Unraveling Non-B DNA Structures in the Era of Telomere-to-Telomere Genomes

Telomere-to-telomere (T2T) genome assemblies now provide a complete representation of genomic sequences, enabling unprecedented exploration of non-B DNA structures-secondary conformations distinct from canonical B-DNA. These fully resolved genomes reveal the true abundance and chromosomal distribution of motifs capable of forming G-quadruplexes, Z-DNA, triplexes, and other noncanonical structures, including within previously inaccessible satellite and repetitive regions. T2T assemblies also illuminate how non-B DNA influences key biological processes such as replication, recombination, chromatin organization, and transcription. Moreover, emerging evidence links non-B DNA structures to genomic instability, mutation hotspots, and disease etiology. Comparative T2T analyses across species are beginning to uncover evolutionary patterns and selection pressures acting on these motifs. Integrating advanced prediction tools, AI-based analyses, and experimental validation promises to clarify the multifaceted roles of non-B DNA in genome function, regulation, and evolution.