Nikol Chantzi1,11, Akshatha Nayak1,11, Fotis A. Baltoumas2,3,11, Eleni Aplakidou2,3, Shiau Wei Liew4,5, Jesslyn Elvaretta Galuh4,5, Michail Patsakis1, Austin Montgomery1, Camille Moeckel1, Ioannis Mouratidis1, Saiful Arefeen Sazed1, Wilfried Guiblet6, Panagiotis Karmiris-Obratański7, Guliang Wang8, Apostolos Zaravinos9,10, Karen M. Vasquez8, Chun Kit Kwok4,5, Georgios A. Pavlopoulos2 and Ilias Georgakopoulos-Soares1 1Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA; 2Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming,” Vari 16672, Greece; 3Department of Basic Sciences, School of Medicine, University of Crete, Heraklion 71003, Greece; 4Department of Chemistry and State Key Laboratory of Marine Environmental Health, City University of Hong Kong, Kowloon Tong, Hong Kong SAR 999077, China; 5Shenzhen Research Institute of the City University of Hong Kong, Shenzhen 518057, China; 6Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA; 7Advanced Manufacturing Laboratory, Department of Manufacturing Systems, Faculty of Mechanical Engineering and Robotics, AGH University of Krakow, Krakow 30-059, Poland; 8Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, Texas 78723, USA; 9Department of Life Sciences, School of Sciences, European University Cyprus, Nicosia 1516, Cyprus; 10Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus

↵11 These authors contributed equally to this work.

Corresponding authors: pavlopoulosfleming.gr, izg5139psu.edu Abstract

G-quadruplex DNA structures exhibit a profound influence on essential biological processes, including transcription, replication, telomere maintenance, and genomic stability. These structures have demonstrably shaped organismal evolution. However, a comprehensive, organism-wide G-quadruplex map encompassing the diversity of life has remained elusive. Here, we introduce Quadrupia, the most extensive and well-characterized G-quadruplex database to date, facilitating the exploration of G-quadruplex structures across the evolutionary spectrum. Quadrupia has identified G-quadruplex sequences in 108,449 reference genomes, with a total of 140,181,277 G-quadruplexes. The database also hosts a collection of 319,784 G-quadruplex clusters of 20 or more members, annotated by taxonomic distributions, multiple sequence alignments, profile hidden Markov models, and cross-references to G-quadruplex 3D structures. Examination of G-quadruplexes across functional genomic elements in different taxa indicates preferential orientation and positioning, with significant differences between individual taxonomic groups. For example, we find that G-quadruplexes in bacteria with a single replication origin display profound preference for the leading orientation. Finally, we experimentally validate the most frequently observed G-quadruplexes using CD-spectroscopy, UV melting, and fluorescent-based approaches.

Footnotes

[Supplemental material is available for this article.]

Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.279790.124.

Freely available online through the Genome Research Open Access option.

Received July 15, 2024. Accepted August 21, 2025.