Garcia A E, Gupta G, Sarma M H, Sarma R H
Theoretical Biology and Biophysics (T-10), Los Alamos National Laboratory, NM 87545.
J Biomol Struct Dyn. 1988 Dec;6(3):525-42. doi: 10.1080/07391102.1988.10506505.
The oligomer d(GCCGCAGC) can adopt two different conformations: i) a duplex with two mismatched A.C base pairs and ii) a hairpin with two C.G base pairs and a single stranded loop. We report molecular mechanics, normal mode analysis, and thermodynamic stability calculations for both structures. We show that the energy-minimized structure and harmonic-dynamics results are in complete agreement with the observed NOE spectrum and imino proton exchange data. We conclude that the high stability of the hairpin structure over the duplex at low salt concentration is due to the higher vibrational entropy contribution to the system free energy by the single stranded loop and to the lack of minor groove phosphate/phosphate electrostatic repulsions that tend to destabilize the duplex.
寡聚体d(GCCGCAGC) 可以采取两种不同的构象：i) 具有两个错配A·C碱基对的双链体，以及ii) 具有两个C·G碱基对和一个单链环的发夹结构。我们报告了这两种结构的分子力学、简正模式分析和热力学稳定性计算。我们表明，能量最小化结构和谐波动力学结果与观察到的NOE谱和亚氨基质子交换数据完全一致。我们得出结论，在低盐浓度下，发夹结构相对于双链体具有高稳定性，这是由于单链环对系统自由能的振动熵贡献更高，以及缺乏倾向于使双链体不稳定的小沟磷酸根/磷酸根静电排斥作用。
