# SWR1_1D_Diffusion_Publication
Codes used to analyze data and generate main figures as seen in manuscript 

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ATP Binding Facilitates Target Search of SWR1 Chromatin Remodeler by Promoting One Dimensional Diffusion on DNA

Claudia C. Carcamo,1Matthew F. Poyton,1Anand Ranjan,2Giho Park,2 Robert K Louder,2Thuc Dzu,2Carl Wu,2**Taekjip Ha1,3*
1 Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. 
2 Johns Hopkins University, Department of Biology, 3400 N Charles St, Baltimore, MD 21218, USA.
3 Howard Hughes Medical Institute, Baltimore, MD 21218, USA. 
*  Corresponding Authors: *tjha@jhu.edu, **wuc@jhu.edu 

Abstract
One-dimensional (1D) target search is a well characterized phenomenon for many DNA binding proteins but is poorly understood for chromatin remodelers. Herein, we characterize the 1D scanning properties of SWR1, a yeast chromatin remodeler that performs histone exchange on +1 nucleosomes adjacent to a nucleosome depleted region (NDR) at promoters. We demonstrate that SWR1 has a kinetic binding preference for DNA of NDR length as opposed to gene-body linker length DNA. Using single and dual color single particle tracking on DNA stretched with optical tweezers, we directly observe SWR1 diffusion on DNA. We found that various factors impact SWR1 scanning, including ATP which promotes diffusion through nucleotide binding rather than ATP hydrolysis.  A DNA binding subunit, Swc2, plays an important role in the overall diffusive behavior of the complex, as the subunit in isolation retains similar, although faster, scanning properties as the whole remodeler.  ATP-bound SWR1 slides until it encounters a protein roadblock, of which we tested dCas9 and nucleosomes. The median diffusion coefficient, 0.024 μm2/sec, in the regime of helical sliding, would mediate rapid encounter of NDR-flanking nucleosomes at length scales found in cells.