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Beyond Crystallography: Investigating the Conformational Dynamics of the Purine Riboswitch

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Non-Protein Coding RNAs

Part of the book series: Springer Series in Biophysics ((BIOPHYSICS,volume 13))

Riboswitches are structured elements located in the 5′-untranslated regions of numerous bacterial mRNAs that serve to regulate gene expression via their ability to specifically bind metabolites. The purine riboswitch ligand-binding domain has emerged as an important model system for investigating the relationship between RNA structure and function. Directed by NMR and crystallographically generated structures of this RNA, a variety of biophysical and biochemical techniques have been utilized to understand its dynamic nature. In this review, we describe these various approaches and what they reveal about the purine riboswitch.

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Abbreviations

2AP:

2-aminopurine

FRET:

fluorescence resonance energy transfer

J:

joining region

L:

loop

NMIA:

N-methylisatoic anhydride

SHAPE:

selective 2′-hydroxyl acylation analyzed by primer extension

smFRET:

single molecule fluorescence resonance energy transfer

TPP:

thiamine pyrophosphate

UTR:

untranslated region

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Author information

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of Colorado-Boulder, Campus Box 215, Cleveland, CO 80309, USA

    Colby D. Stoddard & Dr. Robert T. Batey

Authors
  1. Colby D. Stoddard
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  2. Dr. Robert T. Batey
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Editor information

Editors and Affiliations

  1. Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI, 48109-1055, USA

    Nils G. Walter (Associate Professor of Chemistry) (Associate Professor of Chemistry)

  2. Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA

    Sarah A. Woodson (Professor of Biophysics) (Professor of Biophysics)

  3. Department of Chemistry and Biochemistry, University of Colorado at Boulder, Box 215, Boulder, CO, 80309-0215, USA

    Robert T. Batey (Associate Professor of Chemistry and Biochemistry) (Associate Professor of Chemistry and Biochemistry)

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Stoddard, C.D., Batey, R.T. (2009). Beyond Crystallography: Investigating the Conformational Dynamics of the Purine Riboswitch. In: Walter, N.G., Woodson, S.A., Batey, R.T. (eds) Non-Protein Coding RNAs. Springer Series in Biophysics, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-70840-7_10

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