Detecting polynucleotide motifs: Pentads, hexads, and beyond
Michal Zurkowski, Maja Marusic, Dorota Gudanis-Sobocinska, Marta Szachniuk
TL;DR
This paper introduces a new tool for identifying complex nucleic acid structures called polyads, which are important for genome regulation and stability.
Contribution
The novel contribution is the development and validation of LinkTetrado, a computational tool for detecting and classifying polyadic nucleic acid motifs.
Findings
LinkTetrado identified 25 unique structures containing polyadic motifs in a dataset of 529 nucleic acid structures.
Manual validation confirmed the accuracy of motif assignments with a precision of 0.87.
Previously unreported pentads, hexads, heptads, and octads were found in both DNA and RNA.
Abstract
The structural diversity of nucleic acids extends far beyond the canonical Watson–Crick base pairing, encompassing higher-order motifs, such as triads, tetrads, pentads, hexads, heptads, and octads, which play critical roles in genome regulation and stability. Among these, tetrads – forming the core of G-quadruplexes – and their polyadic extensions have emerged as key determinants in fundamental processes ranging from replication and transcription to telomere maintenance. However, the detection and characterization of these complex motifs in experimental structures remain challenging. To address this, we present LinkTetrado, a computational tool for the automated identification and classification of polyadic motifs in nucleic acid 3D structures. Applied to a curated dataset of 529 nucleic acid structures, LinkTetrado identified 25 unique structures containing such motifs, including…
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
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Taxonomy
TopicsDNA and Nucleic Acid Chemistry · Origins and Evolution of Life · Advanced biosensing and bioanalysis techniques