Optical Graphene-Based Biosensor for Nucleic Acid Detection; Influence of Graphene Functionalization and Ionic Strength.

Diana Becheru,Mariana Ioniţă,Adela Banciu,Jorge Burns,Eugeniu Vasile,George Vlăsceanu

doi:10.3390/ijms19103230

Abstract

A main challenge for optical graphene-based biosensors detecting nucleic acid is the selection of key parameters e.g. graphenic chemical structure, nanomaterial dispersion, ionic strength, and appropriate molecular interaction mechanisms. Herein we study interactions between a fluorescein-labelled DNA (FAM-DNA) probe and target single-stranded complementary DNA (cDNA) on three graphenic species, aiming to determine the most suitable platform for nucleic acid detection. Graphene oxide (GO), carboxyl graphene (GO-COOH) and reduced graphene oxide functionalized with PEGylated amino groups (rGO-PEG-NH2, PEG (polyethylene glycol)) were dispersed and characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The influence of ionic strength on molecular interaction with DNA was examined by fluorescence resonance energy transfer (FRET) comparing fluorescence intensity and anisotropy. Results indicated an effect of graphene functionalization, dispersion and concentration-dependent quenching, with GO and GO-COOH having the highest quenching abilities for FAM-DNA. Furthermore, GO and GO-COOH quenching was accentuated by the addition of either MgCl2 or MgSO4 cations. At 10 mM MgCl2 or MgSO4, the cDNA induced a decrease in fluorescence signal that was 2.7-fold for GO, 3.4-fold for GO-COOH and 4.1-fold for rGO-PEG-NH2. Best results, allowing accurate target detection, were observed when selecting rGO-PEG-NH2, MgCl2 and fluorescence anisotropy as an advantageous combination suitable for nucleic acid detection and further rational design biosensor development.

Highlights

Informative biomarkers, in health and industry sectors, provide opportunities for cost-effective, selective and sensitive biosensing devices
Resorting to a simplified model of nucleic acid-Graphene oxide (GO) interactions [16], we explored the quenching of a fluorescein-labelled DNA (FAM-DNA) probe and detection of the single-stranded complementary DNA (cDNA) target on three types of GO species, not previously compared directly for such purposes (Figure 1), namely; GO, GO-COOH and reduced graphene oxide (rGO)-PEG-NH2 (Figure 2)
As for GO-COOH, the FAM-DNA fluorescence values decreased from 1.15 × 106 ± 5.9 × 104, after 1 h sonication to 1.03 × 106 ± 6.1 × 104 rfu after 2h sonication

Summary

Introduction

In health and industry sectors, provide opportunities for cost-effective, selective and sensitive biosensing devices. Functional nucleic acids (FNA), in particular DNA aptamers, can be conveniently synthesized and readily selected to combine very specific target discrimination with high binding affinity. Graphene-based materials have physiochemical and structural properties well-suited for electrochemical or optical biosensors [3]. A broad range of graphenic species are available for use in optical FNA detection platforms. A common aim is to exploit the graphene oxide (GO)-mediated combination of a strong broad-spectrum fluorescent quenching capacity and different adsorption affinities for FNA aptamers upon target analyte binding [4], making graphene derivatives potent nanomaterials for optical biosensor development [5]. Graphene consists of a single flat sheet of tightly packed carbon atoms arranged in a hexagonal lattice, stable under ambient conditions, bearing highly mobile and extensively-networked π electrons located above and below the graphene sheet [6]

Methods

Results

Conclusion