Static properties of a stacking chain

Polynucleotides are often modeled as the wormlike chain, which characterizes the local stiffness by the bending rigidity. However, some experimental findings unravel that the rigidity arises mainly from the stacking interactions between two consecutive bases along the polynucleotide. Homogeneous polynucleotides such as polydeoxyadenosines can be considered as a stacking chain, in which bases are classified either stacked or free. While a wormlike chain tends to bend evenly due to thermal fluctuations, the bending of a stacking chain requires breakage of a noncovalent chemical bond between consecutive polymer segments. The thermodynamic properties and structures of the stacking chain are investigated by Monte Carlo simulations. Analytical expressions can be obtained if the excluded-volume interaction is neglected. Fundamentally different from the wormlike chain, the crossover of the stacking chain from stiff to flexible polymer is depicted by characteristic temperatures displayed in structural and thermodynamic properties.