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The plasticity of a structural motif in RNA: structural polymorphism of a kink turn as a function of its environment.

ABSTRACT: 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.

SUBMITTER: Daldrop P

PROVIDER: S-EPMC3677246 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature

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The plasticity of a structural motif in RNA: structural polymorphism of a kink turn as a function of its environment.

Daldrop Peter P Lilley David M J DM

RNA (New York, N.Y.) 20130116 3

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 str ...[more]

PMID: 23325110

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