Probing DNA topology using single-molecule biophysics

This experimental PhD project will develop and apply a range of state-of-the-art single-molecule biophysics tools to probe the topology of single molecules of DNA. These will include single-molecule manipulation methods of magnetic and optical tweezers, super-resolution imaging and atomic force microscopy (AFM) imaging on a range of circular DNA molecules covering a large length from small synthetic ‘minicircles’ up to large native ‘plasmids’. Your cutting-edge research will enable unprecedented insight into the biophysical mechanics of single DNA molecules by enabling simultaneous control of molecular torsion and force whilst imaging the dynamic molecular topology. This work complements an EPSRC-funded project that aims to program and predict DNA topology on a broad range of length scales: from model genomes (DNA minicircles with approximately 1 kilo-base-pairs or genetic “sequence letters”) to real bacterial genomes containing several mega-bps (Mbps). The work will be in the group of Prof. Mark Leake and also carried out in collaboration with the group Dr. Agnes Noy through the appointment of an additional Post Graduate Research Assistant for performing complementary computational investigations using molecular dynamics simulations. This proposal falls within the EPSRC’s Grand Challenge “Understanding the Physics of Life” because it addresses an extremely relevant and challenging biological question that needs to be tackled by a physics-based methodology. Although rapid genomic sequencing has led to significant increases in the amount of genetic information available, we are still far from a comprehensive understanding of how DNA operates. For example, recently it has been shown that DNA looping and folding are essential mechanisms in the switching of genes between their on and off states and that different patterns of gene expression are strongly influenced by genomic spatial organisation. This has led to the idea that genetic information is also encoded through DNA topology and mechanics and highlights the importance of studying the mechanical properties of DNA at a molecular level. You will learn to apply existing single-molecule biophysics tools in the Leake group (http://single-molecule-biophysics.org/) in addition to developing new biophysical tools throughout the duration of your project. You will gain direct expertise into the use of molecular manipulation techniques of magnetic and optical tweezers, as well as molecular imaging techniques of super-resolution microscopy. In addition, there will be opportunities to engage in state-of-the-art AFM imaging with our collaborator Prof. Bart Hoogenboom in UCL for a period of up to four months during the project. Although being fundamental research, this study will also impact on the healthcare and synthetic biology sectors because tiny DNA minicircles are being recognised as highly efficient agents for gene therapy and because, through designing genome architecture, we will be able to produce better microorganisms for industrial biosynthesis. This project will give the PhD student a near-unique skill set, combining as it does state-of-the-art experimental skills in a range of cutting-edge single-molecule biophysics tools and techniques. With the current high profile of biological physics within the University, and internationally, we anticipate that this proposal is likely to generate further research collaborations, both within York and elsewhere. Finally, the student will be very employable: the biosciences job market is very strong, and the student will have a ‘unique selling point’ to boost their employment prospects. The PhD studentship will be registered in Physics, hence please apply directly to the Physics Department.