Unraveling siRNA unzipping kinetics with graphene.
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.
Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
Santosh
S
Mogurampelly
Swati
S
Panigrahi
Dhananjay
D
Bhattacharyya
A K
AK
Sood
Prabal K
PK
Maiti
D004247:DNA / Q000737:chemistry; D006108:Graphite / Q000737:chemistry*; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D034741:RNA, Small Interfering / Q000737:chemistry*; D013816:Thermodynamics
D034741:RNA, Small Interfering; D006108:Graphite; D004247:DNA