Computational Characterization of DNA Catenanes

Abstract

DNA catenanes are molecular structures composed of two interlocked circular DNA molecules, held together by a mechanical bond─a topological constraint arising from their mutual interlocking. Using all-atom molecular dynamics simulations, we investigated the structural and dynamical properties of DNA catenanes formed by small double-stranded DNA minicircles. In homocatenanes with mild torsional stress (82 bp–82 bp and 92 bp–92 bp), the minicircles largely retain circular conformations, and the mechanical bond exhibits constrained fluctuations in both bond length and twist angle. Rotational diffusion occurs on the microsecond time scale. In the heterocatenane (76 bp–82 bp), elevated torsional stress promotes kink formation in the 76-bp minicircle, leading to a distorted elliptical shape, enhanced DNA–DNA contacts, and anisotropic relaxation characterized by double-exponential decay in both relative translation and twist. Ion distribution analysis shows Na⁺ enrichment in the interstitial region between the two DNA minicircles, indicating that counterion condensation also occurs within the interlocked structures. Taken together, these results provide quantitative characterization of relative translation, twisting, and rotation in homocatenanes, while for the heterocatenane the emphasis is placed on qualitative interpretation of anisotropic relaxation. This study highlights how DNA conformation and topological constraints shape the structural and dynamic behavior of DNA catenanes.