Adsorption of Polyadenylic acid on graphene oxide: experiments and computer modeling

Abstract

In this work, we study the adsorption of poly(rA) on graphene oxide (GO) using AFM and UV absorption spectroscopies. A transformation of the homopolynucleotide structure on the GO surface is observed. It is found that an energetically favorable conformation of poly(rA) on GO is achieved after a considerable amount of time (days). It is revealed that GO can induce formation of self-structures of single-stranded poly(rA) including a duplex at pH 7. The phenomenon is analyzed by polymer melting measurements and observed by AFM. Details of the noncovalent interaction of poly(rA) with graphene are also investigated using molecular dynamics simulations. The adsorption of (rA)₁₀ oligonucleotide on graphene is compared with the graphene adsorption of (rC)₁₀. DFT calculations are used to determine equilibrium structures and the corresponding interaction energies of the adenine-GO complexes with different numbers of the oxygen-containing groups. The IR intensities and vibrational frequencies of free and adsorbed adenines on the GO surface are calculated. The obtained spectral transformations are caused by the interaction of adenine with GO.

Graphical Abstract

Keywords:

• A-motif
• H-bonding
• noncovalent interaction
• graphene oxide
• polyriboadenilic acid
• adenine
• spectroscopy
• molecular dynamics
• ab initio calculations
• atom force microscopy

Acknowledgements

The authors acknowledge the Computational Center at B. I. Verkin Institute for Low Temperature Physics and Engineering and High Throughput Computing (HTC) at the University of Arizona for providing computer time.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work has been supported by funding from the National Academy of Sciences of Ukraine under Grant no. 0120U100157. This work has been also supported in part by a grant from the National Science Foundation under grant no. 1856702.