Mariusz Popenda1, Joanna Miskiewicz2, Joanna Sarzynska1, Tomasz Zok2,3, Marta Szachniuk1,2. 1. Department of Structural Bioinformatics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland. 2. Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Poznan 60-965, Poland. 3. Poznan Supercomputing and Networking Center, Poznan 61-139, Poland.
Abstract
MOTIVATION: Quadruplexes attract the attention of researchers from many fields of bio-science. Due to a specific structure, these tertiary motifs are involved in various biological processes. They are also promising therapeutic targets in many strategies of drug development, including anticancer and neurological disease treatment. The uniqueness and diversity of their forms cause that quadruplexes show great potential in novel biological applications. The existing approaches for quadruplex analysis are based on sequence or 3D structure features and address canonical motifs only. RESULTS: In our study, we analyzed tetrads and quadruplexes contained in nucleic acid molecules deposited in Protein Data Bank. Focusing on their secondary structure topology, we adjusted its graphical diagram and proposed new dot-bracket and arc representations. We defined the novel classification of these motifs. It can handle both canonical and non-canonical cases. Based on this new taxonomy, we implemented a method that automatically recognizes the types of tetrads and quadruplexes occurring as unimolecular structures. Finally, we conducted a statistical analysis of these motifs found in experimentally determined nucleic acid structures in relation to the new classification. AVAILABILITY AND IMPLEMENTATION: https://github.com/tzok/eltetrado/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Quadruplexes attract the attention of researchers from many fields of bio-science. Due to a specific structure, these tertiary motifs are involved in various biological processes. They are also promising therapeutic targets in many strategies of drug development, including anticancer and neurological disease treatment. The uniqueness and diversity of their forms cause that quadruplexes show great potential in novel biological applications. The existing approaches for quadruplex analysis are based on sequence or 3D structure features and address canonical motifs only. RESULTS: In our study, we analyzed tetrads and quadruplexes contained in nucleic acid molecules deposited in Protein Data Bank. Focusing on their secondary structure topology, we adjusted its graphical diagram and proposed new dot-bracket and arc representations. We defined the novel classification of these motifs. It can handle both canonical and non-canonical cases. Based on this new taxonomy, we implemented a method that automatically recognizes the types of tetrads and quadruplexes occurring as unimolecular structures. Finally, we conducted a statistical analysis of these motifs found in experimentally determined nucleic acid structures in relation to the new classification. AVAILABILITY AND IMPLEMENTATION: https://github.com/tzok/eltetrado/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Mateusz Kudla; Kaja Gutowska; Jaroslaw Synak; Mirko Weber; Katrin Sophie Bohnsack; Piotr Lukasiak; Thomas Villmann; Jacek Blazewicz; Marta Szachniuk Journal: Bioinformatics Date: 2020-12-26 Impact factor: 6.937
Authors: Dana Beseiso; Erin V Chen; Sawyer E McCarthy; Kailey N Martin; Elizabeth P Gallagher; Joanne Miao; Liliya A Yatsunyk Journal: Nucleic Acids Res Date: 2022-03-21 Impact factor: 19.160