Advanced computational frameworks for characterizing abnormal DNA architectures and their implications in genome dynamics

Computational and machine learning approaches are playing a pivotal role in the identification, characterization and targeting of noncanonical DNA structures including G-quadruplexes, Z-DNA, hairpins, and triplexes. These configurations play critical roles in maintaining genomic stability, facilitating DNA repair, and regulating chromatin organization. Although the human genome predominantly adopts the B DNA conformation, evidence indicates that non B DNA forms exert significant influence on gene expression and disease development. This highlights the need for dedicated computational frameworks to systematically investigate these alternative structures. Machine learning models encompassing supervised and unsupervised algorithms such as K Nearest Neighbors, Support Vector Machines, and deep learning architectures including Convolutional Neural Networks have shown considerable potential in predicting sequence motifs predisposed to forming non B DNA conformations. These predictive tools contribute to identifying genomic regions associated with disease susceptibility. Complementary bioinformatics platforms and molecular docking tools, notably AutoDock, along with chemical libraries like ZINC, facilitate the virtual screening of small molecules targeting specific DNA structures. Stabilizers of G quadruplexes, exemplified by CX 5461, have demonstrated therapeutic promise in BRCA deficient cancers, highlighting the translational impact of computational methods on drug discovery. Anticipating DNA structural shifts opens new avenues in personalized medicine for complex diseases, with computational chemistry and machine learning deepening our understanding of DNA topology and guiding smarter ligand design. The integrated approach proposed in this review addresses the previous studies done in this field and highlights the current limitations in structural genomics and advances the development of precision therapeutics aligned with individual genomic profiles.