Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States.
J Am Chem Soc. 2011 Aug 31;133(34):13545-50. doi: 10.1021/ja204413v. Epub 2011 Aug 10.
The DNA-single-walled carbon nanotube (SWCNT) hybrid molecule has attracted significant attention recently for its ability to disperse and sort SWCNTs according to their chirality. Key for utilizing their unique properties is an understanding of the structure of DNA adsorbed on the SWCNT surface, which we study here using molecular simulations. Using replica exchange molecular dynamics (REMD), we explore equilibrium structures formed by single strands of 12-mer oligonucleotides, of varying sequence, adsorbed on a (6,5)-SWCNT. We find a consistent motif in which the DNA strand forms a right-handed helical wrap around the SWCNT, stabilized by "stitches" (hydrogen bonding between distant bases) to itself. Variability among equilibrium populations of DNA self-stitched structures was observed and shown to be directly influenced by DNA sequence and composition. Competition between conformational entropy and hydrogen bonding between bases is predicted to be responsible for the formation of random versus stitched configurations.
DNA-单壁碳纳米管 (SWCNT) 杂化分子因其能够根据手性对 SWCNT 进行分散和分类而受到广泛关注。利用其独特性质的关键是了解吸附在 SWCNT 表面上的 DNA 的结构，我们在这里使用分子模拟研究了这一点。使用复制交换分子动力学 (REMD)，我们探索了吸附在 (6,5)-SWCNT 上的不同序列的 12 聚体单链寡核苷酸形成的平衡结构。我们发现了一个一致的模式，其中 DNA 链形成右手螺旋缠绕在 SWCNT 上，由自身的“缝线”（远距离碱基之间的氢键）稳定。观察到 DNA 自缝合结构的平衡种群中的可变性，并表明其直接受到 DNA 序列和组成的影响。预测构象熵和碱基之间氢键之间的竞争负责形成随机与缝合配置。
