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Related Experiment Video

Updated: Jun 29, 2026

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

Published on: August 27, 2014

How DNA coiling enhances target localization by proteins.

B van den Broek¹, M A Lomholt, S-M J Kalisch

¹Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.

Proceedings of the National Academy of Sciences of the United States of America

|October 8, 2008

Summary

DNA coiling significantly speeds up protein target searching. This facilitated diffusion process, involving DNA-binding proteins like EcoRV, is crucial for rapid genetic processes within cells.

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Area of Science:

Biochemistry
Molecular Biology
Biophysics

Background:

Proteins rapidly locate specific DNA sequences amidst abundant non-specific DNA.
Facilitated diffusion, involving 1D sliding and 3D dissociation/reassociation, is the proposed search mechanism.
The role of DNA conformation in protein search pathways remains largely unexplored.

Purpose of the Study:

To investigate the influence of DNA conformation on the specific association rate of EcoRV restriction enzymes.
To differentiate the contributions of various search pathways, including intersegmental jumping.

Main Methods:

Utilized optical tweezers combined with a rapid buffer exchange system.
Measured EcoRV association times on single DNA molecules as a function of DNA extension.
Analyzed data using an extended facilitated diffusion model.

Main Results:

DNA coiling demonstrably influences the specific association rate of EcoRV restriction enzymes.
Targeting rates nearly doubled when DNA transitioned from an extended to a coiled state, dependent on salt concentration.
Identified that only a subset of enzymes are competent for DNA binding.

Conclusions:

DNA conformation, specifically coiling, plays a significant role in modulating protein-DNA interactions.
Intersegmental jumps are predicted to be a major contributor to target localization speed in cellular environments.
Findings provide insights into the efficiency of genetic processes in crowded cellular conditions.