Microehrology in DNA-hydrogels for Molecular imprinting

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In the past few years DNA has been proven to be a material that allows building almost any nano-sized structures ranging from well-defined sheets, to wires and finite-sized 3D building blocks. In this project the student will use some of the well-established DNA-binding rules to build a new class of 3-dimensional DNA-hydrogels with well-defined structures. These involve the use of the fact that we can form 3-way and 4-way junctions with different strands of single-stranded (ss) DNA and use these then to build 3D structures. Aim is to build in freely dangling ssDNA that is still attached to the network for sensing unknown DNA fragments. Once these fragment bind the viscoelastic properties of the hydrogel will change significantly. In order to test these changes, the student will build up a micro-rheometer based on optically trapping a probe particle, whose fluctuations will be used to extract the viscoelastic properties of the network. We will employ a home-developed algorithm for that [2].Seeman, N. C. Nature 421, 427 (2003); Rothemund, P. W. K. Nature 440, 297 (2006) ; Kershner, R. J. et al. Nature Nanotechnology 4, 557 (2009); Ke, J. et al. Nature Chemistry 6, 994 (2014)[2] T. Yanagishima, D. Frenkel, J. Kotar, and E. Eiser, "Real-time monitoring of complex moduli from micro-rheology", J.Phys.: Condens. Matter, 23, 194118 (2011)