Adsorption of flexible linker for siRNA on carbon nanotube using pyrene anchor: Molecular dynamics simulation

Carbon nanotubes are considered an effective nanoplatform for drug delivery, including therapeutic nucleic acids such as small interfering RNAs (siRNAs), which are used in cancer therapy. In this work, a noncovalent immobilization of a single-stranded oligonucleotide (with 17 nucleotides in length) on the single-walled carbon nanotube (SWNT) surface using a pyrene molecule as an anchor is simulated by molecular dynamics method. This oligonucleotide design supposes the following binding with siRNA ends to provide its keeping near the nanotube surface. In the model, the pyrene molecule is covalently conjugated to the oligonucleotide through an hexaethylene glycol oligomer (EG)6 and attached to the SWNT's surface by means of pi-pi stacking interaction. Structures of the complex and the binding energy of pyrene in the complex with SWNT are determined. Two possible orientations of the oligonucleotide arrangement relative to SWNT were considered: mutually perpendicular orientation and arrangement of an oligonucleotide along the nanotube. In both cases, the pyrene-terminated flexible polyethylene glycol linker plays an important role in keeping the oligonucleotide near the nanotube surface and provides sufficiently rapid adsorption of the biopolymer on SWNT, which is important for the creation of new drug delivery systems into the cell and for biosensor design.