Biology – Quantitative Biology – Biomolecules
Scientific paper
2007-08-08
Nucleic Acids Res. 2008 May 3
Biology
Quantitative Biology
Biomolecules
16 pages, 4 figures
Scientific paper
10.1093/nar/gkn173
Strong experimental and theoretical evidence shows that transcription factors and other specific DNA-binding proteins find their sites using a two-mode search: alternating between 3D diffusion through the cell and 1D sliding along the DNA. We consider the role spatial effects in the mechanism on two different scales. First, we reconcile recent experimental findings by showing that the 3D diffusion of the transcription factor is often local, i.e. the transcription factor lands quite near its dissociation site. Second, we discriminate between two types of searches: global searches and local searches. We show that these searches differ significantly in average search time and the variability of search time. Using experimentally measured parameter values, we also show that 1D and 3D search is not optimally balanced, leading to much larger estimates of search time. Together, these results lead to a number of biological implications including suggestions of how prokaryotes and eukaryotes achieve rapid gene regulation and the relationship between the search mechanism and noise in gene expression.
Mirny Leonid A.
Wunderlich Zeba
No associations
LandOfFree
Spatial effects on the speed and reliability of protein-DNA search does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with Spatial effects on the speed and reliability of protein-DNA search, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Spatial effects on the speed and reliability of protein-DNA search will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-215902