Reduced Graphene Oxide-Oligonucleotide Interfaces: Understanding Based on Electrochemical Oxidation of Guanines

Abstract

Investigation into the interactions between biomolecules DNA/RNA and carbon nanomaterials is very important for applications in bioassays and bioanalysis. Graphene and graphene oxide (GO) have been successfully adopted by exploiting the binding affinity difference between single-stranded oligonucleotides (ssDNA) and double-stranded oligonucleotides (dsDNA) to graphene sheets. In this work, we describe the electrochemical DNA oxidation with [Ru(bpy) 3 ] 2+ to understand the interaction between dsDNA (and corresponding ssDNA) and reduced graphene oxide (rGO). The electrochemical oxidation rate of guanine bases of ssDNA bound to rGO by electrochemically generated [Ru(bpy) 3 ] 3+ was much slower than those unbound to rGO. Our study revealed that ssDNA constrained on rGO was significantly protected from the electron transfer to [Ru(bpy) 3 ] 3+ because of π,π-stacking interaction between nucleobases and rGO. On the other hand, the oxidation rates of 11-, 20-, and 27-mer dsDNA bound to rGO increased relative to those of dsDNA alone, demonstrating that the guanine bases of dsDNA on the interaction with rGO became more accessible to [Ru(bpy) 3 ] 3+ . Our electrochemical data illustrated that dsDNA could be totally or partially dehybridized and bind to rGO to form ssDNA/rGO. Furthermore, absorption, circular dichroism spectra, and fluorescence measurements of ethidium bromide using ssDNA and dsDNA with rGO supported the dehybridization of dsDNA in the presence of rGO.

Multiple gene detection using a selective fluorophore probe–RNA hybridization/graphene oxide quenching system

“…The Cy5 fluorophore probe is quenched by the tight electrostatic interaction due to the π,π-stacking between the nucleobases and GO. 25,29 Later, when the second amplified "N" gene RNAs under the LDT reaction are exposed to the quenched Cy5 probe solution, the Cy5 probe-RNA hybridization occurs due to their H-bond interactions compared to the previous electrostatic-π,π stacking bond of the quenched solution. This incident of fluorophore probe-RNA hybridization turned ON the quenched emission of the Cy5 fluorophore again by releasing its fluorescence at the wavelength of 660 nm.…”

“…By using this pioneering quenching capacity of GO, we execute our fluorometric multiple gene detection by ligationdouble transcription. [25][26][27][28][29][30][31][32][33][34] Our analysis exposes key features of multiple gene detection with high sensitivity and is a step towards a detection system with superior efficiency (Scheme 1).…”

Recent biomedical advancements in graphene oxide- and reduced graphene oxide-based nanocomposite nanocarriers

“…Both GO and rGO have strong interactions with single-stranded DNA (ssDNA) through hydrophobic and π-π stacking interactions [ 109 – 111 ]. However, functionalization with positively charged molecules is necessary for interactions with double-stranded DNA (dsDNA) to allow electrostatic interactions [ 112 – 114 ].…”

Sequence-Independent DNA Adsorption on Few-Layered Oxygen-Functionalized Graphene Electrodes: An Electrochemical Study for Biosensing Application

“…To harness the properties of such interfaces for sensitive biosensing platforms, interactions of nucleic acids with graphene-based surfaces have been extensively studied in two regimes, i.e., physisorption and chemisorption [14]. The interfacing of DNA and graphene surfaces is often achieved by the simple mixing of DNA oligonucleotide solution with graphene solution (a liquid/liquid interface) to form DNA-graphene hybrids [15,16], and DNA self-assembly on graphene electrodes (a liquid/solid interface) [17]. Theoretical studies have confirmed π stacking interactions between hydrophobic DNA basepairs and graphitic carbon rings of graphene as a driving force of adsorption [18][19][20].…”