Surface-Mediated Self-Assembly of Kinetoplast DNA: Depletion-Driven Dimer Formation and Quasi-2D Dynamics

Depletion interactions play a crucial role in the assembly and dynamics of colloidal systems in polymer-rich environments. In this study, we investigate the behavior of asymmetric, soft, colloidal kinetoplast DNA (kDNA) in the presence of linear polymers (linear DNA), focusing on their surface accumulation, orientation, diffusion, and dimer formation. We observe that the kDNAs preferentially migrate to a solid surface with a preferred orientation due to depletion interactions with the substrate, a phenomenon absent in polymer-free conditions. Over time, the kDNAs adopt a stable orientation at the surface, and the orientation of individual kDNAs on the surface adopts a polar order. By analyzing kDNA diffusion both in bulk and on the surface, we find that surface-bound kDNAs exhibit prolonged confinement within the field of view, while bulk kDNAs rapidly diffuse out of view. Additionally, we observe the formation of dimers as kDNAs encounter each other on the surface, driven by depletion forces. The kDNAs within the dimers are able to rotate relative to each other and deform to maximize their interaction energy. Fluorescent labeling of both the polymers and kDNAs reveals polymer exclusion from the kDNA-surface and inter-kDNA regions, confirming depletion-driven attraction. We quantified the depletion attraction by measuring the excluded volume between dimerized kDNAs using confocal fluorescence microscopy. These findings provide insights into depletion-mediated interactions in soft, asymmetric colloids and further establish kDNA as a model system for studying the colloidal behavior of catenated soft particles.