Literature DB >> 19377976

Determining structures of RNA aptamers and riboswitches by X-ray crystallography.

Andrea L Edwards1, Andrew D Garst, Robert T Batey.   

Abstract

Structural biology plays a central role in gaining a full understanding of the myriad roles of RNA in biology. In recent years, innovative approaches in RNA purification and crystallographic methods have lead to the visualization of an increasing number of unique structures, providing new insights into its function at the atomic level. This article presents general protocols which have streamlined the process of obtaining a homogeneous sample of properly folded and active RNA in high concentrations that crystallizes well in the presence of a suitable heavy-atom for phasing. Of particular importance are approaches toward RNA crystallography that include exploring "construct space" as opposed to "condition space". Moreover, development of a highly flexible method for experimentally phasing RNA crystals may open the door to a relatively simple means of solving these structures.

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Year:  2009        PMID: 19377976      PMCID: PMC3156247          DOI: 10.1007/978-1-59745-557-2_9

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  39 in total

1.  Syntheses of RNAs with up to 100 nucleotides containing site-specific 2'-methylseleno labels for use in X-ray crystallography.

Authors:  Claudia Höbartner; Renate Rieder; Christoph Kreutz; Barbara Puffer; Kathrin Lang; Anna Polonskaia; Alexander Serganov; Ronald Micura
Journal:  J Am Chem Soc       Date:  2005-08-31       Impact factor: 15.419

2.  Rapid purification of RNAs using fast performance liquid chromatography (FPLC).

Authors:  Insil Kim; Sean A McKenna; Elisabetta Viani Puglisi; Joseph D Puglisi
Journal:  RNA       Date:  2006-12-18       Impact factor: 4.942

3.  Structure of the S-adenosylmethionine riboswitch regulatory mRNA element.

Authors:  Rebecca K Montange; Robert T Batey
Journal:  Nature       Date:  2006-06-29       Impact factor: 49.962

4.  T7 RNA polymerase produces 5' end heterogeneity during in vitro transcription from certain templates.

Authors:  J A Pleiss; M L Derrick; O C Uhlenbeck
Journal:  RNA       Date:  1998-10       Impact factor: 4.942

5.  Ligand requirements for glmS ribozyme self-cleavage.

Authors:  Tom J McCarthy; Melissa A Plog; Shennen A Floy; Joshua A Jansen; Juliane K Soukup; Garrett A Soukup
Journal:  Chem Biol       Date:  2005-11

6.  The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria.

Authors:  F J Grundy; T M Henkin
Journal:  Mol Microbiol       Date:  1998-11       Impact factor: 3.501

7.  The kink-turn: a new RNA secondary structure motif.

Authors:  D J Klein; T M Schmeing; P B Moore; T A Steitz
Journal:  EMBO J       Date:  2001-08-01       Impact factor: 11.598

8.  A modified procedure for fast purification of T7 RNA polymerase.

Authors:  Y Li; E Wang; Y Wang
Journal:  Protein Expr Purif       Date:  1999-07       Impact factor: 1.650

9.  Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions.

Authors:  Adam Roth; Ali Nahvi; Mark Lee; Inbal Jona; Ronald R Breaker
Journal:  RNA       Date:  2006-02-16       Impact factor: 4.942

10.  Rfam: annotating non-coding RNAs in complete genomes.

Authors:  Sam Griffiths-Jones; Simon Moxon; Mhairi Marshall; Ajay Khanna; Sean R Eddy; Alex Bateman
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

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  23 in total

1.  Basis for ligand discrimination between ON and OFF state riboswitch conformations: the case of the SAM-I riboswitch.

Authors:  Vamsi Krishna Boyapati; Wei Huang; Jessica Spedale; Fareed Aboul-Ela
Journal:  RNA       Date:  2012-04-27       Impact factor: 4.942

2.  Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment.

Authors:  Joseph A Piccirilli; Yelena Koldobskaya
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2011-10-27       Impact factor: 6.237

3.  Structural basis for diversity in the SAM clan of riboswitches.

Authors:  Jeremiah J Trausch; Zhenjiang Xu; Andrea L Edwards; Francis E Reyes; Phillip E Ross; Rob Knight; Robert T Batey
Journal:  Proc Natl Acad Sci U S A       Date:  2014-04-21       Impact factor: 11.205

4.  Structure-guided mutational analysis of gene regulation by the Bacillus subtilis pbuE adenine-responsive riboswitch in a cellular context.

Authors:  Joan G Marcano-Velázquez; Robert T Batey
Journal:  J Biol Chem       Date:  2014-12-30       Impact factor: 5.157

5.  Cobalamin riboswitches exhibit a broad range of ability to discriminate between methylcobalamin and adenosylcobalamin.

Authors:  Jacob T Polaski; Samantha M Webster; James E Johnson; Robert T Batey
Journal:  J Biol Chem       Date:  2017-05-08       Impact factor: 5.157

Review 6.  Advances in methods for native expression and purification of RNA for structural studies.

Authors:  Robert T Batey
Journal:  Curr Opin Struct Biol       Date:  2014-02-28       Impact factor: 6.809

7.  Crystallization and preliminary X-ray diffraction analysis of the barley yellow dwarf virus cap-independent translation element.

Authors:  Jelena J Kraft; Julie A Hoy; W Allen Miller
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-04-21

8.  Soaking Hexammine Cations into RNA Crystals to Obtain Derivatives for Phasing Diffraction Data.

Authors:  Robert T Batey; Jeffrey S Kieft
Journal:  Methods Mol Biol       Date:  2016

9.  Insights into the regulatory landscape of the lysine riboswitch.

Authors:  Andrew D Garst; Ely B Porter; Robert T Batey
Journal:  J Mol Biol       Date:  2012-07-03       Impact factor: 5.469

10.  Divalent Cation Dependence Enhances Dopamine Aptamer Biosensing.

Authors:  Nako Nakatsuka; John M Abendroth; Kyung-Ae Yang; Anne M Andrews
Journal:  ACS Appl Mater Interfaces       Date:  2021-01-07       Impact factor: 9.229

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