Vologodskii A V, Lukashin A V, Anshelevich V V, Frank-Kamenetskii M D
Nucleic Acids Res. 1979 Mar;6(3):967-82. doi: 10.1093/nar/6.3.967.
The effect of superhelicity on the base-pair opening probability and on the probability of occurrence of cruciform states in palindromic regions is theoretically treated. The calculations show that below the superhelix density value of -sigma=0.05 superhelicity does not appreciably affect the characteristics of DNA secondary structure fluctuations. In the range of physiological superhelix densities sigma (-sigma=0.05-0.09) the base-pair opening probability markedly increases. However, within this range of sigma the base-pairs are opened only transiently and permanently open regions are not formed. Permanently opened regions appear at higher negative superhelix densities (-sigma greater than 0.10). At the values of -sigma higher than 0.06 a cruciform structure in the palindromic region centred in position 3965 proves to be the most probable fluctuational disturbance in the 0x174 duplex DNA. Different experimental approaches used for probing the fluctuations in superhelical DNA have been analysed. The results suggest that most direct quantitative information can be derived from data on the nicking of closed DNA by single strand-specific endonucleases. Such data (Wang, 1974) accord with the results of theoretical calculations. Calculations show that, due to base-pair opening, the total free energy of superhelical DNA should depend parabolically on sigma only up to some critical value of sigma=sigmac. If negative superhelicity exceeds this critical value, which under physiological conditions proves to be -sigma=0.085, the free energy should increase linearly with -sigma. The biological role of supercoiling is discussed in the light of obtained results.
从理论上探讨了超螺旋对回文区域碱基对打开概率和十字形结构出现概率的影响。计算结果表明，在超螺旋密度值-sigma = 0.05以下，超螺旋对DNA二级结构波动特性没有明显影响。在生理超螺旋密度sigma范围内（-sigma = 0.05 - 0.09），碱基对打开概率显著增加。然而，在这个sigma范围内，碱基对只是短暂打开，不会形成永久开放区域。永久开放区域出现在更高的负超螺旋密度下（-sigma大于0.10）。在-sigma高于0.06时，以3965位为中心的回文区域中的十字形结构被证明是0x174双链DNA中最可能的波动干扰。分析了用于探测超螺旋DNA波动的不同实验方法。结果表明，最直接的定量信息可以从单链特异性内切核酸酶切割闭环DNA的数据中获得。这些数据（Wang，1974）与理论计算结果一致。计算表明，由于碱基对打开，超螺旋DNA的总自由能仅在sigma达到某个临界值sigmac之前应与sigma呈抛物线关系。如果负超螺旋超过这个临界值，在生理条件下这个临界值为-sigma = 0.085，自由能应与-sigma呈线性增加。根据所得结果讨论了超螺旋的生物学作用。
