Unraveling siRNA unzipping kinetics with graphene

Mogurampelly, Santosh ; Panigrahi, Swati ; Bhattacharyya, Dhananjay ; Sood, A. K. ; Maiti, Prabal K. (2012) Unraveling siRNA unzipping kinetics with graphene Journal of Chemical Physics, 137 (5). Article ID 054903. ISSN 0021-9606

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Official URL: https://aip.scitation.org/doi/full/10.1063/1.47421...

Related URL: http://dx.doi.org/10.1063/1.4742189

Abstract

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.

Item Type:Article
Source:Copyright of this article belongs to American Institute of Physics.
ID Code:113235
Deposited On:24 May 2018 05:38
Last Modified:24 May 2018 05:38

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