2D materials


Graphene, a 2D carbon lattice resembling a honeycomb, has attracted great attention since its discovery in 2004. Due to its unique optoelectronic and mechanical properties, it has been intensively explored worldwide. Among a long list of interesting properties of graphene, there are several which are especially crucial in the fields of single-molecule biosensing, biophysics and super-resolution. Namely, high transparency, zero energy band gap, and the resulting relatively high and frequency-independent absorption in the visible and near-infrared spectral regions. With these characteristics, graphene acts as a broadband, unbleachable and label-free energy acceptor, which strongly quenches fluorescence of the nearby emitters. Their fluorescence can be restored with a displacement from graphene.

Our main motivation to marry graphene with DNA origami nanostructured was twofold. First of all, we were interested in establishing a new approach to position a single emiter with a distance from graphene controlled in nanometer precision, as well as in overcoming the problem of chemical functionalization of graphene for optical biosensing assays. Secondly, with a single-molecule approach, we could study in detail distance dependance of the energy transfer efficiency in broader spectra range, and determine the distance d0. We succesfully realized these tasks by equiping DNA origami nanostructures with several pyrene molecules, that allowed for controlled immobilization of DNA nanopositioners on graphene. Pyrene molecules also serve as a spacer that keeps DNA origami nanostructures undistracted by the strong π–π interactions with the graphene lattice. The measurements of fluorescence intensity and lifetime of single emitters carried out for distances ranging from 3 to 53 nm confirmed the d–4 dependence of the excitation energy transfer to graphene (Figure 1). Moreover, we determined the characteristic distance d0 for 50% efficiency of the energy transfer from single dyes to graphene to be ~18 nm.

Figure 1. Sketches of rectangular-, disc-, and pillar-shaped DNA origami structures. A single ATTO542 fluorophore (green sphere) is positioned at a height of 3 nm, 7 nm, 12 nm, 16 nm, 24 nm, and 53 nm. Orange frame: zoom-in of pyrene-modified (violet) DNA strand protruding from DNA origami nanostructure and interacting with graphene via π–π interactions. Gray bars represent double-stranded DNA.

Measurements performed with such a precision at the single-molecule level required high-quality graphene substrates. We examined 10 methods for graphene transfer and cleaning, while the quality of the samples was validated by atomic force microscopy, fluorescence lifetime imaging, and Raman spectroscopy. As a result, we established the protocol for the transfer of graphene on glass coverslips with a pristine quality.

With the approach described above, the measured fluorescence lifetime and intensity of single emitters may be directly translated into the distance from graphene. Combining these characteristics of graphene with the modularity of self-assembled DNA origami nanopositioners resulted in developing a new type of nanoruler operating at distances up to 40 nm. Following this, we equipped graphene-DNA origami hybrids with a whole series of self-designed static and dynamic structures with fluorescent molecules. Those constructs have been used among the others, to precisely determine the height of molecules with respect to graphene, to visualize the dynamics of DNA nanostructures, and to determine the orientation of Förster-type resonance energy transfer pairs. What is more, we demonstrated a new form of the fluorescence bioassay, as well as single-molecule tracking, and DNA PAINT super-resolution with isotropic 3D-resolution. The range of examples shows the potential of graphene-on-glass coverslips as a versatile platform for single-molecule biophysics, biosensing, and super-resolution microscopy.

Figure 2. DNA origami structures for GET applications. a) Multiple possible binding geometries of the L-shaped DNA origami structure to graphene due to additional 𝜋-𝜋 stacking of the helices. b) Dynamic investigations and a bioassay was realized by adding a tether the L-shaped DNA origami structure. c) As a biosensing assay a dye is more quenched by graphene and after binding of the target strand a higher binding site is accessible (right part of c)). d) For FRET measurements a dynamic DNA origami structure which can transiently bind to two binding sites at different heights. e) The cubic DNA origami structure contains different binding sites only 2.7 nm apart for super-resolution imaging of the z-distance with DNA-PAINT. f) Tracking of a dye was realized by equipping the L-shaped DNA origami structure with three different binding sites.


Discovered in 2011, MXenes are a growing family of multielemental two-dimensional materials based on transition metal carbides. These materials have gained plenty of attention in the last ten years mainly because of their outstanding intercalation properties and high electrical conductivity. More recently, MXenes are also attracting research efforts in optoelectronics because they combine optical transparency and metallic character, together with a high degree of electronic tuneability by the modulation of surface groups. In addition, their clay-like properties and hydrophilicity make them highly mouldable (flexible devices) and easily processable in water without the need of surfactants. This makes the processability of these materials one of the easiest among most 2D materials. All these advantages are being exploited mainly by the energy research community, where MXenes have found their way as prospective battery and supercapacitor materials.

In the Tinnefeld lab, we are interested in looking at MXenes from a different angle. Motivated by their hydrophilicity, clay-like adsorptive properties, near-infrared absorption and plasmonic properties, we want to explore at the single-molecule level how MXenes affect the fluorescence of dye molecules by using DNA origamis as nanopositioning structures. With this, we are looking into MXenes’ properties as sensors or transducers of fluorescence. In other words, we are looking into probing these materials to detect small changes in their vicinity arising from biomolecular interactions at their surface and at what distances this sensitivity occurs. Given their clay-like adsorptive properties and their potential transducer character, our goal is to merge these two features into a system that can easily and sensitively entrap and sense nucleic acids-based interactions taking place at the material-biomolecular interface.


Graphene Energy Transfer for Single-Molecule Biophysics, Biosensing, and Super-Resolution Microscopy

Kamińska, Izabela; Bohlen, Johann; Yaadav, Renukka; Schüler, Patrick; Raab, Mario; Schröder, Tim; Zähringer, Jonas; Zielonka, Karolina; Krause, Stefan; Tinnefeld, Philip

Graphene Energy Transfer for Single-Molecule Biophysics, Biosensing, and Super-Resolution Microscopy Journal Article

In: Advanced Materials, vol. 33, no. 24, pp. 2101099, 2021.

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Graphene-on-Glass Preparation and Cleaning Methods Characterized by Single-Molecule DNA Origami Fluorescent Probes and Raman Spectroscopy

Krause, Stefan; Ploetz, Evelyn; Bohlen, Johann; Schüler, Patrick; Yaadav, Renukka; Selbach, Florian; Steiner, Florian; Kamińska, Izabela; Tinnefeld, Philip

Graphene-on-Glass Preparation and Cleaning Methods Characterized by Single-Molecule DNA Origami Fluorescent Probes and Raman Spectroscopy Journal Article

In: ACS Nano, vol. 15, no. 4, pp. 6430–6438, 2021.

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Kaminska, I.; Bohlen, J.; Rocchetti, S.; Selbach, F.; Acuna, G. P.; Tinnefeld, P.

Distance Dependence of Single-Molecule Energy Transfer to Graphene Measured with DNA Origami Nanopositioners Journal Article

In: Nano Letters, vol. 19, no. 7, pp. 4257–4262, 2019.

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