Gidden Jennifer, Ferzoco Alessandra, Baker Erin Shammel, Bowers Michael T
Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106, USA.
J Am Chem Soc. 2004 Nov 24;126(46):15132-40. doi: 10.1021/ja046433+.
The gas-phase conformations of a series of cytosine/guanine DNA duplexes were examined by ion mobility and molecular dynamics methods. Deprotonated duplex ions were formed by electrospray ionization, and their collision cross sections measured in helium were compared to calculated cross sections of theoretical models generated by molecular dynamics. The 4-mer (dCGCG) and 6-mer (dCGCGCG) duplexes were found to have globular conformations. Globular and helical structures were observed for the 8-mer (dCGCGCGCG) duplex, with the globular form being the more favored conformer. For the 10-mer (dCGCGCGCGCG), 14-mer (dCGCGCGCGCGCGCG), and 18-mer (dCGCGCGCGCGCGCGCGCG) duplexes, only helical structures were observed in the ion mobility measurements. Theory predicts that the helical structures are less stable than the globular forms in the gas phase and should collapse into the globular form given enough time. However, molecular dynamics simulations at 300 K indicate the helical structures are stable in aqueous solution and will retain their conformations for a limited time in the gas phase. The presence of helical structures in the ion mobility experiments indicates that the duplexes retain "solution structures" in the gas phase on the millisecond time scale.
通过离子迁移率和分子动力学方法研究了一系列胞嘧啶/鸟嘌呤DNA双链体的气相构象。通过电喷雾电离形成去质子化的双链体离子，并将其在氦气中测得的碰撞截面与分子动力学生成的理论模型的计算截面进行比较。发现4聚体（dCGCG）和6聚体（dCGCGCG）双链体具有球状构象。在8聚体（dCGCGCGCG）双链体中观察到球状和螺旋结构，其中球状形式是更有利的构象异构体。对于10聚体（dCGCGCGCGCG）、14聚体（dCGCGCGCGCGCGCG）和18聚体（dCGCGCGCGCGCGCGCGCG）双链体，在离子迁移率测量中仅观察到螺旋结构。理论预测，在气相中螺旋结构比球状形式不稳定，并且在足够长的时间后应坍塌成球状形式。然而，300K下的分子动力学模拟表明，螺旋结构在水溶液中是稳定的，并且在气相中会在有限的时间内保持其构象。离子迁移率实验中螺旋结构的存在表明双链体在毫秒时间尺度上在气相中保留了“溶液结构”。
