Using competition assays to quantitatively model cooperative binding by transcription factors and other ligands.

ABSTRACT:

Background

The affinities of DNA binding proteins for target sites can be used to model the regulation of gene expression. These proteins can bind to DNA cooperatively, strongly impacting their affinity and specificity. However, current methods for measuring cooperativity do not provide the means to accurately predict binding behavior over a wide range of concentrations.

Methods

We use standard computational and mathematical methods, and develop novel methods as described in Results.

Results

We explore some complexities of cooperative binding, and develop an improved method for relating in vitro measurements to in vivo function, based on ternary complex formation. We derive expressions for the equilibria among the various complexes, and explore the limitations of bind

SUBMITTER: Peacock J 

PROVIDER: S-EPMC5623634 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature