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Semin Cell Dev Biol. 2018 Jan;73:220-230. doi: 10.1016/j.semcdb.2017.06.028. Epub 2017 Jun 30.

Studying protein-DNA interactions using atomic force microscopy.

Author information

1
Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA.
2
Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA. Electronic address: vanhoutenb@upmc.edu.

Abstract

Atomic force microscopy (AFM) has made significant contributions to the study of protein-DNA interactions by making it possible to topographically image biological samples. A single protein-DNA binding reaction imaged by AFM can reveal protein binding specificity and affinity, protein-induced DNA bending, and protein binding stoichiometry. Changes in DNA structure, complex conformation, and cooperativity, can also be analyzed. In this review we highlight some important examples in the literature and discuss the advantages and limitations of these measurements. We also discuss important advances in technology that will facilitate the progress of AFM in the future.

KEYWORDS:

Atomic force microscopy; Binding specificity; DNA bending; Protein-DNA interaction; Stoichiometry

PMID:
28673677
PMCID:
PMC5762137
DOI:
10.1016/j.semcdb.2017.06.028
[Indexed for MEDLINE]
Free PMC Article

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