Studying the π-π interaction between single-stranded oligonucleotides and single-walled carbon nanotubes by molecular dynamics simulation and density functional theory

Subject Areas :

Mohammad Reza Bozorgmehr ¹ , Maryam Ghanbari Ghanbarloo ² , Ali Morsali ³

1 - Rahnamaee Road, No. 24
2 - Department of chemistry, Islamic Azad University, Mashhad Branch, Mashhad, Iran
3 - Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran

Received: 2023-07-25 Accepted : 2023-10-23 Published : 2023-11-22

Keywords: Drug delivery, Thymine, Biosensor, nucleic acid,

Abstract :

Carbon nanotubes are used in smart drug delivery due to their biocompatibility. However, due to the non-polar nature of these compounds, their use in the in vivo environment is limited. To solve this limitation, functionalization of nanotubes is used. Biological compounds such as nucleic acids are used to functionalize nanotubes. Understanding the interaction mechanism of nanotubes with biological compounds can help in smart drug delivery. In this research, the interaction of four homocopolymers of organic bases adenine, guanine, cytosine and thymine with carbon nanotubes was studied by molecular dynamics simulation and density functional theory. The distance between the two ends of each homocopolymer and the number of atoms of the organic base rings of the homocopolymers were calculated. These two quantities were used to calculate the probability of the system being in different states. Then, the Gibbs free energy for each interaction was calculated using the calculated probabilities. The results show that purine homocopolymers surround the carbon nanotube, while pyrimidine homocopolymers are placed on the surface of the nanotube. The number of monomers with π-π interaction in homocopolymer with guanine 4, adenine 3, cytosine and thymine 2 was obtained.