Date of Award
5-2025
Document Type
Thesis
Degree Name
Master of Science (MS)
Department
Mathematical Sciences
Committee Member
Keisha Cook (Co-Advisor)
Committee Member
Matthew Macauley (Co-Advisor)
Committee Member
Jennifer Mason
Abstract
DNA can be damaged through both internal and external sources. Therefore, cells have created methods to repair DNA damage. In Escherichia coli, the system responsible for DNA repair is termed the SOS response. This system consists of more than 50 genes and contains three main repair pathways: nucleotide excision repair, translesion synthesis, and homologous recombination. The response is initiated when DNA lesions result in the accumulation of single-stranded DNA (ssDNA). The protein RecA is activated by binding to ssDNA and is then denoted RecA*. RecA* assists in the auto-cleavage of LexA which is the primary repressor protein involved in the SOS system. Inactivation of LexA allows for the transcription of operons, such as umuDC, uvrAB, recX, recN, recX, lexA, dinI, and yebG. In this study, we model the behavior of these genes and their gene products during the SOS response using a stochastic model and a Boolean model. In the stochastic model, we observe oscillations in some of the components of the system as well as two distinct responses: one in which DNA is repaired and the other where DNA is not repaired within 330 minutes. We find that the Boolean model exhibits two fixed points when the SOS system is induced which also suggests an oscillatory behavior and/or bistability. We hypothesize that these observations are due to 1) stalling/restarting the replication fork and 2) proteins inhibiting RecA*. In comparing our model to previous experimental results, we observe that it matches these data.
Recommended Citation
Ivey, Gabrianne, "Modeling DNA repair in Escherichia coli using a Boolean and Stochastic Framework" (2025). All Theses. 4470.
https://open.clemson.edu/all_theses/4470
Author ORCID Identifier
https://orcid.org/0000-0002-1618-9587