Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples

Ruszkowska, Agnieszka; Ruszkowski, Milosz; Hulewicz, Jacob P.; Dauter, Zbigniew; Brown, Jessica A.

doi:10.1093/nar/gkz1222

Title: Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples

Journal Article · 12 January 2020 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkz1222 · OSTI ID:1582472

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Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL 60439 USA

Three-dimensional structures have been solved for several naturally occurring RNA triple helices, although all are limited to six or fewer consecutive base triples, hindering accurate estimation of global and local structural parameters. We present an X-ray crystal structure of a right-handed, U•A-U-rich RNA triple helix with 11 continuous base triples. Due to helical unwinding, the RNA triple helix spans an average of 12 base triples per turn. The double helix portion of the RNA triple helix is more similar to both the helical and base step structural parameters of A'-RNA rather than A-RNA. Its most striking features are its wide and deep major groove, a smaller inclination angle and all three strands favoring a C3'-endo sugar pucker. Despite the presence of a third strand, the diameter of an RNA triple helix remains nearly identical to those of DNA and RNA double helices. Contrary to our previous modeling predictions, this structure demonstrates that an RNA triple helix is not limited in length to six consecutive base triples and that longer RNA triple helices may exist in nature. Our structure provides a starting point to establish structural parameters of the so-called ‘ideal’ RNA triple helix, analogous to A-RNA and B-DNA double helices.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: National Institutes of Health (NIH); Henry Luce Foundation; National Cancer Institute (NCI); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: W-31109-ENG-38

OSTI ID:: 1582472

Alternate ID(s):: OSTI ID: 1615847

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 6 Vol. 48; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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