Representative 3D structures of 24-mer C-rich strand of Bcl-2 Oncogene Promoter

Here, we report the representative centroid structures extracted from the conformational clustering analysis of the molecular dynamics trajectory of the 23-mer C-rich DNA sequence (bcl2midG4_C) derived from the promoter region of the human Bcl-2 oncogene. The deposited structures represent the five most populated conformational clusters identified after a 500 ns all-atom molecular dynamics simulation performed to assess the structural stability of the i-motif predicted by AlphaFold 3. Briefly, the initial three-dimensional model of the bcl2midG4_C sequence was generated using AlphaFold 3, which predicted an intramolecular i-motif architecture. The model was subsequently refined through explicit-solvent molecular dynamics simulations using the AMBER22 package and the ff99bsc0 force field. Structural stability was evaluated by monitoring RMSD, RMSF, hydrogen-bond occupancies, and base-stacking interactions. Conformational clustering was then performed using a hierarchical average-linkage algorithm based on the backbone RMSD, partitioning the trajectory into five representative structural clusters. The centroid structure of each cluster is provided in this dataset. The simulations revealed a highly stable i-motif core stabilized by persistent hemiprotonated C·C⁺ base pairs and extensive base stacking, whereas the observed conformational variability was primarily confined to the loop regions. The largest cluster accounted for approximately 76% of the sampled conformations, indicating that the i-motif adopts a well-defined and persistent fold throughout the simulation. These representative structures provide a structural framework for investigating the conformational landscape of the Bcl-2promoter i-motif and may serve as reference models for future computational and experimental studies aimed at understanding i-motif stability, ligand recognition, and the structural consequences of PNA-induced strand displacement in oncogene promoters.