Literature DB >> 29927103

Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays.

Yumeng Hao1, Jen Bohon2, Ryan Hulscher1, Mollie C Rappé1, Sayan Gupta3, Tadepalli Adilakshmi1, Sarah A Woodson1.   

Abstract

RNA footprinting by hydroxyl radical cleavage provides 'snapshots' of RNA tertiary structure or protein interactions that bury the RNA backbone. Generation of hydroxyl radicals with a high-flux synchrotron X-ray beam provides analysis on a short timescale (5-100 msec), which enables the structures of folding intermediates or other transient conformational states to be determined in biochemical solutions or cells. This article provides protocols for using synchrotron beamlines for hydroxyl radical footprinting.
© 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

Entities:  

Keywords:  RNA structure probing; hydroxyl radical footprinting; time-resolved footprinting

Mesh：

Substances：

Year:  2018        PMID： 29927103      PMCID： PMC6057793          DOI： 10.1002/cpnc.52

Source DB:  PubMed          Journal:  Curr Protoc Nucleic Acid Chem        ISSN： 1934-9270


  36 in total

1.  Hydroxyl radical footprinting.

Authors:  W J Dixon; J J Hayes; J R Levin; M F Weidner; B A Dombroski; T D Tullius
Journal:  Methods Enzymol       Date:  1991       Impact factor: 1.600

2.  Hydroxyl radical "footprinting": high-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein.

Authors:  T D Tullius; B A Dombroski
Journal:  Proc Natl Acad Sci U S A       Date:  1986-08       Impact factor: 11.205

3.  Synchrotron X-ray footprinting on tour.

Authors:  Jen Bohon; Rhijuta D'Mello; Corie Ralston; Sayan Gupta; Mark R Chance
Journal:  J Synchrotron Radiat       Date:  2013-11-02       Impact factor: 2.616

4.  Iron(II)-ethylenediaminetetraacetic acid catalyzed cleavage of RNA and DNA oligonucleotides: similar reactivity toward single- and double-stranded forms.

Authors:  D W Celander; T R Cech
Journal:  Biochemistry       Date:  1990-02-13       Impact factor: 3.162

5.  Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting.

Authors:  Ryan M Hulscher; Jen Bohon; Mollie C Rappé; Sayan Gupta; Rhijuta D'Mello; Michael Sullivan; Corie Y Ralston; Mark R Chance; Sarah A Woodson
Journal:  Methods       Date:  2016-03-22       Impact factor: 3.608

6.  SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments.

Authors:  Rhiju Das; Alain Laederach; Samuel M Pearlman; Daniel Herschlag; Russ B Altman
Journal:  RNA       Date:  2005-03       Impact factor: 4.942

7.  DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone.

Authors:  B Balasubramanian; W K Pogozelski; T D Tullius
Journal:  Proc Natl Acad Sci U S A       Date:  1998-08-18       Impact factor: 11.205

8.  Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly.

Authors:  Tadepalli Adilakshmi; Deepti L Bellur; Sarah A Woodson
Journal:  Nature       Date:  2008-09-10       Impact factor: 49.962

9.  DNA conformational changes associated with the cooperative binding of cI-repressor of bacteriophage lambda to OR.

Authors:  D Strahs; M Brenowitz
Journal:  J Mol Biol       Date:  1994-12-16       Impact factor: 5.469

10.  'Footprinting' proteins on DNA with peroxonitrous acid.

Authors:  P A King; E Jamison; D Strahs; V E Anderson; M Brenowitz
Journal:  Nucleic Acids Res       Date:  1993-05-25       Impact factor: 16.971
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  3 in total

1.  Evolution of a virus-like architecture and packaging mechanism in a repurposed bacterial protein.

Authors:  Stephan Tetter; Naohiro Terasaka; Angela Steinauer; Richard J Bingham; Sam Clark; Andrew J P Scott; Nikesh Patel; Marc Leibundgut; Emma Wroblewski; Nenad Ban; Peter G Stockley; Reidun Twarock; Donald Hilvert
Journal:  Science       Date:  2021-06-11       Impact factor: 47.728

2.  Role of Era in assembly and homeostasis of the ribosomal small subunit.

Authors:  Aida Razi; Joseph H Davis; Yumeng Hao; Dushyant Jahagirdar; Brett Thurlow; Kaustuv Basu; Nikhil Jain; Josue Gomez-Blanco; Robert A Britton; Javier Vargas; Alba Guarné; Sarah A Woodson; James R Williamson; Joaquin Ortega
Journal:  Nucleic Acids Res       Date:  2019-09-05       Impact factor: 16.971

Review 3.  Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy.

Authors:  Huaqun Zhang; Sarah C Keane
Journal:  Wiley Interdiscip Rev RNA       Date:  2019-04-25       Impact factor: 9.957
  3 in total

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