Interaction of telomeric i-motif DNA fragments with functionalized carbon nanotubes. Effect of the protonation state of cytosines analyzed using molecular dynamics simulations

In this work, we have used molecular dynamics simulations to provide a quantitative analysis of pH-dependent interactions between human telomeric i-motif DNA and functionalized single-walled carbon nanotubes with different diameters and functional groups. We study two kinds of i-motifs differing by the protonation state of cytosines, i.e. unprotonated ones representative to neutral pH and with half of the cytosines protonated and representative to acidic conditions. We observed that protonated i-motif adsorbs strongly on the nanotubes surfaces, with it`s 3’ and 5’ ends directed towards the surface and that adsorption does not affect the i-motif shape. Additionally, the functionalization of the nanotube tips by amino groups or by guanine containing residues has a negligible effect on either the position of i-motif or on its binding strength. On the other hand, the structure of unprotonated i-motif deteriorates significantly after adsorption on nanotubes and its binding strength is rather high as compared to protonated counterparts. Based on various structural property calculations, we found that (10,0) nanotubes destroy the i-motif shape faster than (20,0). Moreover, the i-motif either tries to wrap the nanotube or migrates to its tip and become immobilized due to interaction with guanine residue localized on the nanotube tip and attempts to incorporate its 3’ end into the nanotube interior. Overall, our study suggests that single-walled carbon nanotubes cannot directly stabilize the structure of unprotonated i-motif due to simple physical interactions being a result of the specific shape of nanotubes.

Acknowledgments

This work was supported by Polish National Science Centre grant 2017/27/B/ST4/00108.