Photochemistry and Spectroscopy Department
Institute of Physical Chemistry, Polish Academy of Sciences
“Graphene biosensors and biophysics”
Project leader: Dr. Izabela Kamińska
Postdoctoral researcher: Dr. Ewa Czechowska
PhD student: Karolina Gronkiewicz
Recruitment/rekrutacja:
Postdoctoral Researcher (https://www.euraxess.pl/pl/node/762489)
Student - scholarship (https://www2.ncn.gov.pl/baza-ofert/?akcja=wyswietl&id=190159)
Project funded by the National Science Center, within the program Sonata 15 2019/35/D/ST5/00958 (1 November 2020 – 31 October 2023).
Single-molecule studies provide detailed and valuable information about complexity and heterogeneity of multi-component systems, otherwise hidden by the ensemble-averaged measurement. This approach has significantly increased the sensitivity of biosensors and devices for molecular diagnostics by lowering the detection limit down to ultralow concentrations. Nowadays, single-molecule measurements are regarded as a critical part of many research fields and have become more and more common, what is undoubtedly related to the advances in nanotechnology and development of new analytical tools. Notwithstanding, the detection of single species, investigation of their properties and simultaneous measurements of many single molecules are still very challenging. This can be fulfilled only with well-designed and fully-controlled functional structures characterized with high homogeneity and reproducibility.
With this project, we aim at establishing a novel platform for the new field of graphene biosensing and biophysics. There are two major players: graphene and DNA origami nanostructures. On one hand, we have a high quality graphene with outstanding optoelectronic properties but chemically inert. On the other hand, we have DNA origami nanostructures folded solely from single-stranded DNA which allows for introduction of almost any entity (for example a chemical group) with very high (nanometer) precision. There is a great interest in both materials due to their unique properties, however it is very challenging to bring them together.
Our newly developed strategy allows for placing functional DNA origami nanostructures on graphene using several pyrene molecules as a universal glue to connect these two materials in a controlled manner, without losing their intrinsic properties. On the way to realize the overarching goal there are several subsidiary goals. At first, we will elaborate the preparation of ultraclean graphene samples, using improved protocols for graphene transfer. At the same time, we would like to reduce production cost, increase throughput, and most importantly make the technology broadly available. Secondly, we aim for DNA origami nanostructures that could act as a platform for biophysical and biosensing applications. We will also develop improved biorecognition units whose functioning will be monitored via interactions with graphene. The last but not least, we will explore new, fascinating biophysical properties of macromolecules which are of biological interest.
Combining optimized graphene substrates and the DNA origami nanostructures, serve new tools at hand that offer exciting applications for biosensing and biophysics, but also for superresolution microscopy, plasmonics, material sciences, and many more.
DNA origami
DNA origami technology has been introduced by Paul Rothemund in 2006.1 He demonstrated that one can design and fabricate two-dimensional structures with nanometer precision using only single-stranded DNA. Self-assembled DNA origami constructs are formed by folding a long circular single-stranded DNA scaffold into a specific shape, with the help of hundreds of small complementary oligonucleotides (staple strands). Each staple strand can be modified to carry different chemical moieties (e.g. dyes, biotin, thiol, etc. – internal modification, during folding process) or act as a specific functional entity (e.g. docking strands for metallic NPs – external modification). The combination of a rigid structure, folded by design, and custom strand modification, allows the construction of devices with an excellent control of the spatial arrangement. Since the first demonstration1, the DNA origami technology has been greatly developed, by creating new design strategies and fabricating more and more advanced three-dimensional constructs.2
DNA origami folding animation
Examples of DNA origami-based constructs:
Useful links:
DNA origami tutorials:
https://www.youtube.com/watch?v=Ek-FDPymyyg&t
https://www.youtube.com/watch?v=noWkRxKYBhU
https://www.youtube.com/watch?v=yPkQsrQwpj8&t
https://www.youtube.com/watch?v=cwj-4Wj6PMc
https://www.youtube.com/watch?v=EabqNaYAI7o
https://www.youtube.com/watch?v=G68D-Dgdkp8
Lecture: "DNA Origami: Folded DNA as a Building Material for Molecular Devices" - Paul Rothemund, Research Professor of Bioengineering, Computing and Mathematical Sciences, and Computation and Neural Systems (links: https://www.youtube.com/watch?v=yPkQsrQwpj8&t)
Graphene
Graphene, 2D carbon lattice resembling a honeycomb, has attracted a great attention since its discovery in 2004. Due to its unique properties, it has been intensively explored worldwide and found applications probably in every branch of science.3 One of the properties of graphene and graphene-related 2D materials (for instance rGO called chemical graphene), which is exploited in the field of optical biosensors is fluorescence quenching due to the very efficient energy transfer.4 These interactions have been studied in detail for single dye molecules and QDs.5,6 It has been demonstrated that the energy transfer to graphene strongly depends on the distance between a molecule and graphene, and on the number of graphene layers.5–7 Graphene-based optical sensors have been applied to detect among others small biomolecules, DNA/RNA or proteins.4
1. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).
2. Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (2009).
3. Ferrari, A. C. et al. Science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems. Nanoscale 7, 4598–4810 (2014).
4. Zhu, C., Du, D. & Lin, Y. Graphene and graphene-like 2D materials for optical biosensing and bioimaging : a review. 2D Mater. 2, 32004 (2015).
5. Gaudreau, L. et al. Universal distance-scaling of nonradiative energy transfer to graphene. Nano Lett. 13, 2030–2035 (2013).
6. Federspiel, F. et al. Distance Dependence of the Energy Transfer Rate from a Single Semiconductor Nanostructure to Graphene. Nano Lett. 15, 1252–1258 (2015).
7. Kaminska, I., Wiwatowski, K. & Mackowski, S. Efficiency of energy transfer decreases with the number of graphene layers. RSC Adv. 6, 102791–102796 (2016).
Publications
1. “Graphene Energy Transfer for Single-Molecule Biophysics, Biosensing & Superresolution Microscopy” I. Kamińska*, J. Bohlen, R. Yaadav, P. Schüler, M. Raab, T. Schröder, J. Zähringer, K. Zielonka, S. Krause and P. Tinnefeld*, Advanced Materials, 2021, 33, 2101099.
2. “Graphene-on-Glass Preparation and Cleaning Methods Characterized by Single-Molecule DNA Origami Fluorescent Probes and Raman Spectroscopy”, S. Krause, E. Ploetz, J. Bohlen, P. Schüler, R. Yaadav, F. Selbach, F. Steiner, I. Kamińska, P. Tinnefeld, ACS Nano 2021, 15, 6430–6438.
Conferences and talks
