Localized vibrational modes at a double‐helix‐single‐strand junction

Abstract

Abstract A vibrational analysis has been performed for a double‐helix–single‐strand junction. A Green's function technique has been used in treating the junction as a defect on an otherwise perfect system of infinite chain homopolymers. We calculate that the hydrogen‐bond stretching at the junction is amplified by a factor of two relative to the interior of the double helix, B poly(dG)–poly(dC). Breathing modes localized near the junction have also been predicted at 77 and 94 wave numbers. The calculated results are shown to be consistent with predictions from recent nmr studies.