AFM Visualization of Protein–DNA Interactions
This chapter outlines the advances in AFM technology in studies of various types of protein–DNA complexes. The sample preparation methods are briefly described and recommendations for the selection of the appropriate methodology are provided. Studies of sequence-specific and non-sequence-specific DNA-binding proteins are limited to a few examples with a focus on recent publications. The AFM studies of complexes of DNA with architectural proteins are limited to SSB protein and chromatin. Special attention is given to time-lapse AFM imaging in aqueous solutions that enables direct observation of protein–DNA dynamics and interactions. A few examples of the application of time-lapse high-speed AFM are provided as well.
KeywordsAtomic Force Microscopy Atomic Force Microscopy Analysis Atomic Force Microscopy Study Architectural Protein Nucleosome Core Particle
I am grateful to Luda Shlyakhtenko for valuable comments and critical reading of the manuscript, and current and former members of the group for their contribution to works incorporated into the manuscript. The work was supported by grants from National Institutes of Health Grants (1P01GM091743-01A1 and 1 R01 GM096039-01A1), US Department of Energy (DE-FG02-08ER64579), National Science Foundation (EPS – 1004094), and Nebraska Research Initiative grant to Y.L.L.
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