Study of the prostate-specific antigen–aptamer stability in the PSA–aptamer-single wall carbon nanotube assembly by docking and molecular dynamics simulation

ABSTRACT

Prostate-specific antigen (PSA) is used to detect prostate cancer. RNA aptamers against this protein have been reported previously. In this work, the stability and interaction mechanism of aptamer with PSA and single-wall carbon nanotube (SWCNT) was studied by computational techniques. Molecular dynamics simulations were used to investigate the interaction of aptamer segments with the surfaces of SWCNT and prostate-specific antigen (PSA) protein in an aqueous solution by two steps. Firstly, the interaction of aptamer and SWCNT was studied by the molecular dynamic simulation method. Our results showed that an aptamer segment can attach to the surface of SWCNT with its helix axis perpendicularly. Our analysis shows that the π–π stacking interactions play an important role in the binding of the aptamer to carbon rings. Secondly, we analysed the interaction of PSA protein with aptamer in the aptamer–SWCNT assemble. We found that the 3D structure of aptamer in the presence of PSA protein and SWCNT was stable. Finally, this study provides evidence about the stability of aptamer as a sensor on the surface of SWCNT (as a fixed surface) for PSA protein as a ligand. This finding can help to improve new biosensors for detecting cancer protein markers.

KEYWORDS:

• Prostate-specific antigen
• molecular dynamics simulation
• aptamer
• biosensor
• single-wall carbon nanotube

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

Financial support for this work was provided by the Research Council of Islamshahr Branch of Islamic Azad University.