How to Read and Write Mechanical Information in DNA Molecules

Abstract

DNA molecules contain a second layer of information on top of the classical genetic information. This second layer is geometrical/mechanical in nature and guides the folding of DNA molecules inside cells. With the help of a new Monte Carlo technique, Mutation Monte Carlo, we demonstrate that the two information layers can be multiplexed (as one can have two phone conversations on the same wire). This allows, for instance, to guide on top of genes the packaging of DNA into nucleosomes with single base-pair precision. By mapping our model onto a probabilistic model we achieve a speed-up that allows for genome-wide calculations. I will show results for genome-wide multiplexing for baker's yeast. In addition, genome wide studies of DNA mechanics for 50 different organisms taught us a simple general rule: around transcription start sites DNA is stiff for unicellular life and soft for multicellular life. The reason for this difference is surprising.