Structural and Dynamic DNA Origami: Design and Applications
Professor Amanda Ellis
University of Canterbury Erskine Fellow Flinders Centre for Nanoscale Science and Technology Flinders University, Adelaide, Australia
Time & Place
Wed, 04 May 2016 12:00:00 NZST in Rutherford Room 531
All are welcome
Structural DNA origami affords a unique opportunity to fold large circular DNA into complex structures by “stapling” with smaller DNA strands at very specific location based on computer modelling and the intrinsic programmable base pairing of DNA nucleobases. This presentation will describe how to make such structures and examine them using gel electrophoresis, scanning electron microscopy and atomic force microscopy. The second part of the talk will focus on DNA manipulation using non-enzymatic dynamic toehold-driven DNA strand displacement reactions. These reactions offer unique advantages in the construction and operation of multi-dimensional DNA nanostructures, DNA computation, bio-sensing as well as nucleic acid sequence analysis. The reactions allow for highly specific and efficient sensing of DNA molecules due to their remarkable ‘zipper-like’ re-hybridisation mechanism. Importantly, this consecutive “base-by-base” uni-directional re-hybridisation permits discrimination of DNA molecules even at the level of single nucleotide polymorphisms (SNPs). The identification of SNPs is an important issue as they are said to give rise to genetic diversity. For example, genetic variations underlie differences in our susceptibility to disease, the severity of illness and the way our body responds to treatments. The detection and discrimination of SNPs within the hyper variable region 1 (HVR-1) of mitochondrial DNA (mtDNA) will be discussed [1,2]. We show the kinetics and kinetic discrimination parameters of these reactions. Other applications of toehold-mediated DNA strand displacement reactions for surface-based DNA sensing will also be discussed, including microfluidic channels and magnetic beads .
 D.A. Khodakov, A.S. Khodakova, D. Huang, A. Linacre, A.V Ellis. Scientific Reports 5 (2015) 8721.
 D.A. Khodakov, A.S. Khodakova, A. Linacre, A.V Ellis. Journal of the American Chemical Society, 135 (2013) 5612–5619.
 D.A. Khodakov, A.S. Khodakova, A. Linacre, A.V Ellis. Analyst, 139 (2014) 3548-3551.
Short Bio: Professor Amanda Ellis graduated with a Ph.D (Applied Chemistry) from the University of Technology, Sydney in 2003. She then undertook two postdocs in the USA, including Rensselaer Polytechnic Institute and New Mexico State University. After these she returned to New Zealand as a Foundation of Research Science and Technology Postdoctoral Research Fellow at Industrial Research Ltd (now Callaghan Innovations). In 2006 Amanda commenced at Flinders University as a teaching/research academic. Since then she has secured over $20M in funding from the ARC and nonARC sources and published over 125 peer-reviewed journal articles (with over 2300 citations) on projects involving novel polymer coatings, functionalised carbon nanotubes and graphene, microfluidics, genotyping and DNA nanotechnology. Currently, she is currently an Australian Research Council Future Fellow (2014-2018), the Deputy Associate Dean of Research for the Faculty of Science and Engineering at Flinders University, a Board Member of the Royal Australian Chemical Institute (RACI), the past-Chair of the RACI National Polymer Division (2013-2015) and a co-founder and executive member of the Australia & New Zealand Micro/Nanofluidics group.