DNA in Tight Spaces

After water and oxygen, DNA is arguably the most famous molecule of life. This is not surprising, as the eye-catching double helix of DNA carries the instructions necessary to manufacture and assemble all the components of a living organism. However, the wealth of information encoded in DNA often overshadows its unusual physical properties, such as same-charge attraction. In this lecture, I will describe my lab’s efforts to characterize the physical properties of DNA through high-end computer simulations and elucidate their effect on DNA's biological function. The topics to be covered include the spatial organization of genomic DNA inside the nucleus, the inside-out conformational dynamics of DNA and its relation to gene transcription, and the first complete all-atom structure of a fully packaged virus particle. The lecture will illustrate how high-end computer simulations can reveal information inaccessible to current experimental probes and provide a forward-looking perspective on modeling an entire biological cell at the all-atom resolution.