We report spontaneous translocation of small interfering RNA (siRNA) inside
carbon nanotubes (CNTs) of various diameters and chirality using all atom
molecular dynamics (MD) 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 shows 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 \tau decreases with the increase of CNT diameter with a
critical diameter of 24 \AA for the translocation. In contrast, double strand
DNA (dsDNA) 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.Comment: Accepted for the Journal of Chemical Physics; 24 pages, 6 figures and
1 tabl
