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Relevant bibliographies by topics / Hydroxyl radical footprinting (HRF)

Academic literature on the topic 'Hydroxyl radical footprinting (HRF)'

Author: Grafiati

Published: 14 March 2023

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Journal articles on the topic "Hydroxyl radical footprinting (HRF)"

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Chea, Emily E., and Lisa M. Jones. "Analyzing the structure of macromolecules in their native cellular environment using hydroxyl radical footprinting." Analyst 143, no. 4 (2018): 798–807. http://dx.doi.org/10.1039/c7an01323j.

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Kiselar, Janna, and Mark R. Chance. "High-Resolution Hydroxyl Radical Protein Footprinting: Biophysics Tool for Drug Discovery." Annual Review of Biophysics 47, no. 1 (May 20, 2018): 315–33. http://dx.doi.org/10.1146/annurev-biophys-070317-033123.

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Abstract:

Hydroxyl radical footprinting (HRF) of proteins with mass spectrometry (MS) is a widespread approach for assessing protein structure. Hydroxyl radicals react with a wide variety of protein side chains, and the ease with which radicals can be generated (by radiolysis or photolysis) has made the approach popular with many laboratories. As some side chains are less reactive and thus cannot be probed, additional specific and nonspecific labeling reagents have been introduced to extend the approach. At the same time, advances in liquid chromatography and MS approaches permit an examination of the labeling of individual residues, transforming the approach to high resolution. Lastly, advances in understanding of the chemistry of the approach have led to the determination of absolute protein topologies from HRF data. Overall, the technology can provide precise and accurate measures of side-chain solvent accessibility in a wide range of interesting and useful contexts for the study of protein structure and dynamics in both academia and industry.

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Carey, M., and S. T. Smale. "Hydroxyl-Radical Footprinting." Cold Spring Harbor Protocols 2007, no. 24 (December 1, 2007): pdb.prot4810. http://dx.doi.org/10.1101/pdb.prot4810.

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Tullius, T. D. "DNA footprinting with hydroxyl radical." Nature 332, no. 6165 (April 1988): 663–64. http://dx.doi.org/10.1038/332663a0.

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Tullius, Thomas D. "DNA Footprinting with the Hydroxyl Radical." Free Radical Research Communications 13, no. 1 (January 1991): 521–29. http://dx.doi.org/10.3109/10715769109145826.

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Leser, Micheal, Jessica R. Chapman, Michelle Khine, Jonathan Pegan, Matt Law, Mohammed El Makkaoui, Beatrix M. Ueberheide, and Michael Brenowitz. "Chemical Generation of Hydroxyl Radical for Oxidative ‘Footprinting’." Protein & Peptide Letters 26, no. 1 (February 13, 2019): 61–69. http://dx.doi.org/10.2174/0929866526666181212164812.

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Background: For almost four decades, hydroxyl radical chemically generated by Fenton chemistry has been a mainstay for the oxidative ‘footprinting’ of macromolecules. Objective: In this article, we start by reviewing the application of chemical generation of hydroxyl radical to the development of oxidative footprinting of DNA and RNA and the subsequent application of the method to oxidative footprinting of proteins. We next discuss a novel strategy for generating hydroxyl radicals by Fenton chemistry that immobilizes catalytic iron on a solid surface (Pyrite Shrink Wrap laminate) for the application of nucleic acid and protein footprinting. Method: Pyrite Shrink-Wrap Laminate is fabricated by depositing pyrite (Fe-S2, aka ‘fool’s gold’) nanocrystals onto thermolabile plastic (Shrinky Dink). The laminate can be thermoformed into a microtiter plate format into which samples are deposited for oxidation. Results: We demonstrate the utility of the Pyrite Shrink-Wrap Laminate for the chemical generation of hydroxyl radicals by mapping the surface of the T-cell co-stimulatory protein Programmed Death – 1 (PD-1) and the interface of the complex with its ligand PD-L1. Conclusion: We have developed and validated an affordable and reliable benchtop method of hydroxyl radical generation that will broaden the application of protein oxidative footprinting. Due to the minimal equipment required to implement this method, it should be easily adaptable by many laboratories with access to mass spectrometry.

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Gerasimova, N. S., and V. M. Studitsky. "Hydroxyl radical footprinting of fluorescently labeled DNA." Moscow University Biological Sciences Bulletin 71, no. 2 (April 2016): 93–96. http://dx.doi.org/10.3103/s0096392516020036.

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Jain, Swapan S., and Thomas D. Tullius. "Footprinting protein–DNA complexes using the hydroxyl radical." Nature Protocols 3, no. 6 (June 2008): 1092–100. http://dx.doi.org/10.1038/nprot.2008.72.

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Nilsen, Timothy W. "Mapping RNA–Protein Interactions Using Hydroxyl-Radical Footprinting." Cold Spring Harbor Protocols 2014, no. 12 (December 2014): pdb.prot080952. http://dx.doi.org/10.1101/pdb.prot080952.

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Leser, Micheal, Jonathan Pegan, Mohammed El Makkaoui, Joerg C. Schlatterer, Michelle Khine, Matt Law, and Michael Brenowitz. "Protein footprinting by pyrite shrink-wrap laminate." Lab on a Chip 15, no. 7 (2015): 1646–50. http://dx.doi.org/10.1039/c4lc01288g.

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Dissertations / Theses on the topic "Hydroxyl radical footprinting (HRF)"

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Asuru, Awuri P. "Applications of X-ray Hydroxyl Radical Protein Footprinting." Case Western Reserve University School of Graduate Studies / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=case1575877091577049.

