Hairpin formation in synthetic oligonucleotides

The structure and dynamics of the homologous series of the (partly) self-complementary DNA fragments, d(ATCCTATnTAGGAT) n = 0-7, were investigated in a combined NMR, T-jump, and optical melting study. It is shown that all compounds in the series may adopt hairpin like conformations, even for n less than 3, although for these smaller n values this only occurs in significant amounts at relatively low concentrations (approximately 10 microM). The enthalpy change accompanying the hairpin-coil melting transition turns out to depend on the number of intervening thymidines, n. It is shown that this does not mean that the enthalpy of loop closure is significantly different from zero, but that loop formation stabilizes the base pair closing the loop. The results indicate that for DNA the optimal loop consists of four or five residues. The observation that hairpins are formed for n less than 3 and that the stability of DNA hairpins is at its maximum for loop lengths of four to five residues is at variance with earlier findings for RNA. In the latter case the optimal loop size consists of six to seven residues, whereas for less than three intervening residues only, dimer, and no hairpin formation, was observed [17, 20]. A direct comparison with RNA behaviour was made by studying r(AUCCUAUT4UAGGAU), T = ribothymidine. In contrast to its DNA analogue, d(ATCCTAT4TAGGAT), the ribo-fragment forms a dimer as well as a hairpin at low (10 microM) concentrations. With the thermodynamic melting parameters deduced from the present experiments the differences between DNA and RNA melting behaviour can be explained.