@article{2dae88ec1da74446a5fe9c9801e42c22,
title = "Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting",
abstract = "The assembly of the Escherichia coli ribosome has been widely studied and characterized in vitro. Despite this, ribosome biogenesis in living cells is only partly understood because assembly is coupled with transcription, modification and processing of the pre-ribosomal RNA. We present a method for footprinting and isolating pre-rRNA as it is synthesized in E. coli cells. Pre-rRNA synthesis is synchronized by starvation, followed by nutrient upshift. RNA synthesized during outgrowth is metabolically labeled to facilitate isolation of recent transcripts. Combining this technique with two in vivo RNA probing methods, hydroxyl radical and DMS footprinting, allows the structure of nascent RNA to be probed over time. Together, these can be used to determine changes in the structures of ribosome assembly intermediates as they fold in vivo.",
keywords = "4-Thiouridine, Dimethylsulfate, Hydroxyl radical footprinting, RNA structure, Ribosome assembly, Synchrotron X-ray beamline",
author = "Hulscher, {Ryan M.} and Jen Bohon and Rapp{\'e}, {Mollie C.} and Sayan Gupta and Rhijuta D'Mello and Michael Sullivan and Ralston, {Corie Y.} and Chance, {Mark R.} and Woodson, {Sarah A.}",
note = "Funding Information: The authors thank Donald Abel, Rich Celestre, and John Toomey for technical assistance. This work was supported by a grant from the National Institutes of Health ( R01 GM60819 to S.A.W.). The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The National Synchrotron Light Source, Brookhaven National Laboratory, was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886. The Center for Synchrotron Biosciences at the National Synchrotron Light Sources is supported by NIBIB under P30-EB0966, with research instrumentation development supported by the National Science Foundation under DBI-1228549. Publisher Copyright: {\textcopyright} 2016 Elsevier Inc.",
year = "2016",
month = jul,
day = "1",
doi = "10.1016/j.ymeth.2016.03.012",
language = "English (US)",
volume = "103",
pages = "49--56",
journal = "Methods",
issn = "1046-2023",
publisher = "Academic Press Inc.",
}