Graphene Near-Field Interactions for the Observation of DNA Hybridization in Aqueous Environment with Nanoscale Resolution

Summary form only given. We demonstrate that near field effects of graphene can be used to measure axial distances optically, well below the diffraction limit, with resolution down to 1 nm. First we fabricate a control sample using Plasma Enhanced - Chemical Vapour Deposition (PE-CVD) to deposit thin layers of SiO
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with known thicknesses on top of a CVD grown graphene sheet, and onto which a 2 nm thin Atto488-doped Poly Vinyl Alcohol (PVA) layer is spin-coated (Fig. 1A). The fluorescence lifetime values scale with the nanoscale distance from graphene, matching a theoretical description published recently by Gaudreau et al.
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(Fig. 1B). We use the established and tested fluorescence lifetime-to-nanoscale distance conversion to develop a genosensor. Our DNA sensor 2 is composed of a fluorophore-labelled DNA -beacon, for which the oligonucleotide sequence is designed to be complementary to a target DNA molecule, 3 here from a specific grape used for Port wine production, that binds to the graphene via a 1-Pyrenebutyric Acid N-Hydroxysuccinimide Ester (PBSE) linker molecule. The chemistry of this linker allows a high accuracy of axial positioning of the fluorophore relative to the graphene (Fig. 1C) in the inactivated state. Using time-lapse Fluorescence Lifetime Imaging Microscopy (FLIM) the distance between the dye and graphene is monitored with nanometric precision. Upon the addition of target DNA the fluorescence lifetime values increase over time, which can be associated with enlarged distances between dye and graphene (Fig. 1D). We explain the increase by a conformational change of the initially folded beacon into a stretched double stranded DNA, which causes a displacement Az of the attached fluorophore away from the graphene surface. We observe a Az of 10.7 ± 0.7 nm (Fig. 1E), which is comparable to the calculated length of the stretched 9.5 nm DNA strand. It can be assumed that the full beacon unfolding only happens in case of complementary analyte DNA interacting with the genosensor. The mm axial resolution allows detecting partial beacon unfoldings, which may be induced by either i) complete mismatch, ii) partial or iii) even single base mismatch caused e.g. by a mutation in the analyte DNA. Our genosensor therefore may pave the way for a mutation sensitive platform which would have relevance in areas ranging from medicine, to food quality control or environment, which shall be evaluated in future work.