A Comprehensive Computational Model to Simulate Transcription Factor Binding in Prokaryotes

摘要

Site specific transcription factors (TF) are proteins that orchestrate transcrip tion by binding to specific target sites on the DNA. This binding can be both sequence- and conformation-specific. However, also non-specific binding with lower affinity can be observed [3]. The number of specific target sites is signifi cantly smaller compared to the number of non-specific sites and, consequently, TF molecules bind, in a first instance, non-specifically to the DNA. Once bound to the DNA the TF molecules perform an one dimensional random walk on the DNA until they either find a target site or unbind from the DNA template. In particular, during the one dimensional random walk on the DNA, a molecule will perform one of the three types of movements: (ⅰ) sliding , (ⅱ) hopping and (ⅲ) jumping [6]. This combination of one and three dimensional diffusion is called facilitated diffusion and it is hypothesised that this speeds up the search process [3,2,5].