Duplex formation and the onset of helicity in poly d(CG)n oligonucleotides in a solvent-free environment
Duplex formation and the onset of helicity in poly d(CG)n oligonucleotides in a solvent-free environment
复制标题
DOI：
10.1021/ja046433
复制
发表时间：
2004-11-24
影响因子：
15
通讯作者：
Bowers, MT
中科院分区：
文献类型：
--
作者：
Gidden, J;Ferzoco, A;Bowers, MT
用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双链的气相构象。通过电喷雾电离形成脱质子双离子，并将其在氦中的碰撞截面与分子动力学理论模型的计算截面进行了比较。发现4-聚体（dCGCG）和6-聚体（dCGCGCG）双聚体具有球状构象。8-聚（dCGCGCGCG）双相结构为球状和螺旋结构，球状构象更受青睐。对于10-聚（dCGCGCGCGCG）、14-聚（dcgcgcgcgcgcg）和18-聚（dcgcgcgcgcgcg）双相化合物，在离子迁移率测量中只观察到螺旋结构。理论预测，螺旋结构在气相中不如球状结构稳定，只要有足够的时间，就会坍塌成球状。然而，在300 K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。离子迁移实验中螺旋结构的存在表明双相化合物在毫秒时间尺度上保持气相的“溶液结构”。
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.