Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
J Chem Phys. 2013 Jan 21;138(3):034901. doi: 10.1063/1.4773302.
We report spontaneous translocation of small interfering RNA (siRNA) inside carbon nanotubes (CNTs) of various diameters and chirality using all atom molecular dynamics simulations with explicit solvent. We use umbrella sampling method to calculate the free energy landscape of the siRNA entry and translocation event. Free energy profiles show that siRNA gains free energy while translocating inside CNT, and barrier for siRNA exit from CNT ranges from 40 to 110 kcal/mol depending on CNT chirality and salt concentration. The translocation time τ decreases with the increase of CNT diameter with a critical diameter of 24 Å for the translocation. In contrast, double strand DNA of the same sequence does not translocate inside CNT due to large free energy barrier for the translocation. This study helps in understanding the nucleic acid transport through nanopores at microscopic level and may help designing carbon nanotube based sensor for siRNA.
我们使用含显式溶剂的全原子分子动力学模拟研究了不同直径和手性的碳纳米管（CNT）内小干扰 RNA（siRNA）的自发转运。我们使用伞状采样法计算了 siRNA 进入和转运事件的自由能景观。自由能曲线表明，siRNA 在 CNT 内转运时获得自由能，而 siRNA 从 CNT 中出来的势垒则取决于 CNT 的手性和盐浓度，范围为 40 到 110 kcal/mol。随着 CNT 直径的增加，转运时间 τ 会减少，对于转运而言，存在一个 24 Å 的临界直径。相比之下，相同序列的双链 DNA 由于转运的自由能势垒较大，因此不会在 CNT 内转运。本研究有助于从微观层面理解核酸通过纳米孔的转运，并可能有助于设计基于碳纳米管的 siRNA 传感器。
