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Polymer architecture plays critical roles in both bulk rheological properties and microscale macromolecular dynamics in entangled polymer solutions and composites. Ring polymers, in particular, have been the topic of much debate due to the inability of the celebrated reptation model to capture their observed dynamics. Macrorheology and differential dynamic microscopy (DDM) are powerful methods to determine entangled polymer dynamics across scales; yet, they typically require different samples under different conditions, preventing direct coupling of bulk rheological properties to the underlying macromolecular dynamics. Here, we perform macrorheology on composites of highly overlapping DNA and dextran polymers, focusing on the role of DNA topology (rings versus linear chains) as well as the relative volume fractions of DNA and dextran. On the same samples under the same conditions, we perform DDM and single-molecule tracking on embedded fluorescent-labeled DNA molecules immediately before and after bulk measurements. We show DNA-dextran composites exhibit unexpected nonmonotonic dependences of bulk viscoelasticity and molecular-level transport properties on the fraction of DNA comprising the composites, with characteristics that are strongly dependent on the DNA topology. We rationalize our results as arising from stretching and bundling of linear DNA versus compaction, swelling, and threading of rings driven by dextran-mediated depletion interactions.
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This content will become publicly available on November 25, 2026
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.
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- Award ID(s):
- 2510937
- PAR ID:
- 10686871
- Publisher / Repository:
- ACS
- Date Published:
- Journal Name:
- Langmuir
- Volume:
- 41
- Issue:
- 46
- ISSN:
- 0743-7463
- Page Range / eLocation ID:
- 31422 to 31432
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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