Next Article in Journal
Structure–Activity Relationship and Molecular Docking of Natural Product Library Reveal Chrysin as a Novel Dipeptidyl Peptidase-4 (DPP-4) Inhibitor: An Integrated In Silico and In Vitro Study
Next Article in Special Issue
Detection of Protein Complexes Based on Penalized Matrix Decomposition in a Sparse Protein–Protein Interaction Network
Previous Article in Journal
Bactericidal Properties of Plants-Derived Metal and Metal Oxide Nanoparticles (NPs)
Previous Article in Special Issue
Small Universal Bacteria and Plasmid Computing Systems
Article Menu
Issue 6 (June) cover image

Export Article

Open AccessArticle
Molecules 2018, 23(6), 1367;

Discovering Structural Motifs in miRNA Precursors from the Viridiplantae Kingdom

Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
Author to whom correspondence should be addressed.
Received: 29 April 2018 / Revised: 1 June 2018 / Accepted: 4 June 2018 / Published: 6 June 2018
(This article belongs to the Special Issue Molecular Computing and Bioinformatics)
Full-Text   |   PDF [1654 KB, uploaded 6 June 2018]   |  


A small non-coding molecule of microRNA (19–24 nt) controls almost every biological process, including cellular and physiological, of various organisms’ lives. The amount of microRNA (miRNA) produced within an organism is highly correlated to the organism’s key processes, and determines whether the system works properly or not. A crucial factor in plant biogenesis of miRNA is the Dicer Like 1 (DCL1) enzyme. Its responsibility is to perform the cleavages in the miRNA maturation process. Despite everything we already know about the last phase of plant miRNA creation, recognition of miRNA by DCL1 in pre-miRNA structures of plants remains an enigma. Herein, we present a bioinformatic procedure we have followed to discover structure patterns that could guide DCL1 to perform a cleavage in front of or behind an miRNA:miRNA* duplex. The patterns in the closest vicinity of microRNA are searched, within pre-miRNA sequences, as well as secondary and tertiary structures. The dataset consists of structures of plant pre-miRNA from the Viridiplantae kingdom. The results confirm our previous observations based on Arabidopsis thaliana precursor analysis. Hereby, our hypothesis was tested on pre-miRNAs, collected from the miRBase database to show secondary structure patterns of small symmetric internal loops 1-1 and 2-2 at a 1–10 nt distance from the miRNA:miRNA* duplex. View Full-Text
Keywords: miRNA biogenesis; structural patterns; DCL1 miRNA biogenesis; structural patterns; DCL1

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary material


Share & Cite This Article

MDPI and ACS Style

Miskiewicz, J.; Szachniuk, M. Discovering Structural Motifs in miRNA Precursors from the Viridiplantae Kingdom. Molecules 2018, 23, 1367.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics



[Return to top]
Molecules EISSN 1420-3049 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top