Simplified Method in Polynucleotide Helix-Coil Transition Theory Including Binding of Complementary Monomer

Abstract

The grand partition function for a long linear system of alternating α and β sequences with the restraint of a fixed number, N _αβ, of αβ boundaries depends in an extremely simple way on the α-sequence and β-sequence grand partition functions, ξ_α and ξ_β. When the restraint is removed, we have μαβ = 0, where μαβ is the chemical potential conjugate to N _αβ. The grand partition function and the condition μαβ = 0 lead to the fundamental relation 1 = ξ_αξ_βz², where z = e^-ωαβ^/κT and ωαβ = boundary free energy. This is a generalization of an earlier equation of Hill, and is equivalent to a result due to Lifson. Binding of a substrate does not affect the argument: the new component is simply included in ξα and ξβ. A model for the binding of adenosine on poly(U) is used as an example.

• generalized Ising systems
• Lifson and Zimm
• adenosine + poly(U)