A Raman Spectroscopic Study on Conformations of DNA Oligomers: A Dominant Effect of an AA:TT Sequence Over Those of AT:AT and TA:TA Sequences on Determining Conformations of DNA Duplexes

Abstract

Abstract The conformations of the following ten DNA oligomers in solution have been studied by a Raman spectroscopy; d(ATAT)2, d(TATA)2, d(AATT)2, d(TTAA)2, d(TTATATAA)2, d(AATTAATTAATT)2 (dodecamer 1), d(CGCGATATCGCG)2, d(CGCGTATACGCG)2, d(CGCGAATTCGCG)2, and d(CGCGTTAACGCG)2 (dodecamer 2–5). Each oligomer takes on the B form under low salt conditions, although some differences within a B form family are detected. Among four tetramers, only d(ATAT)2 gives an indication of a salt-induced conformational change under high salt conditions. D(TTATATAA)2 which contains the d(ATAT)2 sequence at the center, however, does not give an indication of a salt-induced conformational change, revealing that the inherent character of the d(ATAT)2 sequence is suppressed by the addition of d(AA):d(TT) sequences at both ends. It is in the same context that the conformation of dodecamer 1 is identical to that of poly(dA):poly(dT) but that it is different from that of poly(dA-dT):poly(dA-dT), indicating that the conformation o...