Complex Thermodynamic Behavior of Single-Stranded Nucleic Acid Adsorption to Graphene Surfaces

Abstract

In just over a decade since its discovery, research on graphene has exploded due to a number of potential applications in electronics, materials, and medicine. In its water-soluble form of graphene oxide, the material has shown promise as a biosensor due to its preferential absorption of single-stranded polynucleotides and fluorescence quenching properties. The rational design of these biosensors, however, requires an improved understanding of the binding thermodynamics and ultimately a predictive model of sequence-specific binding. Toward these goals, here we directly measured the binding of nucleosides and oligonucleotides to graphene oxide nanoparticles using isothermal titration calorimetry and used the results to develop molecular models of graphene-nucleic acid interactions. We found individual nucleosides binding KD values lie in the submillimolar range with binding order of rG < rA < rC < dT < rU, while 5mer and 15mer oligonucleotides had markedly higher binding affinities in the range of micromolar and submicromolar KD values, respectively. The molecular models developed here are calibrated to quantitatively reproduce the above-mentioned experimental results. For oligonucleotides, our model predicts complex binding features such as double-stacked bases and a decrease in the fraction of graphene stacked bases with increasing oligonucleotide length until plateauing beyond ∼10-15 nucleotides. These experimental and computational results set the platform for informed design of graphene-based biosensors, further increasing their potential and application.

Dynamic Cooperation of Hydrogen Binding and π Stacking in ssDNA Adsorption on Graphene Oxide

“…Along these lines, it has been shown experimentally that individual nucleosides binding to GO lie in the submillimolar range with binding order of rG < rA < rC < dT < rU using isothermal titration calorimetry in aqueous solutions. [4] Thisr esult is inconsistent with the experimental results [5] and the theoretical calculations [6] of nucleobases on graphene surfaces. The interactionb etween the ssDNA segment and graphene/GO has also been experimentally and theoretically studied, and the hydrophobic, [2f, 7] hydrogen bonding, [8] and p-p stacking interactions [5, 8b] have been regarded as important factors.…”

“…Clearly, to improve the application of DNA‐based functional structures, it is important to understand how DNA interacts with graphene/GO. Along these lines, it has been shown experimentally that individual nucleosides binding to GO lie in the submillimolar range with binding order of rG<rA<rC<dT<rU using isothermal titration calorimetry in aqueous solutions . This result is inconsistent with the experimental results and the theoretical calculations of nucleobases on graphene surfaces.…”

Advances in RNA molecular dynamics: a simulator's guide to RNA force fields

“…Given the lack of an universally agreed upon model that accurately captures Mg 2+ ion–RNA interactions as has been discussed above, motifs that are strongly ion‐dependent (i.e., kink‐turns, quadruplexes) should be avoided. RNA–ligand and RNA–surface interactions are in principle possible to simulate, although any material capable of significant stacking (i.e., graphene) requires calibrations beyond the ‘automated’ parameterization schemes, preferably utilizing experimental binding data. Due to the current difficulties in describing base‐pairing energetics, atomistic simulations cannot yet be used to melt duplexes or observe conformational equilibria involving base‐pairing rearrangements at this time.…”

tRNA Modification Detection Using Graphene Nanopores: A Simulation Study

“…The conformation adopted by the nucleosides in the heterogeneous environment of the nanopore is going to be highly dependent on the models used for nucleoside–graphene interactions. The interaction of individual nucleosides to graphene was shown to be highly over stabilized using the default AMBER parameters [ 49 ]. Therefore, we used the newly developed AMBER-type force field parameters for nucleoside–graphene interactions, which employed gas phase quantum mechanical calculations, and calibrated against experimental thermodynamic results [ 49 ].…”

“…The interaction of individual nucleosides to graphene was shown to be highly over stabilized using the default AMBER parameters [ 49 ]. Therefore, we used the newly developed AMBER-type force field parameters for nucleoside–graphene interactions, which employed gas phase quantum mechanical calculations, and calibrated against experimental thermodynamic results [ 49 ]. The calibrated force field was shown to reproduce the thermodynamic behavior of nucleosides and oligonucleotides at the graphene surface, an important parameter for characterizing the structure and interactions of nucleic acids at graphene–water interfaces.…”