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DNA Tetrahedra as Sensors – nanotechnology platforms for plants

Principal Supervisor: Professor Rachel O’Reilly, Department of Chemistry, University of Birmingham

Co-supervisors: Dr Tom Wilks (Birmingham); Prof Richard Napier (School of Life Sciences, Warwick)

PhD project title: DNA Tetrahedra as Sensors – nanotechnology platforms for plants

University of Registration: University of Birmingham

Project outline:

DNA tetrahedra1were first reported by the Turberfield group in 2005 – they are formed in a single step from four component strands. The assembly process is straightforward and high-yielding, making them attractive for nanotechnology applications. In addition, the 3’ and 5’ ends of the strands can be moved around the structure to achieve a high degree of control over the placement of functional groups – for example fluorophores.

Proposed Work

DNA tetrahedra constitute a versatile nanostructure to build a sensor around. While there are several examples of their use in mammalian cell lines1, there is no evidence that anyone has ever considered applying them in plant cells. Yet their size and likely stability suggest they may be perfect vehicles for novel nanobiosensors. This could be fertile ground as we will be able to start with novel, proof-of-principle experiments. In particular:

  1. Do tetrahedra have the same resistance to the DNA-degrading enzymes present in plant tissue as they do to those in mammalian cells?
  2. Can tetrahedra cross the plant cell wall?
  3. Where are tetrahedra preferentially accumulated in plant tissues?
  4. Are the concentrations of tetrahedra required for plant cell studies workable from a cost point of view?

Proof-of-principle experiments include:

  1. A study of degradation rates of tetrahedra, DNA hairpins, duplex and single stranded DNA and larger DNA origami structures in plant cell lysates. Assay using electrophoresis and FRET.
  2. A study of tetrahedron localisation in plant tissue. Synthesise a fluorescent tetrahedron and incubate it with either whole roots or suspensions of plant cells, then examine using confocal microscopy.
  3. If the results of these studies are positive then progress to testing a sensor, for example one incorporating the ATP aptamer, which could be benchmarked against existing technologies.
  4. Deploy aptamers selective for e.g. hormones in order to provide biosensors for in situ, real-time monitoring of biological signals.
  5. Additional questions which could be addressed include addressable tetrahedra for cell type/compartmental analyses; biosensor formats including microscopy and electrochemistry; alternative aptamer selections etc.
References:
  1. Nat. Nanotechnol.2012, 7, 389–393; ACS Appl. Mater. Interfaces2016, 8, 4378–4384; Chem. Commun.2013,49, 2010; Angew. Chemie - Int. Ed.2012, 51, 9020–9024.

BBSRC Strategic Research Priority: Food Security & Molecules, Cells and Systems

Techniques that will be undertaken during the project:
  • Polymer chemistry
  • Synthetic chemistry
  • Analytical chemistry
  • Molecular biology
  • Biophysics
  • Plant physiology, confocal and associated microscopies
  • DNA nanotechnology

Contact: Professor Rachel O’Reilly, University of Birmingham