1. Structural Biology and Molecular Biophysics
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Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer

Research Article
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Cite this article as: eLife 2015;4:e12362 doi: 10.7554/eLife.12362

Abstract

The thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in mRNA that modifies gene expression in response to TPP concentration. Its specificity is dependent upon conformational changes that take place within its aptamer domain. Here, the role of tertiary interactions in ligand binding was studied at the single-molecule level by combined force spectroscopy and Förster resonance energy transfer (smFRET), using an optical trap equipped for simultaneous smFRET. The 'Force-FRET' approach directly probes secondary and tertiary structural changes during folding, including events associated with binding. Concurrent transitions observed in smFRET signals and RNA extension revealed differences in helix-arm orientation between two previously-identified ligand-binding states that had been undetectable by spectroscopy alone. Our results show that the weaker binding state is able to bind to TPP, but is unable to form a tertiary docking interaction that completes the binding process. Long-range tertiary interactions stabilize global riboswitch structure and confer increased ligand specificity.

Article and author information

Author details

  1. Van K Duesterberg

    Biophysics Program, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Irena T Fischer-Hwang

    Department of Electrical Engineering, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Christian F Perez

    Department of Physics, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Daniel W Hogan

    Department of Applied Physics, Stanford University, Stanford, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Steven M Block

    Department of Applied Physics, Stanford University, Stanford, United States
    For correspondence
    sblock@stanford.edu
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Antoine M van Oijen, University of Groningen, Netherlands

Publication history

  1. Received: October 16, 2015
  2. Accepted: December 27, 2015
  3. Accepted Manuscript published: December 28, 2015 (version 1)
  4. Version of Record published: February 23, 2016 (version 2)

Copyright

© 2015, Duesterberg et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Further reading

Further reading

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