ENERGETICS OF THE STRAND SEPARATION TRANSITION IN SUPERHELICAL DNA
ENERGETICS OF THE STRAND SEPARATION TRANSITION IN SUPERHELICAL DNA
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DOI：
10.1016/0022-2836(92)90404-8
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发表时间：
1992-06-05
影响因子：
5.6
通讯作者：
BENHAM, CJ
中科院分区：
文献类型：
--
作者：
BENHAM, CJ
本文通过对实验数据的分析，确定了控制超螺旋链分离转变的三个自由能参数的值。这些是引发分离运行所需的自由能a、与包括分离位点的两个单股的股间缠绕相关的扭转刚度C以及与残余连接相关的二次自由能的系数K。在该分析中使用的实验数据是在pBR 322 DNA分子中发生的链分离的位置和相对量以及测量的残留连接，两者都在负连接差异范围内进行评价。所使用的分析方法对待链分离作为一个杂聚的，合作的，两个状态的过渡到一个扭转变形的替代构象，这发生在一个环状DNA分子的约束下，其连接数的恒定性。这些参数在实验条件下的测定值（T= 310 K，pH = 7.0，单价阳离子浓度= 0.01 m）面积= 10.84（±0.2）kcal/mol，C= 2.5（± 0.3）× 10− 13 erg/rad 2和K = 2350（±80）RT/N，其中N是以碱基对表示的分子长度。这些自由能参数被结合到不同分子中的超螺旋链分离的分析中，并且在不同于它们的评估中所使用的那些条件的其它条件下。首先，温度依赖性的过渡处理，然后超螺旋链分离进行了分析，在一系列的DNA分子具有系统的序列修饰，这些理论分析的结果与实验进行了比较。在所有的分子中，在实验中看到的连接差异的范围内预测过渡。此外，它发生在分析预测的特定序列位置处，并且在每个位置处具有大约预测的相对转变量。已知的敏感性，这种转变的温度变化和小的序列修改的预测在定量精确的方式由理论结果。这些理论方法所证明的高精度为筛选DNA序列中易受超螺旋链分离影响的位点提供了一种工具，其中一些可能具有调节或其他生物学意义。
In this paper the values of three free energy parameters governing the superhelical strand separation transition are determined by analysis of available experimental data. These are the free energy,a, needed to initiate a run of separation, the torsional stiffness,C, associated with interstrand winding of the two single strands comprising a separated site and the coefficient,K, of the quadratic free energy associated to residual linking. The experimental data used in this analysis are the locations and relative amounts of strand separation occurring in the pBR322 DNA molecule and the measured residual linking, both evaluated over a range of negative linking differences. The analytic method used treats strand separation as a heteropolymeric, co-operative, two-state transition to a torsionally deformable alternative conformation, which takes place in a circular DNA molecule constrained by the constancy of its linking number. The values determined for these parameters under the experimental conditions (T= 310 K, pH = 7.0, monovalent cation concentration = 0.01m) area= 10.84(±0.2) kcal/mol,C= 2.5(± 0.3) × 10−13erg/rad2andK= 2350(±80)RT/N, whereNis the molecular length in base-pairs.In order to assess the accuracy of the author's theoretical methods, these free energy parameters are incorporated into the analysis of superhelical strand separation in different molecules and under other conditions than those used in their evaluation. First, the temperature dependence of transition is treated, then superhelical strand separation is analyzed in a series of DNA molecules having systematic sequence modifications, and the results of these theoretical analyses are compared with those from experiments. In all molecules, transition is predicted in the range of linking differences where it is seen experimentally. Moreover, it occurs at the specific sequence locations that the analysis predicts, and with approximately the predicted relative amounts of transition at each location. The known sensitivities of this transition to changes of temperature and to small sequence modifications are predicted in a quantitatively precise manner by the theoretical results. The demonstrated high-level precision of these theoretical methods provides a tool for the screening of DNA sequences for sites susceptible to superhelical strand separation, some of which may have regulatory or other biological significance.