Dependence of defect-mediated hydrogen-bond melting in the DNA double helix on the size of an induced defect

This paper studies the defect-mediated melting of a DNA double helix resulting from the occurrence of small melted regions (MR’s) in the helix. We choose MR’s of small and medium sizes and model the DNA replicating fork as an infinite MR. We watch the H bond of these systems stretch as temperature increases until these DNA molecules break down (melt). For all systems we find that the H-bond stretch vibrations near the open region are enhanced not only by proximity to an open section itself but also by the anharmonic properties of the H bonds. In addition, the H-bond stretch amplitudes increase slightly with the size of the finite MR’s and are considerably lower than those of the replicating fork. Finally we find that the melting temperature decreases very slowly with finite MR sizes, especially for small MR defects. This suggests that the calculation on single-base-pair MR’s give the same melting temperature as somewhat larger MR’s. Since small MR’s are more probable one can predict a unique melting temperature.