Relevant bibliographies by topics / Hydroxyl radical footprinting (HRF)

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters

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

Author: Grafiati
Published: 14 March 2023
Last updated: 31 July 2025

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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 (2018): 315–33. http://dx.doi.org/10.1146/annurev-biophys-070317-033123.

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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 l
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Carey, M., and S. T. Smale. "Hydroxyl-Radical Footprinting." Cold Spring Harbor Protocols 2007, no. 24 (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 (1988): 663–64. http://dx.doi.org/10.1038/332663a0.

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Leser, Micheal, Jessica R. Chapman, Michelle Khine, et al. "Chemical Generation of Hydroxyl Radical for Oxidative ‘Footprinting’." Protein & Peptide Letters 26, no. 1 (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 appli
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Tullius, Thomas D. "DNA Footprinting with the Hydroxyl Radical." Free Radical Research Communications 13, no. 1 (1991): 521–29. http://dx.doi.org/10.3109/10715769109145826.

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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 (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 (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 (2014): pdb.prot080952. http://dx.doi.org/10.1101/pdb.prot080952.

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Leser, Micheal, Jonathan Pegan, Mohammed El Makkaoui, et al. "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, generate
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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™. 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. 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. 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. 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. 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. 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. 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. Elsevier, 1993. http://dx.doi.org/10.1016/b978-0-12-586500-5.50010-2.

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Kolb, Annie. "Hydroxyl radical footprinting." In DNA-Protein Interactions. Oxford University PressOxford, 2000. http://dx.doi.org/10.1093/oso/9780199636921.003.0012.

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Abstract Hydroxyl radicals have now been used for more than 15years to probe the structure of various macromolecules. They have also been widely used to footprint DNA-protein and RNA-protein complexes (1, 2). Hydroxyl radicals are w1y small, comparable in size to a water molecule, are most commonly generated from FeEDTA in solution by an innocuous and inexpensive procedure (see Protocols 2 and 3) <md are capable of cutting the DNA or RNA backbone at eve1y accessible nucleotide without sequence specificity (3-5). A footprinting reagent in which the .EDTA moiety is coupled to an intercala
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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. Elsevier, 1991. http://dx.doi.org/10.1016/0076-6879(91)08021-9.

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