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The partly self-complementary DNA octamer d(m5C-G-m5C-G-T-G-m5C-G) was

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By means of one‐ and two‐dimensional NMR spectroscopy the solution structures of the partly self‐complementary octamer d(m5C‐G‐m5C‐G‐A‐G‐m5C‐G) were investigated. It is shown that this DNA fragment, under conditions of high DNA concentration (8 mM DNA) and/or high ionic strength prefers to adopt a duplex structure. At low DNA concentration (0.4 mM DNA), the duplex exists in a 1:1 slow equilibrium with a monomeric hairpin form. Addition of salt destabilizes the hairpin structure in favour of the dimer. At high temperatures the hairpin form, as well as the dimer structure, exist in a fast equilibrium with the random‐coil form. For the hairpin/random‐coil equilibrium a Tm of 329 K and a ΔH° of ‐121 kJ · mol−1 were deduced. These thermodynamic parameters are independent of the DNA concentration, as is expected for a monomeric structure. For the dimer to coil transition a Tm of 359 K(1 M DNA) and a ΔH° of ‐285 kJ · mol duplex−1 were derived. The thermodynamic data of the hairpin‐coil transition mutually agree with those recently reported for the hairpin to random coil equilibrium of the DNA octamer d(m5C‐G‐m5C‐G‐T‐G‐m5C‐G) [Orbons, L. P. M., van der Marel, G. A., van Boom, J. H. & Altona, C. (1987) J. Biomol. Struct. Dyns. 4, 939–963]. It is demonstrated that the dimer structure exhibits B‐DNA characteristics, as is witnessed by the NOESY experiments and the analysis of the proton‐proton coupling data. It is shown that the base‐pair formation of the G × A mismatches is anti‐anti. A comparison of 1H and 31P chemical‐shift data of the title compound with those of a well‐characterized B‐DNA structure reveals large differences in the dm5C(3)‐dG(4)‐dA(5) part of the mismatched dimer structure. These differences apparently indicate some major local structural changes due to the incorporation of the G × A mismatches. Under the most extreme conditions used (i.e. up to 3 M NaCl or 75% CH3OH in the presence of 10 mM MgCl2) no Z‐DNA structure was observed. It is shown that the structural features of the hairpin form of the title compound mimic those of the hairpin structure of d(m5C‐G‐m5C‐G‐T‐G‐m5C‐G). An energy‐minimized model of the hairpin form is given.