Dynamics of entangled DNA: Similarities to and differences from with synthetic polymers

Significance 

Deoxyribonucleic acid (DNA) is fundamental for replication and transfer of genetic materials in living organisms and an in-depth understanding of DNA dynamics is consequently important to molecular biology and biophysics because it provides a basis for understanding genome sequencing and genetic engineering. Because DNA is always highly condensed in in vivo studies, knowledge of the entangled dynamics of DNA solutions forms an important piece of the required information about the cell replication mechanism. Associated with this is the potential use of DNA as a model for understanding polymer dynamics that has attracted significant research attention owing to its ideal monodisperse molecular weight distribution and the extreme size of the molecules. At the same time the rheological properties of entangled DNA solutions based on dynamic measurements remain largely underexplored. This can be attributed to both the difficulty of obtaining sufficient sample quantities of DNA that results from extensive measurement needs to adequately characterize the complicated dependence of the entanglement behavior on various parameters such as concentration, polydispersity and molecular weight. The entangled regime is identified in a polymer solution occurs when chains are overlapped enough to store shear energy due to a high polymer concentration. The dynamics in an entangled solution are thought to be similar to those of a polymer melt that do not have any solvent contribution.

Herein, Dr. Sourya Banik, Dr. Dejie Kong, Professor Michael J. San Francisco and Professor Gregory B. McKenna from Texas Tech University developed a concentration dependent model for lambda DNA in the entangled state. Lambda DNA is the genome of bacteriophage and has a molar mass of ~30 million g/mol; hence the entangled states can be achieved even in low concentration conditions. More importantly, the lambda DNA is ideally monodispersed and has a PDI of 1. The linear viscoelastic properties were reported by conducting rheological measurements in oscillatory shear conditions. The properties of the entangled DNA were then compared with the behavior of the conventional polymers. Corresponding author Professor McKenna is now affiliated with North Carolina State University and is widely recognized for the development and use of novel experimental methods for the investigation of the rheological properties of complex fluids and polymers.

The research team findings showed the surprising result that monodisperse lambda DNA exhibited high strain sensitivity in the reported dynamics, leading to the shrinking of the linear viscoelastic region upon reduction of the angular frequency. On comparing with previously published data reported by Teixeira et.al. (Macromolecules, 2007), it was confirmed that those measurements were conducted in the nonlinear viscoelastic region. Further exploration, that is currently being expanded upon, found that the strain sensitivity in entangled DNA can be controlled by changing the polydispersity of the sample.

The time-concentration superposition principle was observed to be valid in the terminal zone signifying the time dependent dynamics could be correlated with the concentration dependent dynamics even for semi-flexible chains like double stranded DNA. Several crucial rheological parameters like the rubbery plateau modulus, terminal relaxation time, and zero-shear viscosity were obtained from the oscillatory shear experiments. The concentration dependence of the crossover and plateau moduli agreed well with the concentration dependence of the time-concentration shift factors. The consistency of the scaling exponents with the experimental relationships suggested the applicability of different approaches for analysis. The plateau modulus scaling with concentration was consistent with the Colby-Rubinstein blob model for concentrated solutions. The terminal relation time exhibited a crossover in its concentration dependence from   to , similar to the unentangled-to-entangled crossover in most synthetic polymer solutions. A high concentration dependence of the zero-shear viscosity  was observed experimentally. The zero-shear viscosity scaling was interpreted to be observed only in very high molecular weight solutions at sufficiently high concentrations. A Reptation/Tube model-based framework like the Likhtman-McLeish model for the linear dynamics of entangled linear polymers could only describe the DNA behavior at low concentrations, indicating the important role of the constraint release mechanism variation in determining the slow relaxation. Owing to the strong nonlinearity reported in this study, the authors pointed out the possibility of unique dynamics of lambda DNA being nonreptative in nature, which could enhance its application in polymers. Despite the strong nonlinearity, the empirical Cox-Merz equivalence was established for relationship between the DNA dynamics and the steady flow properties.

In summary, the Texas Tech University research team reported on the rheological response of concentrated solutions of lambda DNA in buffered aqueous solutions. Rheological properties of DNA were determined via dynamic measurements. The scaling laws (functional relationship) of entangled DNA not only provided insights into the DNA dynamics that are relevant to behavior within a cell but also provide insights for the dynamics of similar materials like polyelectrolytes, concentrated solutions, and ultra-high molecular weight polymer solutions and melts as well as soft entangled systems like hydrogels.

The original research article is published in the research journal, Macromolecules.

Reference

Banik, S., Kong, D., San Francisco, M., & McKenna, G. (2021). Monodisperse Lambda DNA as a Model to Conventional Polymers: A Concentration-Dependent Scaling of the Rheological PropertiesMacromolecules, 54(18), 8632-8654.

Go To Macromolecules

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