Conformation and Rheological Properties of Calf-Thymus DNA in Solution

Abstract

Abstract:Studies of DNA molecule behavior in aqueous solutions performed through different approaches allow assessment of the solute-solvent interactions and examination of the strong influence of conformation on its physicochemical properties, in the presence of different ionic species and ionic concentrations. Firstly, the conformational behavior of calf-thymus DNA molecules in TE buffer solution is presented as a function of temperature. Secondly, their rheological behavior is discussed, as well as the evidence of the critical concentrations, i.e., the overlap and the entanglement concentrations (C* and C e , respectively) from steady state flow and oscillatory dynamic shear experiments. The determination of the viscosity in the Newtonian plateau obtained from flow curves η ( 9 γ) allows estimation of the intrinsic viscosity and the specific viscosities at zero shear when C[η] < 40. At end, a generalized master curve is obtained from the variation of the specific viscosity as a function of the overlap parameter C [η]. The variation of the exponent s obtained from the power law η~9 γ´s for both flow and dynamic results is discussed in terms of Graessley's analysis. In the semi-dilute regime with entanglements, a dynamic master curve is obtained as a function of DNA concentration (C DNA > 2.0 mg/mL) and temperature (10˝C < T < 40˝C).

Nucleic acids complexation with cationic elastin-like polypeptides: Stoichiometry and stability of nano-assemblies

“…We used calf thymus DNA, from Sigma-Aldrich (FR), with an average molecular weight of 6,559,500 g/mol [59]. The pUC19 plasmid (2,985 bp) was purified from an E. coli culture with the Midiprep Macherey Nagel kit according to the manufacturer's instructions.…”

“…DNA/ELPs complexes were prepared by using calf-thymus DNA (CT-DNA) solutions with a concentration of 0.01 mg/mL, which is 23 times lower than the average of the overlap concentration (C*) of this nucleic acid sample [59]. C* corresponding to the threshold between dilute polymer solutions, where the coiled chains are separated from one another, and more concentrated solutions, where the chains overlap [59].…”

“…DNA/ELPs complexes were prepared by using calf-thymus DNA (CT-DNA) solutions with a concentration of 0.01 mg/mL, which is 23 times lower than the average of the overlap concentration (C*) of this nucleic acid sample [59]. C* corresponding to the threshold between dilute polymer solutions, where the coiled chains are separated from one another, and more concentrated solutions, where the chains overlap [59]. Since CT-DNA is a well-known and characterized nucleic acid sample [59,75,81], it was used as model of nucleic acid in order to study the role of electrostatic interactions between positively-charged ELPs and DNA in the stoichiometry during the CT-DNA /ELPs complexation process.…”

“…C* corresponding to the threshold between dilute polymer solutions, where the coiled chains are separated from one another, and more concentrated solutions, where the chains overlap [59]. Since CT-DNA is a well-known and characterized nucleic acid sample [59,75,81], it was used as model of nucleic acid in order to study the role of electrostatic interactions between positively-charged ELPs and DNA in the stoichiometry during the CT-DNA /ELPs complexation process. As mentioned in the methods section, slow dropwise mixing of positively charged ELPs derivatives to a negatively charged DNA solution was performed to avoid the aggregate formation [63][64][65].…”

Direct determination of molecular weight distribution of calf‐thymus DNAs and study of their fragmentation under ultrasonic and low‐energy infrared irradiations. A charge detection mass spectrometry investigation

“…Thus, it has been widely used as a DNA sample, such as testing anti‐dsDNA antibody activity, nuclease activity, DNA binding anticancer agents and DNA binding agents that modulate DNA structure and function. CT‐DNA is also used in physicochemical studies of DNA behavior in solution, in particular conformation and rheological properties . Recently, the interaction of silver (Ag) clusters with CT‐DNA has been used as an efficient template method to prepare luminescent Ag clusters …”