Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules

Lin Huang (Lead / Corresponding author), Xinli Liao, Mengxiao Li, Jia Wang, Xuemei Peng, Timothy J. Wilson, David M. J. Lilley (Lead / Corresponding author)

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Abstract

k-Turns are widespread key architectural elements that occur in many classes of RNA molecules. We have shown previously that their folding properties (whether or not they fold into their tightly kinked structure on addition of metal ions) and conformation depend on their local sequence, and we have elucidated a series of rules for prediction of these properties from sequence. In this work, we have expanded the rules for prediction of folding properties, and then applied the full set to predict the folding and conformation of four probable k-turns we have identified amongst 224 structured RNA species found in bacterial intergenenic regions by the Breaker lab (1). We have analyzed the ion-dependence of folding of the four k-turns using fluorescence resonance energy transfer, and determined the conformation of two of them using X-ray crystallography. We find that the experimental data fully conform to both the predicted folding and conformational properties. We conclude that our folding rules are robust, and can be applied to new k-turns of unknown characteristics with confidence. [Abstract copyright: © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.]
Original languageEnglish
Pages (from-to)5916-5924
Number of pages9
JournalNucleic Acids Research
Volume49
Issue number10
Early online date12 May 2021
DOIs
Publication statusPublished - 4 Jun 2021

Keywords

  • RNA structure
  • kink-turn
  • RNA folding
  • X-ray crystallography

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