Kozyavkin S A, Naritsin D B
Institute of Molecular Genetics, USSR Academy of Sciences, Moscow.
J Biomol Struct Dyn. 1986 Feb;3(4):689-704. doi: 10.1080/07391102.1986.10508456.
The kinetic analysis of individual helix-coil subtransitions were performed by comparing melting and renaturation profiles obtained at different temperature change rates. The duration of the three transition stages and its dependence on temperature and ionic strength were determined for a T7 phage DNA fragment. The obtained temperature dependence of the melting time for a stretch flanked by melted regions is in quantitative agreement with that predicted by the theory of slow processes (V.V. Anshelevich, A.V. Vologodskii, A.V. Lukashin, M.D. Frank-Kamenetskii, Biopolymers 23, 39 (1984)). The reasons are discussed for the increasing relaxation time of this stretch in the middle of its transition with decreasing ionic strength. The zipping kinetics of a melted region under essentially nonequilibrium conditions was examined for T7 fragment and pAO3 DNAs. The obtained temperature dependence of the zipping time is in quantitative agreement with calculations based on the theory of slow processes. The renaturation times of stretches flanked by helical regions proved fairly small even at a low ionic strength. These times are several orders of magnitude smaller than the renaturation times of the same stretches with one helical boundary. A formal application of the theory of slow processes failed to account for the small renaturation times of stretches that are zipped from both ends. This is probably due to the non-allowance for the changing entropy of the loop linking two helix-coil boundaries migrating towards each other. Slow processes have been revealed in the intramolecular melting of Col E1 DNA at a high ionic strength. The reason for the long relaxation time of one subtransition is the large size of the loop that separates the melting stretch from the helical part of the molecule. This result can be accounted for by the theory of slow processes.
通过比较在不同温度变化速率下获得的解链和复性曲线，对单个螺旋-线圈亚转变进行动力学分析。针对T7噬菌体DNA片段，确定了三个转变阶段的持续时间及其对温度和离子强度的依赖性。对于由解链区域侧翼的一段序列，所获得的解链时间对温度的依赖性与慢过程理论（V.V.安舍列维奇、A.V.沃洛戈德斯基、A.V.卢卡申、M.D.弗兰克-卡缅涅茨基，《生物聚合物》23, 39 (1984)）所预测的结果在定量上相符。讨论了在转变过程中该片段中间部分随着离子强度降低弛豫时间增加的原因。在基本非平衡条件下，研究了T7片段和pAO3 DNA的解链区域的拉链动力学。所获得的拉链时间对温度的依赖性与基于慢过程理论的计算结果在定量上相符。事实证明，即使在低离子强度下，由螺旋区域侧翼的片段的复性时间也相当短。这些时间比具有一个螺旋边界的相同片段的复性时间小几个数量级。慢过程理论的形式应用无法解释从两端拉链的片段的短复性时间。这可能是由于未考虑连接两个相互靠近的螺旋-线圈边界的环的熵变。在高离子强度下，已在Col E1 DNA的分子内解链中揭示了慢过程。一个亚转变的弛豫时间长的原因是将解链片段与分子的螺旋部分隔开的环的尺寸大。这一结果可用慢过程理论来解释。
