Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
J Chem Phys. 2012 Aug 7;137(5):054903. doi: 10.1063/1.4742189.
Using all atom molecular dynamics simulations, we report spontaneous unzipping and strong binding of small interfering RNA (siRNA) on graphene. Our dispersion corrected density functional theory based calculations suggest that nucleosides of RNA have stronger attractive interactions with graphene as compared to DNA residues. These stronger interactions force the double stranded siRNA to spontaneously unzip and bind to the graphene surface. Unzipping always nucleates at one end of the siRNA and propagates to the other end after few base-pairs get unzipped. While both the ends get unzipped, the middle part remains in double stranded form because of torsional constraint. Unzipping probability distributions fitted to single exponential function give unzipping time (τ) of the order of few nanoseconds which decrease exponentially with temperature. From the temperature variation of unzipping time we estimate the energy barrier to unzipping.
利用全原子分子动力学模拟，我们报告了小干扰 RNA（siRNA）在石墨烯上的自发解链和强结合。我们基于色散校正密度泛函理论的计算表明，与 DNA 残基相比，RNA 的核苷与石墨烯具有更强的吸引力。这些更强的相互作用迫使双链 siRNA 自发解链并结合到石墨烯表面。解链总是从 siRNA 的一端开始，在解开几个碱基对后传播到另一端。当两端都解开时，由于扭转约束，中间部分仍然保持双链形式。拟合到单指数函数的解链概率分布给出了解链时间（τ），约为几个纳秒，其随温度呈指数下降。从解链时间随温度的变化，我们估计了解链的能垒。
