Statics of DNA Deformations

DNA is a deformable molecule. The term “deformable” implies phenomena rooted in the collective behavior of many atoms, and a description based on concepts of continuum and statistical mechanics. Long DNA molecules are an excellent experimental system to study the equilibrium conformations and dynamics of long, flexible molecules. This chapter discusses the following: DNA melting, the zipper model, experimental melting curves, base pairing and base stacking as separate, Hamiltonian formulation of the zipper model, 2 × 2 model, nearest neighbor model, connection to nonlinear dynamics, linear and nonlinear elasticity of DNA, bending modulus and persistence length, measurements of DNA elasticity (short and long molecules), the Euler instability, and the DNA yield transition.