Novel features for identifying A-minors in three-dimensional RNA molecules |
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| Institution: | 1. Bioinformatics Program, New Jersey Institute of Technology, Newark, NJ 07102, USA;2. Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA;3. Departments of Biology, Mathematics and Computer Science, Wilkes University, Wilkes-Barre, PA 18766, USA;4. Computer Science Department, New Jersey Institute of Technology, Newark, NJ 07102, USA;1. Plant Physiology Laboratory, Federal University of Pernambuco, Department of Botany, Recife, PE 50670901, Brazil;2. Plant Physiology Laboratory, Federal University of Alagoas, Maceió, AL, Brazil;3. Department of Chemistry, Federal Rural University of Pernambuco, Recife, PE, Brazil;1. Department of Education Administration, Mayo Clinic, Rochester, MN, United States;2. Department of Nursing, Mayo Clinic, Rochester, MN, United States;3. Division of General Internal Medicine, Mayo Clinic, Rochester, MN, United States;1. Department of Chemistry, Bhaskaracharya College of Applied Sciences (University of Delhi), Sector-2, Dwarka, New Delhi, 110075, India;2. Present Address: Institut de La Matie''re Condense et des Nanosciences (IMCN), Universite’ Catholique de Louvain (UCL), Place Louis Pasteur 1, 1348, Louvain-la-Neuve, Belgium;3. Rudraksh Proudhyogiki Sangathan, Delhi, India;1. WSP Analysis and Strategy, Arenavägen 7, 121 77 Johanneshov, Sweden;2. Transport Analysis, Rosenlundsgatan 54, 118 63 Stockholm, Sweden;1. Kazan Federal University, Institute of Chemistry, Kremlevskaya Str. 18, 420008 Kazan, Russia;2. Jan Długosz University, Faculty of Science and Technology, al. Armii Krajowej 13/15, 42-200 Częstochowa, Poland |
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| 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. |
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| Keywords: | RNA tertiary interactions Tertiary motifs Three-dimensional RNA structure |
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