Stretching DNA to quantify non-specific protein binding

• Type of Material: Article
• Authors: Sachin Goyal, Emory University; Chandler Fountain, Emory University; David Dunlap, Emory University; Fereydoon Family, Emory University; Laura Finzi, Emory University
• Language: English
• Date: 2012-07
• Publisher: American Physical Society
• Publication Version: Final Published Version
• Copyright Statement: © 2012 American Physical Society
• Final Published Version (URL): http://pre.aps.org/abstract/PRE/v86/i1/e011905
• Title of Journal or Parent Work: Physical Review E
• ISSN: 1539-3755
• Volume: 86
• Issue: 1
• Start Page: 011905
• End Page: 011905
• Grant/Funding Information: This work was supported by NIH RGM084070A to LF.
• Research Categories: Biology, Cell; Biology, Physiology

Abstract

Non-specific binding of regulatory proteins to DNA can be an important mechanism for target search and storage. This seems to be the case for the lambda repressor protein (CI), which maintains lysogeny after infection of E. coli. CI binds specifically at two distant regions along the viral genome and induces the formation of a repressive DNA loop. However, single-molecule imaging as well as thermodynamic and kinetic measurements of CI-mediated looping show that CI also binds to DNA non-specifically, and that this mode of binding may play an important role in maintaining lysogeny. This paper presents a robust phenomenological approach using a recently developed method based on the partition function, which allows calculation of the number of proteins bound non-specifically to DNA from measurements of the DNA extension as a function of applied force. This approach was used to analyze several cycles of extension and relaxation of λ-DNA performed at several CI concentrations to measure the dissociation constant for non-specific binding of CI (~100 nM), and to obtain the first measurement of the induced DNA compaction (~10%) by CI.