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Solution AFM Studies of Human Swi-Snf and Its Interactions with MMTV DNA and Chromatin

H. Wang ^*, R. Bash ^* , S. M. Lindsay ^*   and D. Lohr 

^* Arizona Biodesign Institute, Department of Chemistry and Biochemistry, and Department of Physics and Astronomy, Arizona State University, Tempe, Arizona 85287

Correspondence: Address reprint requests to S. M. Lindsay, Arizona Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601. Tel.: 480-965-4691; Fax: 480-727-2378; E-mail: stuart.lindsay{at}asu.edu.

ATP-dependent nucleosome remodeling complexes are crucial for relieving nucleosome repression during transcription, DNA replication, recombination, and repair. Remodeling complexes can carry out a variety of reactions on chromatin substrates but precisely how they do so remains a topic of active inquiry. Here, a novel recognition atomic force microscopy (AFM) approach is used to characterize human Swi-Snf (hSwi-Snf) nucleosome remodeling complexes in solution. This information is then used to locate hSwi-Snf complexes bound to mouse mammary tumor virus promoter nucleosomal arrays, a natural target of hSwi-Snf action, in solution topographic AFM images of surface-tethered arrays. By comparing the same individual chromatin arrays before and after hSwi-Snf activation, remodeling events on these arrays can be monitored in relation to the complexes bound to them. Remodeling is observed to be: inherently heterogeneous; nonprocessive; able to occur near and far from bound complexes; often associated with nucleosome height decreases. These height decreases frequently occur near sites of DNA release from chromatin. hSwi-Snf is usually incorporated into nucleosomal arrays, with multiple DNA strands entering into it from various directions, + or – ATP; these DNA paths can change after hSwi-Snf activation. hSwi-Snf appears to interact with naked mouse mammary tumor virus DNA somewhat differently than with chromatin and ATP activation of surface-bound DNA/hSwi-Snf produces no changes detectable by AFM.

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