Microehrology in DNA-hydrogels for Molecular imprinting
Lead Research Organisation:
University of Cambridge
Department Name: Physics
Abstract
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)
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)
Organisations
People |
ORCID iD |
| Erika Eiser (Primary Supervisor) | |
| Iliya Stoev (Student) |
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| EP/N509620/1 | 01/10/2016 | 30/09/2022 | |||
| 1805384 | Studentship | EP/N509620/1 | 01/10/2016 | 31/03/2020 | Iliya Stoev |
| Description | This award has been used for the successful characterisation of the mechanical response of self-assembling DNA networks. We used the base complementarity of DNA in order to build higher-order structures, which then possess thermal responsiveness. By using rheology, a branch of physics studying how materials respond to external stimuli through the application of a force, we successfully characterised the relaxation dynamics and interactions between the main constituents in DNA hydrogels. As a result, we showed how introducing flexibility into this type of transient networks leads to suppression of gelation, which is otherwise known to occur in DNA hydrogels due to the formation of hydrogen bonds between base pairs. We hope that in the future this discovery will facilitate the more informed design of smart materials based on DNA nanotechnology. |
| Exploitation Route | The flexibility in the design and synthesis of DNA sequences can be used in conjunction with our findings for gaining control over the macroscopic phases that result on combining short oligonucleotides. In this way, the future use of DNA nanotechnology for creating self-assembling structures will benefit from firm understanding of the structure and dynamics of these phases, elucidated through our microrheology research here. |
| Sectors | Agriculture, Food and Drink,Construction,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology,Other |
| URL | https://pubs.rsc.org/en/content/articlelanding/2019/sm/c9sm01398a#!divAbstract |