Translocation and encapsulation of siRNA inside carbon nanotubes

Abstract

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 τdecreases with the increase of CNT diameter with a critical diameter of 24 Åfor 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.

Accepted for the Journal of Chemical Physics; 24 pages, 6 figures and 1 table

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Cited by in corpus (3)

• Endohedral confinement of a DNA dodecamer onto pristine carbon nanotubes and the stability of the canonical B form
• Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA
• Nanoscopic Characterization of DNA within Hydrophobic Pores:Thermodynamics and Kinetics