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Research Article

High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

  • Kevin A Wilkinson,

    Affiliation: Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America

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  • Robert J Gorelick,

    Affiliation: AIDS Vaccine Program, SAIC-Frederick, National Cancer Institute-Fredrick, Frederick, Maryland, United States of America

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  • Suzy M Vasa,

    Affiliation: Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina, United States of America

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  • Nicolas Guex,

    Affiliation: Swiss Institute of Bioinformatics, Lausanne, Switzerland

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  • Alan Rein,

    Affiliation: HIV Drug Resistance Program, National Cancer Institute-Fredrick, Frederick, Maryland, United States of America

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  • David H Mathews,

    Affiliation: Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, United States of America

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  • Morgan C Giddings,

    Affiliations: Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina, United States of America, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America, Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina, United States of America

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  • Kevin M Weeks mail

    To whom correspondence should be addressed. E-mail: weeks@unc.edu

    Affiliation: Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America

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  • Published: April 29, 2008
  • DOI: 10.1371/journal.pbio.0060096

About the Authors

Kevin A Wilkinson, Kevin M Weeks
Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
Robert J Gorelick
AIDS Vaccine Program, SAIC-Frederick, National Cancer Institute-Fredrick, Frederick, Maryland, United States of America
Suzy M Vasa, Morgan C Giddings
Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina, United States of America
Nicolas Guex
Swiss Institute of Bioinformatics, Lausanne, Switzerland
Alan Rein
HIV Drug Resistance Program, National Cancer Institute-Fredrick, Frederick, Maryland, United States of America
David H Mathews
Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, United States of America
Morgan C Giddings
Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, United States of America
Morgan C Giddings
Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina, United States of America

Corresponding Author

Email: weeks@unc.edu

Competing Interests

KAW, SMV, NG, MCG and KMW have applied for a patent related to some of the technology described in this work.

Author Contributions

KAW, RJG, AR, and KMW conceived and designed the experiments. KAW and RJG performed the experiments. KAW, SMV, and KMW analyzed the data. RJG, SMV, NG, DHM, and MCG contributed materials and analysis tools. KAW and KMW wrote the paper with contributions from RJG, SMV, NG, AR, DHM, and MCG.