Open Access Nano Review

Stretching and immobilization of DNA for studies of protein–DNA interactions at the single-molecule level

JiHoon Kim1, VenkatRam Dukkipati2, Stella W Pang2 and Ronald G Larson1*

Author Affiliations

1 Department of Chemical Engineering, University of Michigan, Ann Arbor, 48109, MI, USA

2 Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, MI, USA

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Nanoscale Research Letters 2007, 2:185-201  doi:10.1007/s11671-007-9057-5

Published: 18 April 2007

Abstract

Single-molecule studies of the interactions of DNA and proteins are important in a variety of biological or biotechnology processes ranging from the protein’s search for its DNA target site, DNA replication, transcription, or repair, and genome sequencing. A critical requirement for single-molecule studies is the stretching and immobilization of otherwise randomly coiled DNA molecules. Several methods for doing so have been developed over the last two decades, including the use of forces derived from light, magnetic and electric fields, and hydrodynamic flow. Here we review the immobilization and stretching mechanisms for several of these techniques along with examples of single-molecule DNA–protein interaction assays that can be performed with each of them.

Keywords:
DNA; Single-molecule; Proteins; DNA–protein interactions