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

Abstract

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.

Authors:
ORCiD logo [1]; ORCiD logo [2];  [1]; ORCiD logo [2]; ORCiD logo [1]
  1. Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
  2. Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL 60439 USA
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH); Henry Luce Foundation; National Cancer Institute (NCI); USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1582472
Alternate Identifier(s):
OSTI ID: 1615847
Grant/Contract Number:  
R00GM111430; W-31-109-Eng-38
Resource Type:
Published Article
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Name: Nucleic Acids Research Journal Volume: 48 Journal Issue: 6; Journal ID: ISSN 0305-1048
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Ruszkowska, Agnieszka, Ruszkowski, Milosz, Hulewicz, Jacob P., Dauter, Zbigniew, and Brown, Jessica A. Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples. United Kingdom: N. p., 2020. Web. doi:10.1093/nar/gkz1222.
Ruszkowska, Agnieszka, Ruszkowski, Milosz, Hulewicz, Jacob P., Dauter, Zbigniew, & Brown, Jessica A. Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples. United Kingdom. doi:10.1093/nar/gkz1222.
Ruszkowska, Agnieszka, Ruszkowski, Milosz, Hulewicz, Jacob P., Dauter, Zbigniew, and Brown, Jessica A. Mon . "Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples". United Kingdom. doi:10.1093/nar/gkz1222.
@article{osti_1582472,
title = {Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples},
author = {Ruszkowska, Agnieszka and Ruszkowski, Milosz and Hulewicz, Jacob P. and Dauter, Zbigniew and Brown, Jessica A.},
abstractNote = {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.},
doi = {10.1093/nar/gkz1222},
journal = {Nucleic Acids Research},
number = 6,
volume = 48,
place = {United Kingdom},
year = {2020},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1093/nar/gkz1222

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Cited by: 1 work
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