Radical cationic repair process of cissyn thymine dimer has been investigated when (1) sugar-phosphate backbones were substituted by hydrogen atoms, (2) phosphate group was substituted by two hydrogen atoms each on a sugar ring and (3) sugar-phosphate backbone was taken into account. The effect of the interactions between N1 and N1′ lone pairs and the C6-C6′ antibonding orbital are the most important evidences for the cleavage of the C6-C6′ bond in the first step of radical cationic repair mechanism in the absence of the sugar-phosphate backbone. The impact of the N1 and N1′ lone pairs on the C6-C6′ bond cleavage decreases and the energy barrier of the cleavage of that bond significantly increases in the presence of the deoxynucleoside sugars and the sugar-phosphate backbone.