Method for calculating the effects of a dynamic entity interacting with poly(dT-dA)⋅poly(dT-dA): A dynamic enhancer-repressor action

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Abstract
The Green-function technique is used to study the interbase H-bond stretch poly(dT-dA)⋅poly(dT-dA) (where dT is deoxythymine and dA is deoxyadenine) when an effective enzyme is attached to the helix. Four different one-hydrogen-bond attachment points are studied, and two different two-atom attachment points are studied. The enzyme attachments are allowed to oscillate at an unassumed resonant frequency associated with a thermally activated enzyme. This is equivalent in the Green-function formalism to a physical simulation of a simple enzyme attachment to a large DNA helix. The frequency dependence of hydrogen-bond thermal mean motion seems to be a key to the distinction between a dynamic repressor and enhancer action. The response is enhanced interbase hydrogen-bond-stretch amplitude when the effective enzyme attachment to the helix in poly(dT-dA)⋅poly(dT-dA) is oscillating at frequencies that are near the interbase breathing mode of the helix. When the effective enzyme attachment is oscillating at frequencies far removed from the breathing mode of the helix, the response is usually repressed interbase hydrogen-bond stretch. Spectral density therefore may be a signature of protein enhancer or repressor action. A two-attachment effective enzyme is simulated, and it is shown that it can be approximated by the two individual one-point attachments if the force constant attaching them is small.