The shape and stiffness of the DNA
double helix depends on the underlying sequence of base pairs. This allows
to put mechanical cues on genomes that guide the folding of DNA molecules in
cells. Specifically, DNA is wrapped around protein cylinders and the mechanical
cues can direct the positions of the resulting complexes, called nucleosomes.
Using a coarse-grained nucleosome model we were able to recover the well-known
nucleosome sequence preferences (Eslami-Mossallam 2016).
As our model is purely mechanical we can conclude that these sequence preference are mainly mechanical in
nature.
However, DNA carries genetic information, the genes that encode for proteins. Does this mean that
mechanical cues cannot be written on top of genes? We demonstrated that the degeneracy of the genetic
code (64 codons encode for only 20 amino acids) allows to put cues freely on top
of genes (Eslami-Mossallam 2016).
This is an example of multiplexing, as we know it from daily life technology, e.g.
radio channels on the same wire. Speaking of radio channels: this work has been featured at
BBC World Service.
For details check out:
B. Eslami-Mossallam, R. D. Schram, M. Tompitak, J. van Noort and H. Schiessel:
Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach, PLoS ONE
11, e0156905 (2016)
M. Zuiddam, R. Everaers and H. Schiessel:
Physics behind the mechanical nucleosome positioning code, Phys. Rev. E
96, 052412 (2017)
M. Zuiddam and H. Schiessel: Shortest paths through synonymous genomes, Phys. Rev. E
99, 012422 (2019)
