Principal Supervisor: Professor Tim Dafforn, School of Biosciences
Co-supervisor: Professor James Tucker, School of Chemistry; Dr. Pola Oppenheimer, School of Chemical Engineering
PhD project title: Nano-construction using Viral “Lego”
University of Registration: University of Birmingham
One of the aims of Synthetic Biology is to build complex bio-machines using the simple building blocks of life. This includes developing complex genetic circuits from much simpler promoters and regulators, complex biosynthetic pathways from collections of enzymes and novel nanoparticles from assemblies of DNA or proteins. In this project we aim to explore how viruses can be used as components in bionanoassembly.
In our laboratory we have worked on the use of filamentous bacteriophage (M13)1-3 in the production of novel bioassays and sensors. This has culminated in the production of a flexible assay system that can be used to rapidly detect human and plant pathogens. As part of this research we have developed a number of chemical methods that allow us to attach a range of moieties to the surface of the virus (including small molecules, DNA and other proteins). These methods have allowed us to explore whether these viruses can be assembled to form new materials and structures that can be applied to applications from bioelectronics and photonics to liquid crystals. Most recently this has allowed us to produce the first “Star” shaped viral assembly. In this project we propose to build on these findings to develop an assembly system were the viral particles can be viewed as nano-scale “Lego” blocks that can be put together to form new structures with novel properties.
The project will be split into 3 sections.
1) Previous work by our group has shown that we can “program” the assembly of viral superstructures using dye molecules as cross-linkers. These new structures are likely to have exciting properties. In this section you will examine these properties to determine whether they might be used in devices such as sensors.
2) Our preliminary work provides the potential to add affinity tags to the virus allowing it to assemble on surfaces. We will explore whether this can be used to develop novel electronic devices (e.g. viral switches and transistors).
3) The previous sections are concerned with the development of essentially 2 dimensional assemblies. In the final phase of the project we will explore whether the viruses can be assembled into 3 dimension arrays using DNA strands or oligomeric proteins as hubs around which the viruses will assemble. Selective trapping and control of light propagation might enable engineering the fundamental properties (i.e., speed, wavelength, frequency) of electromagnetic waves to produce effects that are impossible with conventional optics. One of the main obstacles to realize these concepts is the enormous difficulty to fabricate periodic three-dimensional (3D) nanostructures to a high level of atomic precision. This unconventional interdisciplinary route incorporating elements of Biosciences, Chemistry, Nanofabrication and Engineering will allow the use of nanoscale engineering methods available to biochemists to enable the arrangement of nanometric components with characteristic length scales ranging from a few to several hundreds of nanometres and control over variation of dielectric contrast for a broad range of biotechnological applications including, 3D optical effects and applications associated with them such as, the reverse Doppler effect, camouflaging, optical tunneling devices, compact resonators and highly directional optical sources. Carefully designed miniaturised platforms from viral self-assembly will enable the next-generation biotechnologies fulfilling multitude criteria.
Taken together this PhD project will provide the foundation for a future where M13 will be an important component in bionanoengineering.
- Pacheco-Gómez R, Kraemer J, Stokoe S, England HJ, Penn CW, Stanley E, Rodger A, Ward J, Hicks MR, Dafforn TR. Detection of pathogenic bacteria using a homogeneous immunoassay based on shear alignment of virus particles and linear dichroism. Anal Chem. 2012 Jan 3;84(1):91-7.
- Carr-Smith J., Pacheco-Gómez R., Little H.A., Hicks M.R., Sandhu S., Steinke N., Smith D.J., Rodger A., Goodchild S.A., Lukaszewski R.A., Tucker J.H.R, Dafforn T.R. “Polymerase Chain Reaction on a Viral Nanoparticle.” ACS Synth. Biol. 2015, 4, 1316-1325.
- Daniela P. Lobo, Alan M. Wemyss, David J. Smith, Anne Straube, Kai B. Betteridge, Andrew H.J. Salmon, Rebecca R. Foster, Hesham E. Elhegni, Simon C. Satchell, Haydn A. Little, Raúl Pacheco-Gómez, Mark J. Simmons, Matthew R. Hicks, David O. Bates, Alison Rodger, Timothy R. Dafforn, and Kenton P. Arkill, (2015) Direct detection and measurement of wall shear stress using a filamentous bio-nanoparticle. Nano Research 2015, 8(10):3307–3315
BBSRC Strategic Research Priority: Industrial Biotechnology and Bioenergy
Techniques that will be undertaken during the project:
- Bacterial culturing
- Spectroscopy including Circular dichroism, Fluorescence and absorbance
- Structural techniques including TEM, STEM, SAXS, AFM
- DNA synthesis
- Optical Characterisation including Fourier-transform infrared and UV-Vis spectrometer , Raman Spectroscopy
- Protein Expression and Purification
- Bioconjugation chemistry
- Bacteriophage M13 engineering
- Linear Dichroism Spectroscopy (including instrument development)
Contact: Professor Tim Dafforn, School of Biosciences