Unique insight into protein-DNA interactions from single molecule atomic force microscopy

Disha Mohan Bangalore; Ingrid Tessmer; Disha Mohan Bangalore; Ingrid Tessmer

doi:10.3934/biophy.2018.3.194

AIMS Biophysics

2018, Volume 5, Issue 3: 194-216. doi: 10.3934/biophy.2018.3.194

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Unique insight into protein-DNA interactions from single molecule atomic force microscopy

Disha Mohan Bangalore ,
Ingrid Tessmer ^,

Rudolf Virchow Center for Experimental Biomedicine, Josef Schneider Str. 2, 97080 Würzburg, Germany

Received: 07 July 2018 Accepted: 17 September 2018 Published: 21 September 2018

Protein-DNA interactions are pivotal for many essential biological processes. Atomic force microscopy (AFM) imaging of protein-DNA systems involved in DNA target site search, identification, and processing by proteins has contributed invaluable information to our understanding of the underlying mechanisms. The single molecule 3D resolution of AFM enables us to uncover stoichiometries and conformational properties of protein-DNA complexes. Its molecular resolution places AFM at the interface between the atomic resolution achievable by crystallography and the comparably poor (typically > hundred nanometers) spatial resolution of optical microscopy. Furthermore, the transient character of protein interactions with nonspecific DNA sites, for example during their target site search renders these complexes difficult to resolve by standard ensemble methods. Here, we review current applications and capabilities of as well as novel advances in AFM imaging in protein-DNA interaction studies.
- atomic force microscopy (AFM),
- protein-DNA interactions,
- single molecule methods
Citation: Disha Mohan Bangalore, Ingrid Tessmer. Unique insight into protein-DNA interactions from single molecule atomic force microscopy[J]. AIMS Biophysics, 2018, 5(3): 194-216. doi: 10.3934/biophy.2018.3.194

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Abstract

Protein-DNA interactions are pivotal for many essential biological processes. Atomic force microscopy (AFM) imaging of protein-DNA systems involved in DNA target site search, identification, and processing by proteins has contributed invaluable information to our understanding of the underlying mechanisms. The single molecule 3D resolution of AFM enables us to uncover stoichiometries and conformational properties of protein-DNA complexes. Its molecular resolution places AFM at the interface between the atomic resolution achievable by crystallography and the comparably poor (typically > hundred nanometers) spatial resolution of optical microscopy. Furthermore, the transient character of protein interactions with nonspecific DNA sites, for example during their target site search renders these complexes difficult to resolve by standard ensemble methods. Here, we review current applications and capabilities of as well as novel advances in AFM imaging in protein-DNA interaction studies.

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