Photochemistry and Spectroscopy Department
Institute of Physical Chemistry, Polish Academy of Sciences
"Single-biomolecule optical sensors based on DNA origami"
Project leader: Dr. Izabela Kamińska
PhD student: Karolina Zielonka
Master student: Magdalena Sobieska
Master student: Bartłomiej Bałamut
Project funded by the Foundation for Polish Science, within the program HOMING/2017-4/3242E8.
The ultimate goal of the project is detection of viral DNA at the single-molecule level. The newly designed sensors will be self-assembled, using the DNA origami technique to arrange individual components: metallic nanoparticles, graphene and a sensing elements, for example a DNA hairpin loop. You can find more here.
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 demonstration,1 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:
How to design DNA origami, caDNAno tutorials 1 and 2
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
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:
I. Kamińska*, J. Bohlen, S. Rocchetti, F. Selbach, G. P. Acuna, P. Tinnefeld, "Distance dependence of single-molecule energy transfer to graphene measured with DNA origami nano-positioners", Nano Letters 19 (2019) 4257-4262.
Conferences and talks:
1. Graphene Week 2019, Helsinki (Finland), "DNA origami-based nanopositioners for single-molecule sensing on graphene", oral presentation (Izabela Kamińska).
2. MAF 219, San Diego (USA), "DNA origami-based nanopositioners for single-molecule studies on graphene", poster (Izabela Kamińska).
3. Polish Photoscience Seminars 2019, Świętokrzyska Polana (Poland) "DNA Origami-based nanoantennas and nanopositioners for single-molecule studies", oral presentation (Aleksandra Bednarz).
4. IPC PAS Microsymposium 2019, "DNA Origami-based nanoantennas and nanopositioners for single-molecule studies", poster (Aleksandra Bednarz)
Collaborations:
Prof. Philip Tinnefeld
Prof. Guillermo P. Acuna
O projekcie można posłuchać w audycji Wieczór Odkrywców, w Programie Pierwszym Polskiego Radia, tu