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. 2013 Apr 27;41(12):6045–6057. doi: 10.1093/nar/gkt324

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© The Author(s) 2013. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — Modeling C-dependent RM systems. (A) Core circuit, generalized for C-dependent systems. In this initial model, C and R are combined (as R) since, in virtually all known C-dependent systems, they are cotranscribed. Chromosomal DNA is represented as P (Protectively methylated) U (Unprotected) and Q (cleaved). Other variables are defined on the left of the figure. N represents nucleotide pools (NTPs and dNTPs, as appropriate), whereas A represents aminoacyl-tRNA pools. (B, C) Simulations were carried out at two different fixed values of phi (gene copy number): B = 11 copies, C = 8 copies.