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Chiang, Cheryl. "Mapping DNA structure & protein-DNA interactions using hydroxyl radical footprinting & high-throughput sequencing." Thesis, 2016. https://hdl.handle.net/2144/17701.

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Development of biochemical techniques to examine chromatin structure and protein-DNA interactions on a global scale has allowed for extensive characterization of functional and regulatory elements essential to cellular biological processes. In particular, chromatin accessibility and susceptibility to damage, coupled with high-throughput sequencing, have served as means for characterizing these elements. To better understand protein occupancy in relation to chromatin architecture, a technique that can impartially probe DNA structure at high resolution is required. The hydroxyl radical, generated from a modified Fenton reaction or ɣ-irradiation of water molecules, is a chemical tool used for probing nucleic acid structure, and capable of mapping protein-DNA binding sites at single-nucleotide resolution. Adapting hydroxyl radical footprinting for analysis by high-throughput sequencing (OH-seq) aims to provide a detailed profile of the chromatin landscape in whole genomes. Initial development of OH-seq was carried out on a model system using synthetic oligonucleotides to mimic a hydroxyl radical damage site. The single-strand break was enzymatically converted to a double-strand break to allow for end-repair and ligation to a sequencing adapter. This dissertation describes the further development of OH-seq in vitro, and the optimization of this technique for application to whole genomes in vivo. To show that OH-seq can successfully map protein-DNA interactions, the technique was tested on the well characterized λ repressor-operator complex. Analyses for sequencing libraries, tagging single- and double-strand breaks created from hydroxyl radical cleavage of plasmid DNA in the absence and presence of λ repressor, show footprints similar to those from previous studies. Application of OH-seq to human and S. cerevisiae genomes captured double-strand breaks in genomic DNA following ɣ-irradiation of cells. Analyses examining the damage profile across aggregated transcription start sites and nucleosome positions in the human genome reveal high damage at promoters, and highly periodic nucleosomal footprints. OH-seq profiles for select transcription factors in yeast show distinct footprints comparable to those from other genome-wide studies. These preliminary results show the potential OH-seq has for characterizing chromatin structure and protein-DNA interactions. Further optimization will make the technique a useful addition to the current repertoire of tools for studying genome structure and function.
2018-08-11T00:00:00Z

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Rogozina, Anastasia [Verfasser]. "The pathway to transcriptionally active Escherichia coli RNAP-T7A1 promoter complex formation : positioning of RNAP at the promoter using X-ray hydroxyl radical footprinting / Anastasia Rogozina." 2009. http://d-nb.info/1000278395/34.

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Books on the topic "Hydroxyl radical footprinting (HRF)"

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Hiley, Shawna Lynn. Structure and folding of the Neurospora VS ribozyme: Hydroxyl radical footprinting and photocrosslinking analyses. 2003.

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Book chapters on the topic "Hydroxyl radical footprinting (HRF)"

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Jagannathan, Indu, and Jeffrey J. Hayes. "Hydroxyl Radical Footprinting of Protein-DNA Complexes." In Methods in Molecular Biology™, 57–71. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-015-1_5.

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Costa, Maria, and Dario Monachello. "Probing RNA Folding by Hydroxyl Radical Footprinting." In Methods in Molecular Biology, 119–42. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-667-2_7.

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Ellis, Michael J., Ryan S. Trussler, Joseph A. Ross, and David B. Haniford. "Probing Hfq:RNA Interactions with Hydroxyl Radical and RNase Footprinting." In Methods in Molecular Biology, 403–15. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-2214-7_24.

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Martin, Joshua S., Paul Mitiguy, and Alain Laederach. "Modeling RNA Folding Pathways and Intermediates Using Time-Resolved Hydroxyl Radical Footprinting Data." In Nucleic Acids and Molecular Biology, 319–34. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-25740-7_15.

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Lai, Stella M., and Venkat Gopalan. "Using an L7Ae-Tethered, Hydroxyl Radical-Mediated Footprinting Strategy to Identify and Validate Kink-Turns in RNAs." In Methods in Molecular Biology, 147–69. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0716-9_9.

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Lai, Stella M., and Venkat Gopalan. "Correction to: Using an L7Ae-Tethered, Hydroxyl Radical-Mediated Footprinting Strategy to Identify and Validate Kink-Turns in RNAs." In Methods in Molecular Biology, C1. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0716-9_17.

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Zhu, Yi, Tiannan Guo, and Siu Kwan Sze. "Elucidating Structural Dynamics of Integral Membrane Proteins on Native Cell Surface by Hydroxyl Radical Footprinting and Nano LC-MS/MS." In Methods in Molecular Biology, 287–303. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-319-6_22.

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BASHKIN, JOHN S., and THOMAS D. TULLIUS. "Hydroxyl Radical Footprinting." In Footprinting of Nucleic Acid-Protein Complexes, 75–106. Elsevier, 1993. http://dx.doi.org/10.1016/b978-0-12-586500-5.50010-2.

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Dixon, Wendy J., Jeffrey J. Hayes, Judith R. Levin, Margaret F. Weidner, Beth A. Dombroski, and Thomas D. Tullius. "[19] Hydroxyl radical footprinting." In Protein \3- DNA Interactions, 380–413. Elsevier, 1991. http://dx.doi.org/10.1016/0076-6879(91)08021-9.

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Shcherbakova, Inna, and Somdeb Mitra. "Hydroxyl-Radical Footprinting to Probe Equilibrium Changes in RNA Tertiary Structure." In Methods in Enzymology, 31–46. Elsevier, 2009. http://dx.doi.org/10.1016/s0076-6879(09)68002-2.

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