Double-stranded DNA as a model polymer: validation through rheological characterization
thesisposted on 23.02.2017 by Pan, Sharadwata
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Solutions of double-stranded DNA (ds-DNA) have been investigated in the presence of excess salt to represent a model neutral polymer system. However, very recently, there have also been some contrary discussions regarding the suitability of using ds-DNA as a model polymer, based on scaling arguments and simulations. Here, we report systematic experimental investigations of dilute and semidilute unentangled ds-DNA solutions, to test the hypothesis that ds-DNA is a model polymer. In addition, we have meticulously characterized the behaviour of ds-DNA solutions far from equilibrium, in shear and extensional flows. In order to study the behaviour of ds-DNA to compare with well known results from neutral polymers, we first characterize its solutions close to equilibrium. We use the solvent quality parameter z and the dimensionless concentration c/c* (where c* is the overlap concentration), as the scaling variables. We have determined the Theta-temperature of DNA in Tris-EDTA buffer under excess salt conditions to be around 15 degree Celsius, and provide the formula to determine z for DNA of any molecular weight at any temperature above the theta temperature. We also show that the temperature crossover for dilute DNA solutions of various molecular weights (from 2.9 to 289 kilobasepairs) for the second virial coefficient, the hydrodynamic radius and the viscosity radius agree with the scaling behaviour of neutral synthetic polymers. The scaling behavior of the zero shear rate viscosity of semidilute DNA solutions, in the double crossover regime driven by temperature and concentration, is shown to have a power law dependence on the scaled concentration c/c*, with an effective exponent that depends on z, in agreement with reported Brownian dynamics simulations of flexible polymer chains. Away from equilibrium, in shear flow, the shear rate dependence of viscosity for semidilute and dilute DNA solutions, at various temperatures and concentrations, can be collapsed onto master curves when interpreted in terms of a different relaxation time based Weissenberg number. In extensional flow, the concentration dependence of the steady state uniaxial extensional viscosities of semidilute DNA solutions has been studied and compared with theoretical predictions. The material functions obtained in this work will also provide benchmark data that are useful for the characterization of industrially important semidilute systems. Equilibrium rheological characterization carried out on dilute and semidilute DNA solutions, investigated under excess salt conditions, show a remarkable agreement with other neutral synthetic polymers, asserting that DNA can be used as a model polymer for rheological studies. Thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy of the Indian Institute of Technology Bombay, India and Monash University, Australia.