Vibrational fluctuations of the hydrogen bonds around a nucleation defect of melting in poly(dG)-poly(dC)

Vibrational fluctuations of the hydrogen bonds around a nucleation defect of strand-separation melting of a DNA polymer, poly(dG)-poly(dC) (dG denotes repeating guanine bases on one strand and dC the repeating cytosine bases on the other strand), are analyzed at 293 and 340 K using a modified self-consistent phonon theory with a complex Green’s function. At 293 K the helix is very stable and the important frequency band for fluctuation is the band between 60 and 120 ${\mathrm{cm}}^{\mathrm{-}1}$. This is the same important band as that for the fluctuation of the hydrogen bonds which are far from the defect. At 340 K, near the temperature at which the hydrogen-bond instability in the neighboring cells to the defect occurs, there are two important frequency bands. One is the band between 60 and 120 ${\mathrm{cm}}^{\mathrm{-}1}$ which is essential for the fluctuation of the bond near the major groove. A second band is the band under 20 ${\mathrm{cm}}^{\mathrm{-}1}$ which is critical for the fluctuation of the bond near the minor groove. We also explain the directional effects around the defect when the instability of the bonds begins to occur based on the roles of the particular phonons.