Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID.

ABSTRACT: Hydroxyl-radical footprinting (HRF) is a powerful method for probing structures of nucleic acid-protein complexes with single-nucleotide resolution in solution. To tap the full quantitative potential of HRF, we describe a protocol, hydroxyl-radical footprinting interpretation for DNA (HYDROID), to quantify HRF data and integrate them with atomistic structural models. The stages of the HYDROID protocol are extraction of the lane profiles from gel images, quantification of the DNA cleavage frequency at each nucleotide and theoretical estimation of the DNA cleavage frequency from atomistic structural models, followed by comparison of experimental and theoretical results. Example scripts for each step of HRF data analysis and interpretation are provided for several nucleosome systems; they can

SUBMITTER: Shaytan AK 

PROVIDER: S-EPMC6322412 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature