Vibrational fluctuations of hydrogen bonds in a DNA double helix with alternating TA type inserts

The Green's function technique is applied to a study of breathing modes in a DNA double helix which contains a region of different base pairs from the rest of the double helix. The calculation is performed on an alternating poly(dC-dG).poly(dC-dG) helix in the B conformation with four consecutive base pairs replaced by a model of a biological promoter region with four alternating T-A,A-T base pairs, henceforth referred to as (TATA)2. The average stretch of interbase hydrogen bonds is found to be amplified around the insert. This is likely related to the (TATA)2 insert having a lower stability against hydrogen bond melting than the two semi-infinite poly(dC-dG).poly(dC-dG) helices. The insert region may be considered to be a site of enhanced tendency to melt in such a helix. The results show that an alternating AT insert of four base pairs has a larger average hydrogen bond stretch inside and outside the insert region than the average hydrogen bond stretch inside and outside an insert of four consecutive A-T base pairs, henceforth referred to as (AAAA).(TTTT). Calculations are performed which show that the enhancement of the average hydrogen bond stretch around an alternating TA type insert is greatly dependent upon the local modes and not the inband modes. The amount of local mode enhanced average stretch is explored as a function of insert size.