Novel features for identifying A-minors in three-dimensional RNA molecules

Palak Sheth, Miguel Cervantes-Cervantes, Akhila Nagula, Christian Laing, Jason T.L. Wang

Research output: Contribution to journalArticlepeer-review

Abstract

RNA tertiary interactions or tertiary motifs are conserved structural patterns formed by pairwise interactions between nucleotides. They include base-pairing, base-stacking, and base-phosphate interactions. A-minor motifs are the most common tertiary interactions in the large ribosomal subunit. The A-minor motif is a nucleotide triple in which minor groove edges of an adenine base are inserted into the minor groove of neighboring helices, leading to interaction with a stabilizing base pair. We propose here novel features for identifying and predicting A-minor motifs in a given three-dimensional RNA molecule. By utilizing the features together with machine learning algorithms including random forests and support vector machines, we show experimentally that our approach is capable of predicting A-minor motifs in the given RNA molecule effectively, demonstrating the usefulness of the proposed approach. The techniques developed from this work will be useful for molecular biologists and biochemists to analyze RNA tertiary motifs, specifically A-minor interactions.

Original languageEnglish (US)
Pages (from-to)240-245
Number of pages6
JournalComputational Biology and Chemistry
Volume47
DOIs
StatePublished - 2013

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Organic Chemistry
  • Computational Mathematics

Keywords

  • RNA tertiary interactions
  • Tertiary motifs
  • Three-dimensional RNA structure

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