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A Packing-Density Metric for Exploring the Interior of Folded RNA Molecules

Authors

  • Jason P. Schwans,

    1. Howard Hughes Medical Institute, The University of Chicago, Department of Biochemistry and Molecular Biology and Department of Chemistry, 5841 S. Maryland Avenue, MC1028, Chicago, Il 60637, USA, Fax: (+1) 773-702-0271
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  • Nan-Sheng Li,

    1. Howard Hughes Medical Institute, The University of Chicago, Department of Biochemistry and Molecular Biology and Department of Chemistry, 5841 S. Maryland Avenue, MC1028, Chicago, Il 60637, USA, Fax: (+1) 773-702-0271
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  • Joseph A. Piccirilli Prof.

    1. Howard Hughes Medical Institute, The University of Chicago, Department of Biochemistry and Molecular Biology and Department of Chemistry, 5841 S. Maryland Avenue, MC1028, Chicago, Il 60637, USA, Fax: (+1) 773-702-0271
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  • We thank Rui Sousa for the gift of the Y639F T7 RNA polymerase plasmid, Kara Juneau and Tom Cech for the ΔC209 P4-P6 plasmid, Cecilia Cortez and Shirshendu Deb for assistance with nucleoside synthesis, Joe Olvera for technical assistance, and Cheryl Small for assistance with manuscript preparation. We also thank members of the Piccirilli group and the reviewers for their comments on the manuscript. N.S.L. is a Research Specialist, and J.A.P. is an Associate Investigator of the Howard Hughes Medical Institute.

Abstract

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Die komplizierten Architekturen von RNA-Molekülen weisen häufig ausgedehnte dicht gepackte Kontaktflächen auf. Die Faltung der gut definierten P4-P6-RNA-Domäne wurde mithilfe einer Reihe von 2′-modifizierten Nucleotiden mit ähnlichen Molekülvolumina gestört. Die dabei erhaltenen Faltungsinterferenzen (siehe Bild) spiegeln die räumliche Umgebung der 2′-Hydroxygruppen wider und definieren damit ein Maß für die Packungsdichte.

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