Effect of selective substitution of 5-bromocytosine on conformation of DNA triple helices

Three tripler DNAs containing 5-bromocytosine[C-Br] were studied by vibrational spectroscopy and molecular modelling. Firstly, three oligodeoxypyrimidines of 5'-(TC)3-T4-((CT)-C-Br)3 [(CC)-C-Br], 5'-((TC)-C-Br)3-T4-(CT)3 [(CC)-C-Br] and 5'-((TC)-C-Br)3-T4-((CT)-C-Br)3 [(CC)-C-Br-C-Br] were synthesized and then reacted with an oligodeoxypurine of 5'-(AG)(3) at pH=4.5 in phosphate buffer respectively to form three comparative hairpin tripler named CY,YC and YY. The results of FT-Raman and IR revealed that YY is almost in A-like form, CY and YC are combinations of A-like form and B-like form, but A-form dominates in CY while B-form is equivalent as A-form in YC. The result is consistent with the theoretical analysis.