Next Generation Biophysics to study DNA: in vitro, in silico and in the living cell
The biological functions of DNA rely not just on its raw nucleotide sequence but also on a suite of proteins which interact with DNA. Many of these interactions have a significant influence on the topology of DNA and its subsequent role inside living cells: several basic, essential processes such as DNA replication, transcription and gene regulation are all dependent in highly sensitive ways upon these often complex and heterogeneous binding and dissociation events. Here I will discuss some of our insights in this area, which have all stemmed from the development and application of in vitro, in silico and in vivo methods, that could, perhaps, be thought of as emerging from the growing toolkit of ‘next generation biophysics’. This powerful combinatorial approach has enabled us to shed some light into the role of shape of DNA in regards to its biological function at the level of single, functional molecules.