A quasi-cyclic RNA nano-scale molecular object constructed using kink turns

Lin Huang, David M. J. Lilley (Lead / Corresponding author)

Research output: Contribution to journalArticle

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118 Downloads (Pure)

Abstract

k-Turns are widespread RNA architectural elements that mediate tertiary interactions. We describe a double-kink-turn motif comprising two inverted k-turns that forms a tight horse-shoe structure that can assemble into a variety of shapes by coaxial association of helical ends. Using X-ray crystallography we show that these assemble with two (dumbell), three (triangle) and four units (square), with or without bound protein, within the crystal lattice. In addition, exchange of a single basepair can almost double the pore radius or shape of a molecular assembly. On the basis of this analysis we synthesized a 114 nt self-complementary RNA containing six k-turns. The crystal structure of this species shows that it forms a quasi-cyclic triangular object. These are randomly disposed about the three-fold axis in the crystal lattice, generating a circular RNA of quasi D3 symmetry with a shape reminiscent of that of a cyclohexane molecule in its chair conformation. This work demonstrates that the k-turn is a powerful building block in the construction of nano-scale molecular objects, and illustrates why k-turns are widely used in natural RNA molecules to organize long-range architecture and mediate tertiary contacts.

Original languageEnglish
Pages (from-to)15189-15195
Number of pages7
JournalNanoscale
Volume8
Issue number33
Early online date10 Aug 2016
DOIs
Publication statusPublished - 7 Sep 2016

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RNA
Crystal lattices
Complementary RNA
Molecules
X ray crystallography
Conformations
Crystal structure
Association reactions
Cyclohexane
Proteins
circular RNA

Cite this

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A quasi-cyclic RNA nano-scale molecular object constructed using kink turns. / Huang, Lin; Lilley, David M. J. (Lead / Corresponding author).

In: Nanoscale, Vol. 8, No. 33, 07.09.2016, p. 15189-15195.

Research output: Contribution to journalArticle

TY - JOUR

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AU - Lilley, David M. J.

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AB - k-Turns are widespread RNA architectural elements that mediate tertiary interactions. We describe a double-kink-turn motif comprising two inverted k-turns that forms a tight horse-shoe structure that can assemble into a variety of shapes by coaxial association of helical ends. Using X-ray crystallography we show that these assemble with two (dumbell), three (triangle) and four units (square), with or without bound protein, within the crystal lattice. In addition, exchange of a single basepair can almost double the pore radius or shape of a molecular assembly. On the basis of this analysis we synthesized a 114 nt self-complementary RNA containing six k-turns. The crystal structure of this species shows that it forms a quasi-cyclic triangular object. These are randomly disposed about the three-fold axis in the crystal lattice, generating a circular RNA of quasi D3 symmetry with a shape reminiscent of that of a cyclohexane molecule in its chair conformation. This work demonstrates that the k-turn is a powerful building block in the construction of nano-scale molecular objects, and illustrates why k-turns are widely used in natural RNA molecules to organize long-range architecture and mediate tertiary contacts.

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