Journal
RNA
Volume 19, Issue 3, Pages 357-364Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1261/rna.036657.112
Keywords
k-turn; RNA structure; RNA-protein interaction; SAM-I riboswitch
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Funding
- Cancer Research UK
- EPSRC [EP/J017094/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [B17092] Funding Source: researchfish
- Cancer Research UK [11722] Funding Source: researchfish
- Engineering and Physical Sciences Research Council [EP/J017094/1] Funding Source: researchfish
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The k-turn is a widespread structural motif that introduces a tight kink into the helical axis of double-stranded RNA. The adenine bases of consecutive G.A pairs are directed toward the minor groove of the opposing helix, hydrogen bonding in a typical A-minor interaction. We show here that the available structures of k-turns divide into two classes, depending on whether N3 or N1 of the adenine at the 2b position accepts a hydrogen bond from the O2' at the -1n position. There is a coordinated structural change involving a number of hydrogen bonds between the two classes. We show here that Kt-7 can adopt either the N3 or N1 structures depending on environment. While it has the N1 structure in the ribosome, on engineering it into the SAM-I riboswitch, it changes to the N3 structure, resulting in a significant alteration in the trajectory of the helical arms.
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