Rau D C, Klotz L C
Biophys Chem. 1978 Mar;8(1):41-51. doi: 10.1016/0301-4622(78)85021-2.
DNA renaturations under nucleation-rate-limiting conditions on simple DNA such as bacterial and bacteriophage DNA show significant deviation from ideal second-order kinetics when followed by optical density measurements at 260 nm. Ideal second-order kinetics yield linear plots when the data is plotted in the standard reciprocal second-order (RSO) manner. The observed deviations from ideal second-order behavior take the form of steadily downward-curving RSO plots. In this paper, experiments are presented for E. coli and T2 DNA documenting this non-ideal behavior. Since experiments using T4, T5 and B, subtilis DNA yield identical non-ideal behavior, this behavior appears to be a property of DNA renaturation followed by optical density, not a peculiarity of a particular DNA. Identical non-ideal behavior is also seen in kinetics followed by S1 nuclease assay. A theory is developed to explain this deviation from ideal second-order kinetics. The theory also explains why kinetics followed by hydroxyapatite chromatography show nearly ideal second-order kinetics. In contrast to the approach taken by others in developing equations that describe S1 nuclease monitored reactions, our view is that nonideal second-order kinetics are fundamentally due to the reacton of free single strands to yield partially helical duplex species. Later reactions of these species tend to reduce the deviations from non-ideal second-order kinetics.
在成核速率限制条件下，对诸如细菌和噬菌体DNA等简单DNA进行的DNA复性实验，当通过在260nm处测量光密度来跟踪时，显示出与理想二级动力学有显著偏差。当以标准的倒数二级（RSO）方式绘制数据时，理想的二级动力学产生线性图。观察到的与理想二级行为的偏差表现为RSO图稳步向下弯曲的形式。在本文中，展示了针对大肠杆菌和T2 DNA的实验，记录了这种非理想行为。由于使用T4、T5和枯草芽孢杆菌DNA进行的实验产生了相同的非理想行为，这种行为似乎是DNA复性后光密度测量的一种特性，而不是特定DNA的特性。在通过S1核酸酶测定跟踪的动力学中也观察到相同的非理想行为。提出了一种理论来解释这种与理想二级动力学的偏差。该理论还解释了为什么通过羟基磷灰石色谱跟踪的动力学显示出近乎理想的二级动力学。与其他人在推导描述S1核酸酶监测反应的方程时所采用的方法不同，我们的观点是，非理想二级动力学从根本上是由于游离单链反应产生部分螺旋双链体物种所致。这些物种的后续反应倾向于减少与非理想二级动力学的偏差。
