Probing the Interaction of Nucleobases and Fluorophore‐Tagged Nucleobases with Graphene Surface: Adsorption and Fluorescence Studies

Abstract

Adsorption of a fluorophore‐labeled DNA oligonucleotide by graphene nano‐probes is of interest to exploit as bio‐sensing material. This work reports the fluorescence properties of fluorophore tagged nucleobases on the graphene surface computationally. The interaction of nucleobases and fluorophore tagged nucleobases to the graphene surface examined using M062X/6‐31G(d) level of theory in the gas phase and ethanol solvent. The binding energies of nucleobases on the graphene surface in the gas phase follows the order: G>A≥C≥T in agreement with the previous reports. The slab model calculations performed with LDA/PWC/DND level of theory also revealed a similar binding affinity on the graphene surface in the gas phase. The fluorescence of benzoxazole as fluorophore tagged with nucleobase on graphene surface was investigated using TD‐DFT M06‐2X/6‐31G(d) level of theory. The binding preference of the fluorophore tagged nucleobases is not significantly different in ethanol solvent. The aromaticity of the nucleobases tagged fluorophore on the graphene surface was investigated by NICS (1) and NICS (1)zz calculations and the aromaticity was found to be increased upon interaction with the graphene surface. The fluorescence quenching upon binding of fluorophore tagged nucleobases on graphene surface revealed the importance of purine nucleobases and found to be more prominent with guanine tagged fluorophore.

Graphene: From Solid Support for Nucleobase Assisted Self-Assemblies to Functional Material for DNA Sequencing

“…The calculations all indicate a very strong π–π interaction between the nucleobase and the graphene surface, with the face of the nucleobase lying almost flat on the surface. − It also emerges that the binding energies follow the trend guanine > adenine > thymine > cytosine, irrespective of the method used for the calculation. Ab initio methods are generally employed to investigate the interaction of only one nucleobase with a graphene sheet or patch of graphene in a gas phase environment.…”

Insight into the Sensing Behavior of DNA Probes Based on MOF–Nucleic Acid Interaction for Bioanalysis

“…During the strategies above, DNA probes should have appropriate interactions/affinity with the nanomaterials used. Otherwise, the adsorption and desorption behaviors of DNA probes will be greatly influenced and ultimately affect sensing performance. , For instance, the weak interaction with nanomaterials could result in high background and long reaction time. Since most of the commonly used nanomaterials are negatively charged at neutral pH, DNA as a polyanion needs to overcome long-ranged electrostatic repulsion to be adsorbed onto these nanomaterials. − In contrast, excessive adsorption forces weakened the signal changes in response to target stimuli. , To achieve excellent analytical performance, substantial endeavors have been exploited to regulate the DNA–nanomaterials interactions by replacing or modifying the used nanomaterials, − while little attention has been paid to the sensing mechanism, the influence by DNA structures (different structured DNA has distinct adsorption characteristics onto nanomaterials), and other factors, which need systematic investigations using an ideal material as a model.…”

“…Otherwise, the adsorption and desorption behaviors of DNA probes will be greatly influenced and ultimately affect sensing performance. 10,11 For instance, the weak interaction with nanomaterials could result in high background and long reaction time. Since most of the commonly used nanomaterials are negatively charged at neutral pH, DNA as a polyanion needs to overcome long-ranged electrostatic repulsion to be adsorbed onto these nanomaterials.…”