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

Шайтан, А.К.; Xiao, H.; Армеев, Г.А.; Gaykalova, D.A.; Комарова, Г.А.; Carl, W.; Студитский, В.М.; Landsman, D.; Panchenko, A.R.

Авторы: Шайтан А.К., Xiao H., Армеев Г.А., Gaykalova D.A., Комарова Г.А., Carl Wu, Студитский В.М., Landsman D., Panchenko A.R.
Журнал: Nature Protocols
Том: 13
Номер: 1
Год издания: 2018
Издательство: Nature Publishing Group
Местоположение издательства: United Kingdom
Первая страница: 2535
Последняя страница: 2556
DOI: 10.1038/s41596-018-0048-z
Аннотация: Hydroxyl-radical footprinting (HRF) is a powerful method to probe 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 it with atomistic structural models. The stages of the HYDROID protocol include extraction of the lane profiles from gel images, quantification of the DNA cleavage frequency at every nucleotide, and theoretical estimation of the DNA cleavage frequency from atomistic structural models followed by comparison of experimental and theoretical results. Example scripts for every step of HRF data analysis and interpretation are provided for several nucleosome systems; they can be easily adapted to analyze user data. As input HYDROID requires polyacrylamide gel electrophoresis images of HRF products and optionally may use a molecular model of the DNA-protein complex. The HYDROID protocol can be used to quantify HRF over DNA regions of up to 100 nucleotides per gel image. In addition it can be applied to the analysis of RNA-protein complexes and free RNA or DNA molecules in solution. Compared to other methods, HYDROID is unique in its ability to simultaneously integrate HRF data with the analysis of atomistic structural models. HYDROID is freely available at https://github.com/ncbi/HYDROID. The complete protocol takes approximately ~ 3 hours. Users should be familiar with the command line interface, the Python scripting language and PDB file formats. A graphical user interface with basic functionality (HYDROID_GUI) is also available.
Добавил в систему: Шайтан Алексей Константинович

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

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