Model of DNA dynamics and replication

Abstract

Before DNA replication can be initiated a definite number of adenosine triphosphate (ATP) containing pre-replication protein complexes (pre-RCs) must be assembled and bound to DNA like in a super-critical mass. A chemically driven dynamics of the Ginzburg-Landau (GL) type is derived, using the non-equilibrium equation for binding of pre-RCs to DNA and a probabilistic conformational distribution of these protein complexes. This dynamics, in which the DNA-protein system behaves like a nonlinear elastically braced string (NEBS), can control the cell cycle via conformational transitions such that G(2) cells contain exactly twice as much DNA as G(1) cells. After adjustment of previously-made derivations, the model is compared with cell growth data from the T lymphocyte MLA-144.

Keywords: DNA compaction; DNA condensation; DNA conformation; DNA dynamics; DNA folding; DNA packing; DNA replication; Ginzburg-Landau model; cell cycle regulation; commitment; elastically braced string; initiation; initiator protein assembly; non-equilibrium dynamics; origin recognition; pre-replication complex; reaction coordinate; termination.