Theoretical and Computational Modeling of Target-Site Search Kinetics In Vitro and In Vivo

• Published in: Biophysical journal Vol. 101; no. 4; pp. 856 - 865
• Main Authors: Koslover, Elena F., Díaz de la Rosa, Mario A., Spakowitz, Andrew J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 17.08.2011; Biophysical Society; The Biophysical Society
• Subjects: Binding sites; Biophysics; Computer Simulation; Deoxyribonucleic acid; Diffusion; DNA; DNA - chemistry; DNA - metabolism; DNA-binding proteins; DNA-Binding Proteins - metabolism; Escherichia coli - metabolism; Escherichia coli Proteins - metabolism; Facilitated Diffusion; genome; Genomes; in vitro studies; Kinetics; Lac Repressors - metabolism; Models, Molecular; Nucleic Acid; Nucleic Acid Conformation; Proteins; Time Factors; transcription factors
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/j.bpj.2011.06.066

Access to genetically encoded data depends on the dynamics of DNA-binding proteins searching for specific target sites in the genome. This search process is thought to occur by facilitated diffusion—a combination of three-dimensional diffusion and one-dimensional sliding. Although facilitated diffusion is capable of significantly speeding up the search in vitro, the importance of this mechanism in vivo remains unclear. We use numeric simulations and analytical theory to model the target-search dynamics of DNA-binding proteins under a wide range of conditions. Our models reproduce experimental measurements of search-rate enhancement within bulk in vitro experiments, as well as the target search time for transcription factors measured in vivo. We find that facilitated diffusion can accelerate the search process only for a limited range of parameters and only under dilute DNA conditions. We address the role of DNA configuration and confinement, demonstrating that facilitated diffusion does not speed up the search on coiled versus straight DNA. Furthermore, we show that, under in vivo conditions, the search process becomes effectively diffusive and is independent of DNA configuration. We believe our results cast in a new light the role of facilitated diffusion in DNA targeting kinetics within the cell.