Binding of Nucleobases with Single-Walled Carbon Nanotubes

TL;DR

This study combines computational and experimental methods to analyze how different nucleobases bind to single-walled carbon nanotubes, revealing the dominant van-der-Waals interactions and the influence of solvation effects on binding affinity.

Contribution

It provides a comprehensive comparison of nucleobase binding energies to SWNTs using ab-initio calculations and experimental calorimetry, highlighting the role of van-der-Waals forces and solvation.

Findings

G has the highest binding energy in gas phase

Solvation effects alter the binding sequence to T > A > C

Experimental binding sequence matches computational predictions for T > A > C

Abstract

We have calculated the binding energy of various nucleobases (guanine (G), adenine (A), thymine (T) and cytosine (C)) with (5,5) single-walled carbon nanotubes (SWNTs) using ab-initio Hartre-Fock method (HF) together with force field calculations. The gas phase binding energies follow the sequence G $>$ A $>$ T $>$ C. We show that main contribution to binding energy comes from van-der Wall (vdW) interaction between nanotube and nucleobases. We compare these results with the interaction of nucleobases with graphene. We show that the binding energy of bases with SWNTs is much lower than the graphene but the sequence remains same. When we include the effect of solvation energy (Poisson-Boltzman (PB) solver at HF level), the binding energy follow the sequence G $>$ T $>$ A $>$ C $>$, which explains the experiment\cite{zheng} that oligonucleotides made of thymine bases are more effective in dispersing the SWNT in aqueous solution as compared to poly (A) and poly (C). We also demonstrate experimentally that there is differential binding affinity of nucleobases with the single-walled carbon nanotubes (SWNTs) by directly measuring the binding strength using isothermal titration (micro) calorimetry. The binding sequence of the nucleobases varies as thymine (T) $>$ adenine (A) $>$ cytosine (C), in agreement with our calculation.