Our bodies may never stop surprising us with their complexity and perfect mechanics. In its complexity, there are biological functions which occur out of equilibrium, converting chemical to mechanical energy. Due to the importance of DNA it is imperative to study the biological functions that occur in this macromolecule which involves proteins. This is because proteins can activate indispensable processes such as DNA replication and gene expression. If one immerses into literature related to the mechanics of biological processes there is actually not that much information regarding these systems. Nevertheless, given the importance of these processes it would be interesting to be able to create a model that describes the necessary physical parameters that dominate. DNA chains contain nucleotides which have three groups: a phosphate group, a sugar group and a nitrogenous base. The bases can be identified as adenine, guanine, thymine and cytosine. Even though some models in literature lack completeness in terms of the mechanical description of the polymer, the model presented by Knotts et al., provides a model that takes into account fusion, hybridization and salt effects. The model is based on three sections that describe a nucleotide, accounting for the charges involved in the molecule. It would be interesting to be able to develop a bead-spring model that can represent these groups and be able to replicate these phenomena computationally.
Image represents the idea behind the model proposed.
- Knotts IV, Thomas A., et al. “A coarse grain model for DNA.” The Journal of chemical physics 126.8 (2007): 084901.
- Monico, C., Capitanio, M., Belcastro, G., Vanzi, F., & Pavone, F. S. (2013). Optical methods to study protein-DNA interactions in vitro and in living cells at the single-molecule level. International journal of molecular sciences, 14(2), 3961-3992.