Dynamics of the B-A transition of DNA double helices
Dynamics of the B-A transition of DNA double helices
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DOI：
10.1093/nar/gkh551
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发表时间：
2004-04-01
影响因子：
14.9
通讯作者：
Porschke, D
中科院分区：
文献类型：
--
作者：
Jose, D;Porschke, D
虽然从B-DNA双螺旋结构到a -形式的转变对于生物功能是必不可少的，正如许多蛋白质- dna复合物中a -形式的存在所表明的那样，但这种转变的动力学尚未得到解决。根据分子动力学模拟，这种转变预计在几纳秒的时间范围内。在停止流动实验中，DNA样品与乙醇混合诱导的B-A转变在死时间内完成，表明反应速度比类似的0.2 ms快。该反应采用电场跳变技术，通过偶极子拉伸力将a -型转化为b -型来感应跃迁。Poly[d(a - t)]被确立为一个有利的模型体系，因为它的过渡具有特别高的协同性，而且它的光谱特征允许分离潜在的副反应。在poly[d(A-T)]的情况下，观察到的时间常数与1600 bp相似，在10 mus左右的范围内。另外一个时间常数约为100 μ s的过程可能是由于成核作用。同样的时间常数（在实验精度+/-10%范围内）被观察到的聚[d(a - t)]样品与70 bp相似。在通常用于研究B-A跃迁的低盐条件下，时间常数几乎与离子强度无关。实验数据表明，在B-A跃迁中存在明显的激活屏障，并且螺旋态彼此明显分离，这与分子动力学模拟的预测相反。
Although the transition from the B-DNA double helix to the A-form is essential for biological function, as shown by the existence of the A-form in many protein-DNA complexes, the dynamics of this transition has not been resolved yet. According to molecular dynamics simulations the transition is expected in the time range of a few nanoseconds. The B-A transition induced by mixing of DNA samples with ethanol in stopped flow experiments is complete within the deadtime, showing that the reaction is faster than similar to0.2 ms. The reaction was resolved by an electric field jump technique with induction of the transition by a dipole stretching force driving the A- to the B-form. Poly[d(A-T)] was established as a favourable model system, because of a particularly high cooperativity of the transition and because of a spectral signature allowing separation of potential side reactions. The time constants observed in the case of poly[d(A-T)] with similar to1600 bp are in the range around 10 mus. An additional process with time constants of similar to100 mus is probably due to nucleation. The same time constants (within experimental accuracy +/-10%) were observed for a poly[d(A-T)] sample with similar to70 bp. Under low salt conditions commonly used for studies of the B-A transition, the time constants are almost independent of the ionic strength. The experimental data show that a significant activation barrier exists in the B-A transition and that the helical states are clearly separated from each other, in contrast to predictions by molecular dynamics simulations.