Mesoscopic irreversible thermodynamics of aging kinetics of alpha polypeptides [DNA] under various constraints: Special reference to the simple spring mechanics

Abstract

The mesoscopic irreversible thermodynamic treatment of α-polypeptides and the helical polynucleotides (DNA) furnishes two sets of analytical expressions, which allow us not only to analyze the reversible force–extension experiments performed by atomic force microscopy (AFM) but also to predict the irreversible “aging” kinetics of the single-stranded and double-stranded polynucleotides (ssDNA and dsDNA) helical conformations exposed to aqueous solutions and applied static stress systems under the various constraints. The present physicochemical cage model emphasizes the fact that the global Helmholtz free energy of the helical conformation acts not only under the stored “intrinsic” unusual torsional and bending elastic energies inherited by the unfolded helical structure of the amino-acid (peptides) or the nucleic-acid (nucleotide) backbone but also reveals the importance of the interfacial Helmholtz free energy density associated with the interaction of the side-wall branches within the surrounding aqueous solutions. The analytical expression obtained for the unfolding force vs extension (FE) shows a strong non-linear elasticity behavior under the twist angle constraint when the interfacial Helmholtz energy term is incorporating into the scenario. This behavior is in excellent quantitative agreement with the AFM test results obtained by Idiris et al. (2000) on the poly-L-glutamic acid [Glu(n)-Cys] exposed to aqueous solutions, which show that acidity increases the degrees of helicity.