这个周期内，聚合物经历三个不同阶段：简单的V形构型、生长的树和衰减的树。对于线性聚合物，由于自由端对动力学产生的额外扰动，这种周期性不太明显。圆形聚合物约30%的时间处于简单的V形构型，与分子量无关（线性聚合物为10%）。
