Cubero E, Luque F J, Orozco M
Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain.
J Am Chem Soc. 2001 Dec 5;123(48):12018-25. doi: 10.1021/ja011200t.
Poly d(A:T) parallel-stranded DNA duplexes based on the Hoogsteen and reverse Watson-Crick hydrogen bond pairing are studied by means of extensive molecular dynamics (MD) simulations and molecular mechanics coupled to Poisson-Boltzmann (MM-PB/SA) calculations. The structural, flexibility, and reactivity characteristics of Hoogsteen and reverse Watson-Crick parallel duplexes are described from the analysis of the trajectories. Theoretical calculations show that the two parallel duplexes are less stable than the antiparallel Watson-Crick duplex. The difference in stability between antiparallel and parallel duplexes increases steadily as the length of the duplex increases. The reverse Watson-Crick arrangement is slightly more stable than the Hoogsteen duplex, the difference being also increased linearly with the length of the duplex. A subtle balance of intramolecular and solvation terms is responsible for the preference of a given helical structure.
基于Hoogsteen和反向沃森-克里克氢键配对的聚d(A:T)平行链DNA双链体，通过广泛的分子动力学（MD）模拟以及与泊松-玻尔兹曼耦合的分子力学（MM-PB/SA）计算进行研究。通过对轨迹的分析，描述了Hoogsteen和反向沃森-克里克平行双链体的结构、柔韧性和反应性特征。理论计算表明，这两种平行双链体比反平行沃森-克里克双链体稳定性更低。随着双链体长度增加，反平行双链体和平行双链体之间的稳定性差异稳步增大。反向沃森-克里克排列比Hoogsteen双链体稍微稳定一些，这种差异也随着双链体长度线性增加。分子内和溶剂化项之间的微妙平衡决定了特定螺旋结构的偏好。
