G4All: a database of experimentally confirmed G-quadruplex-forming sequences

Abstract

G-quadruplexes (G4s) are non-canonical nucleic acid structures with critical roles in gene regulation, genomic stability, and disease, making them prime targets for therapeutic and biotechnological applications. However, the absence of a curated, centralized, experimentally validated repository of short (mostly synthetic) G4-forming sequences, paired with appropriate single-stranded or hairpin controls, has limited reproducibility and hindered progress in the field. Here, we introduce G4All, a comprehensive, curated database of G4-forming short DNA and RNA sequences, complemented by rigorously selected non-G4 controls, all studied under roughly similar experimental conditions (around 100 mM potassium ion at near neutral pH). G4All consolidates sequences validated by diverse experimental methods, including circular dichroism, NMR, UV spectroscopy, with standardized annotations for topology, thermal stability, and experimental conditions. By providing both positive and negative datasets, G4All enables rigorous comparative analyses, assay benchmarking, and the development of predictive models. The database supports a broad range of applications, from fundamental studies of G4 biophysics to the rational design of aptamers, as well as benchmarking prediction algorithms. Future developments will expand G4All to include user-submitted datasets and more RNA sequences. Freely accessible, G4All offers a searchable interface and downloadable datasets, establishing a community-driven hub to accelerate discovery and standardization in G4 research. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/743020v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@111d015org.highwire.dtl.DTLVardef@74447corg.highwire.dtl.DTLVardef@13c5642org.highwire.dtl.DTLVardef@432469_HPS_FORMAT_FIGEXP M_FIG C_FIG