Within the nucleus of each cell lies DNA � an unfathomably long, twisted, and intricately coiled molecule � segments of which make up the genes that provide the instructions that a cell needs to operate. How a cell stores the genetic information inside the nucleus is complicated by the necessity of maintaining accessibility to DNA for genetic processing. In order to gain insight into the roles played by both DNA and proteins in reading and compacting the genome, our group has developed new computational methodologies to take account of the sequence-dependent structural and energetic features of DNA and to simulate the dynamic, three-dimensional configurations of long, fluctuating, protein-decorated strands of DNA. Our coarse-grained approach allows us to determine the effects of nucleotide sequence, individual proteins, and their chemical modifications on overall genomic structure and function. The talk will focus on our recent treatment of the communication between proteins attached to precisely constructed stretches of DNA and chromatin. Our simulations account for the enhancement in communication detected experimentally as well as the critical roles played by electrostatic interactions in this signaling. The molecular states captured in the simulations offer new insights into the ways that the DNA and various proteins contribute to long-range communication along the genome.

Insights into DNA packaging and gene expression revealed from computer simulation

246th National Meeting (2013)

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