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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 of d(AATTAATTAATT)2 is determined by the overwhelmingly dominant effect of the d(AA):d(TT) sequence over those of d(AT):d(AT) and d(TA):d(TA) sequences. Among dodecamers 2–5, only d(CGCGTATACGCG)2 gives an indication of the salt-induced B-Z transition. For the other dodecamers, the central tetramers which are composed of A:T base pairs hinder the transition which the d(CGCG)2 sequences at both ends tend to undergo. The exclusive observation of the indication of the transition in d(CGCGTA-it is reasonable that the indication of the B-Z transition is detected only in d(CGCGTATACGCG)2. We have already shown that the d(TATA)2 is the most unstable among the four tetramers. It can not form a duplex. In other words, the d(TATA)2 sequence in the d(CGCGTATACGCG)2 does not restrict strongly the conformations of the d(CGCG)2 portions at both ends to B form. This might be another aspect of the exclusive observation of the B-Z transition in d(CGCGTATACGCG)2.