Physisorption of nucleobases on graphene: Density-functional calculations

Abstract

We report the results of our first-principles investigation on the interaction of the nucleobases adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) with graphene, carried out within the density functional theory framework, with additional calculations utilizing Hartree-Fock plus second-order Møller-Plesset perturbation theory. The calculated binding energy of the nucleobases shows the following hierarchy: G > T ≈ C ≈ A > U, with the equilibrium configuration being very similar for all five of them. Our results clearly demonstrate that the nucleobases exhibit significantly different interaction strengths when physisorbed on graphene. The stabilizing factor in the interaction between the base molecule and graphene sheet is dominated by the molecular polarizability that allows a weakly attractive dispersion force to be induced between them. The present study represents a significant step towards a first-principles understanding of how the base sequence of DNA can affect its interaction with carbon nanotubes, as observed experimentally. PACS numbers: 68.43.-h, 81.07.De, 82.37.RsDNA-coated carbon nanotubes represent a hybrid system which unites the biological regime and the nanomaterials world. They possess features which make them attractive for a broad range of applications, e.g., as an efficient method to separate carbon nanotubes (CNTs) according to their electronic properties [1, 2, 3], as highly specific nanosensors, or as an in vivo optical detector for ions. Potential applications of single-stranded DNA (ss-DNA) covered CNTs range from electron sensing of various odors [4], to probing conformational changes in DNA triggered by shifts in the surrounding ionic concentration [5], and detection of hybridization between complementary strands of DNA [6,7]. The interaction of DNA with CNT is not limited to the outer surface of the tube; it has also been experimentally demonstrated that ssDNA can be inserted into a CNT [8], further enhancing the potential applications of this nano-bio system.The details of the interaction of DNA with CNTs have not yet been fully understood, though it is generally assumed to be mediated by the π-electron networks of the base parts of DNA and the graphene-like surface of CNTs. One would like to obtain a better understanding of the binding mechanism, and the relative strength of base-CNT binding as it is indicated experimentally from sequence-dependent interactions of DNA with CNTs [3,4]. In this Letter, we present the results of our first-principles study of the interaction of nucleobases with a graphene sheet as a significant step towards a deeper understanding of the interaction of ssDNA with * Corresponding authors. CNTs.Previous theoretical studies focused on the adsorption of the nucleobase adenine on graphite [9]. In the present study, we have considered all five nucleobases of DNA and RNA, namely the two purine bases adenine (A) and guanine (G), and the three pyrimidine bases cytosine (C), thymine (T), and uracil (U). Our specific interest is to assess the subtl...

First-principles study of physisorption of nucleic acid bases on small-diameter carbon nanotubes

“…For G, we find from the Bader analysis that the CNT possesses an excess charge of −0.08 e and correspondingly a slight depletion of electrons on G by +0.08 e. For A with CNT, −0.05 e were found to have been transferred from the nucleic acid base to the CNT. These results should be compared with our corresponding findings from the interaction of nucleic acid bases with a flat graphene sheet [15], where merely 0.02 e were transferred in the case of G.…”

“…Following a similar procedure employed in our previous study with graphene [15], we started by carrying out the optimization process as follows: (i) an initial force relaxation calculation step to determine the preferred orientation and optimum height of the planar base molecule relative to the surface of the CNT; (ii) a curved slice of the potential energy surface was then explored by translating the relaxed base molecules parallel to the CNT surface covering a surface area 4.26Å in height, 70…”

Graphene nanodevices for DNA sequencing

“…Several mechanisms have been discussed, including π-π stacking, electrostatic, van der Waals, and hydrophobic interactions [92]. The main contribution is attributed to π-π bonding, which explains why ssDNA binds more strongly to graphene than dsDNA where the bases are hydrogen bonded and stacked within the helical structure [93,94]. The interaction strengths of the different bases with graphene vary as it depends on the polarizability of the DNA bases [93,95].…”

“…The interaction strengths of the different bases with graphene vary as it depends on the polarizability of the DNA bases [93,95]. Both theoretical and experimental studies report that guanine binds most strongly to graphene while A, T and C have lower and similar interaction strengths [93,[96][97][98][99][100].…”

Adsorption and Desorption of DNA on Graphene Oxide Studied by Fluorescently Labeled Oligonucleotides

“…31 Previous work has focused on characterization of the adsorption of single nucleotides or nucleosides by atomic force microscopy (AFM), 32 isothermal titration calorimetry, 33 and theoretical calculations. [34][35][36] It was concluded that non-electrostatic interactions dominate the binding, 32 and the purine bases bind more strongly than the pyrimidines. 33,35,36 The adsorption of DNA on carbon nanotubes has also been studied.…”