DNA‐Length‐Dependent Fluorescence Signaling on Graphene Oxide Surface

Abstract

Graphene has attracted an immense amount of research interest due to its unique electrical, mechanical, optical, and surface properties. [1][2][3][4] In addition, with its superior fluorescence quenching and adsorption capacity, graphene has been increasingly used for making biosensors, [5][6][7][8] drug delivery vehicles, [9, 10] and imaging agents. [10,11] To disperse in an aqueous solution, graphene oxide (GO) with surface carboxyl and hydroxyl groups is often prepared.GO is also an excellent quencher for adsorbed fluorophores with quenching efficiency approaching 100%. [12][13][14] At the same time, GO selectively adsorbs non-structured and single-stranded DNA (ssDNA), [15,16] which can subsequently desorb upon forming double-stranded (dsDNA) or well-folded structures. Based on these understandings, many optical sensors have been designed for the detection of metal ions, [12,17,18] small molecules, [11, 19, 20] [14, 21] [6, 13, 22-24] proteins, and nucleic acids. For example, adsorption of a fluorophorelabeled probe DNA resulted in quenched fluorescence. In the presence of its complementary DNA (cDNA), the fluorescence was recovered due to duplex formation and subsequent desorption. In this This is the peer reviewed version of the following article: Huang, P.-J. J., & Liu, J. (2012 Submitted to -2 -process, the fluorophore-to-GO distance increased from zero to infinity to achieve the maximal fluorescence enhancement. In addition to GO, many other carbon based nanomaterials including carbon nanotubes, [25][26][27][28][29] mesoporous carbon, [30] carbon nanoparticles [31,32] and water soluble nano-C60 [33] have also been tested for similar applications.On the other hand, little is known about DNA length-dependent fluorescence quenching within a few nanometers from the GO surface. Such information is important for rational design of covalently linked probes. Compared to physisorbed probes, covalent sensors are reversible, regenerable, less prone to non-specific probe displacement, and allow continuous monitoring under flow conditions. [34] In addition, studying distance-dependent fluorescence properties are crucial for the fundamental understanding of DNA/GO interaction and its quenching mechanism. Theoretical calculations predicted that quenching by graphene follows a d -4 dependency, where d is the fluorophore-to-graphene distance. [35,36] This is formally similar to the so-called nanosurface energy transfer (NSET) studied using gold nanoparticles as quencher. [37][38][39][40] Seo and co-workers recently measured the fluorescence intensity of Cy3.5 nearby GO separated by up to 18 base pairs (bp) of DNA, where immobilization was achieved via adsorption of a five-adenine overhang.[41]For a systematic study, we employed eight amino and 6-carboxyfluorescein (FAM) dual-labeled DNAs with varying FAM positions (see Figure 1D for the DNA sequences). TheDNAs were respectively reacted with GO in the presence of EDC to form covalent amide linkages ( Figure 1A, step 1), such that the FAM and GO were separated by...

Fluorescent sensors using DNA-functionalized graphene oxide

“…Fan and co-workers described that the different dyes linked to DNA can also be efficiently quenched by GO [49]. Theoretic calculations show that graphene is a long-ranged dynamic quencher and its quenching efficiency follows d -4 dependency, where d is the distance between fluorophore and graphene [63][64][65][66]62,67]. In comparison, molecular quenchers usually follow a d -6 dependency, and thus they are more short-ranged quenchers.…”

Molecular Beacon Lighting up on Graphene Oxide

“…We recently attached a set of amino and FAM (6-carboxyfluorescein) dual labeled DNAs to GO using EDC (1-ethyl-3-(3dimethyllaminopropyl)carbodiimide hydrochloride) as the coupling agent and measured distancedependent fluorescence energy transfer to GO after adding an excess amount of cDNA. 45 This work has established the useful distance range for fluorescence signaling on GO and suggested the feasibility of designing covalent fluorescent probes. However, important analytical questions such as sensitivity, specificity, non-specific probe displacement, and sensor regeneration have not been tested.…”

Intracellular Detection of ATP Using an Aptamer Beacon Covalently Linked to Graphene Oxide Resisting Nonspecific Probe Displacement

“…First, GO is an efficient and general fluorescence quencher and all tested fluorophores are strongly quenched nearby the GO surface. [12][13][14][15] Second, the affinity of DNA adsorption on GO is intermediate via π-π stacking and hydrogen bonding. The binding is strong enough to allow a low background signal, while still weak enough to allow quick probe desorption in the presence of target molecules.…”